Chlorine in PDB 4k6o: X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
All present enzymatic activity of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution:
2.4.2.3;
Protein crystallography data
The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution, PDB code: 4k6o
was solved by
I.I.Prokofev,
A.A.Lashkov,
A.G.Gabdoulkhakov,
C.Betzel,
A.M.Mikhailov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
40.28 /
1.17
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
93.012,
97.100,
93.017,
90.00,
119.99,
90.00
|
R / Rfree (%)
|
10.8 /
12.8
|
Other elements in 4k6o:
The structure of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution also contains other interesting chemical elements:
Chlorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Chlorine atom in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
(pdb code 4k6o). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the
X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution, PDB code: 4k6o:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Chlorine binding site 1 out
of 12 in 4k6o
Go back to
Chlorine Binding Sites List in 4k6o
Chlorine binding site 1 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl301
b:29.2
occ:1.00
|
H
|
A:SER45
|
2.3
|
11.4
|
0.3
|
H
|
A:SER45
|
2.3
|
11.4
|
0.7
|
HA
|
A:ALA44
|
2.7
|
11.7
|
1.0
|
O
|
A:HOH665
|
2.9
|
38.2
|
1.0
|
O
|
A:HOH572
|
3.0
|
26.4
|
1.0
|
N
|
A:SER45
|
3.1
|
9.5
|
1.0
|
HG
|
A:SER45
|
3.2
|
15.3
|
0.3
|
O
|
A:HOH671
|
3.3
|
31.9
|
1.0
|
HZ
|
A:PHE42
|
3.3
|
14.9
|
1.0
|
CA
|
A:ALA44
|
3.5
|
9.7
|
1.0
|
HB1
|
A:ALA44
|
3.6
|
13.6
|
1.0
|
O
|
A:SER45
|
3.6
|
12.7
|
1.0
|
C
|
A:ALA44
|
3.8
|
8.9
|
1.0
|
O
|
A:HOH794
|
3.8
|
43.7
|
1.0
|
HE1
|
A:HIS46
|
3.9
|
18.4
|
0.5
|
OG
|
A:SER45
|
3.9
|
12.8
|
0.3
|
CB
|
A:ALA44
|
4.0
|
11.3
|
1.0
|
HE2
|
A:PHE42
|
4.0
|
14.5
|
1.0
|
CZ
|
A:PHE42
|
4.0
|
12.4
|
1.0
|
CE1
|
A:HIS46
|
4.1
|
15.3
|
0.5
|
HB3
|
A:SER45
|
4.1
|
15.0
|
0.7
|
CA
|
A:SER45
|
4.1
|
10.8
|
0.3
|
CA
|
A:SER45
|
4.1
|
10.9
|
0.7
|
HB2
|
A:ALA44
|
4.2
|
13.6
|
1.0
|
C
|
A:SER45
|
4.3
|
11.8
|
1.0
|
CE2
|
A:PHE42
|
4.3
|
12.1
|
1.0
|
NE2
|
A:HIS46
|
4.4
|
16.1
|
0.5
|
O
|
A:HOH772
|
4.4
|
44.9
|
1.0
|
HE2
|
A:HIS46
|
4.4
|
19.3
|
0.5
|
CB
|
A:SER45
|
4.6
|
11.7
|
0.3
|
O
|
A:LEU43
|
4.6
|
13.1
|
1.0
|
CB
|
A:SER45
|
4.6
|
12.5
|
0.7
|
N
|
A:ALA44
|
4.7
|
9.4
|
1.0
|
ND1
|
A:HIS46
|
4.7
|
14.2
|
0.5
|
HB3
|
A:ALA44
|
4.9
|
13.6
|
1.0
|
O
|
A:HOH656
|
4.9
|
35.6
|
1.0
|
HD1
|
A:HIS46
|
4.9
|
17.1
|
0.5
|
HA
|
A:SER45
|
5.0
|
13.0
|
0.3
|
HA
|
A:SER45
|
5.0
|
13.1
|
0.7
|
O
|
A:ALA44
|
5.0
|
9.7
|
1.0
|
HB3
|
A:SER45
|
5.0
|
14.0
|
0.3
|
HB2
|
A:SER45
|
5.0
|
15.0
|
0.7
|
|
Chlorine binding site 2 out
of 12 in 4k6o
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Chlorine Binding Sites List in 4k6o
Chlorine binding site 2 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl302
b:15.8
occ:0.66
|
O
|
A:HOH491
|
2.5
|
17.8
|
1.0
|
H
|
A:ASP26
|
2.6
|
10.8
|
1.0
|
H
|
A:GLY25
|
2.6
|
9.5
|
1.0
|
O
|
B:HOH531
|
2.7
|
23.7
|
1.0
|
O
|
A:HOH478
|
3.0
|
18.6
|
1.0
|
HG3
|
A:ARG29
|
3.1
|
20.7
|
1.0
|
HB2
|
A:PRO24
|
3.1
|
9.7
|
1.0
|
N
|
A:GLY25
|
3.3
|
7.9
|
1.0
|
O
|
A:HOH612
|
3.3
|
37.8
|
1.0
|
HB3
|
A:ASP26
|
3.4
|
12.9
|
1.0
|
N
|
A:ASP26
|
3.4
|
9.0
|
1.0
|
HH22
|
B:ARG47
|
3.5
|
17.8
|
0.6
|
HA2
|
A:GLY92
|
3.5
|
14.5
|
0.4
|
HB2
|
A:ASP26
|
3.6
|
12.9
|
1.0
|
HA2
|
A:GLY92
|
3.6
|
11.6
|
0.6
|
HA3
|
A:GLY25
|
3.9
|
10.3
|
1.0
|
CB
|
A:ASP26
|
3.9
|
10.7
|
1.0
|
CB
|
A:PRO24
|
3.9
|
8.1
|
1.0
|
CA
|
A:GLY25
|
4.0
|
8.6
|
1.0
|
NH2
|
B:ARG47
|
4.0
|
14.8
|
0.6
|
HB3
|
A:PRO24
|
4.0
|
9.7
|
1.0
|
HA
|
A:PRO24
|
4.0
|
9.0
|
1.0
|
CG
|
A:ARG29
|
4.0
|
17.3
|
1.0
|
HB2
|
A:ARG29
|
4.1
|
16.3
|
1.0
|
C
|
A:PRO24
|
4.2
|
7.4
|
1.0
|
C
|
A:GLY25
|
4.2
|
8.8
|
1.0
|
HH21
|
B:ARG47
|
4.2
|
17.8
|
0.6
|
HE
|
A:ARG29
|
4.2
|
23.5
|
1.0
|
CA
|
A:PRO24
|
4.2
|
7.5
|
1.0
|
O
|
A:VAL91
|
4.2
|
8.8
|
1.0
|
HA3
|
A:GLY92
|
4.2
|
14.5
|
0.4
|
CA
|
A:ASP26
|
4.3
|
9.3
|
1.0
|
CA
|
A:GLY92
|
4.3
|
12.1
|
0.4
|
HA3
|
A:GLY92
|
4.3
|
11.6
|
0.6
|
O
|
A:HOH592
|
4.4
|
19.2
|
0.7
|
H
|
A:THR93
|
4.4
|
13.5
|
0.4
|
CA
|
A:GLY92
|
4.4
|
9.6
|
0.6
|
HG2
|
A:ARG29
|
4.5
|
20.7
|
1.0
|
O
|
A:HOH477
|
4.5
|
17.5
|
1.0
|
CB
|
A:ARG29
|
4.5
|
13.6
|
1.0
|
HH12
|
B:ARG47
|
4.6
|
15.8
|
0.6
|
HB3
|
A:ARG29
|
4.6
|
16.3
|
1.0
|
HG23
|
A:THR93
|
4.7
|
14.7
|
0.4
|
HH12
|
B:ARG47
|
4.7
|
17.2
|
0.4
|
HG13
|
A:VAL91
|
4.7
|
10.2
|
1.0
|
CZ
|
B:ARG47
|
4.8
|
13.8
|
0.6
|
NE
|
A:ARG29
|
4.9
|
19.6
|
1.0
|
O
|
A:HOH625
|
4.9
|
30.5
|
1.0
|
H
|
A:THR93
|
4.9
|
8.5
|
0.6
|
HA2
|
A:GLY25
|
4.9
|
10.3
|
1.0
|
O
|
A:ASP26
|
4.9
|
9.1
|
1.0
|
CD
|
A:ARG29
|
4.9
|
19.3
|
1.0
|
NH1
|
B:ARG47
|
4.9
|
14.3
|
0.4
|
|
Chlorine binding site 3 out
of 12 in 4k6o
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Chlorine Binding Sites List in 4k6o
Chlorine binding site 3 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl309
b:21.4
occ:0.97
|
H
|
A:PHE133
|
2.3
|
6.7
|
1.0
|
O
|
F:HOH440
|
2.4
|
5.3
|
0.6
|
O
|
A:HOH602
|
2.6
|
28.9
|
1.0
|
HG21
|
F:THR110
|
2.8
|
10.0
|
1.0
|
HB2
|
A:PHE133
|
2.9
|
7.7
|
1.0
|
HG1
|
F:THR110
|
3.0
|
9.0
|
1.0
|
HA
|
A:ASP132
|
3.1
|
6.0
|
1.0
|
O
|
A:HOH519
|
3.1
|
15.8
|
1.0
|
N
|
A:PHE133
|
3.1
|
5.5
|
1.0
|
HA2
|
F:GLY153
|
3.3
|
6.5
|
1.0
|
O
|
F:HOH440
|
3.4
|
14.3
|
0.4
|
HB2
|
F:MET152
|
3.6
|
7.7
|
1.0
|
CB
|
A:PHE133
|
3.6
|
6.4
|
1.0
|
HB3
|
A:PHE133
|
3.7
|
7.7
|
1.0
|
CG2
|
F:THR110
|
3.7
|
8.3
|
1.0
|
HB3
|
F:MET152
|
3.7
|
7.7
|
1.0
|
O
|
F:MET152
|
3.8
|
7.6
|
1.0
|
OG1
|
F:THR110
|
3.8
|
7.5
|
1.0
|
CA
|
A:ASP132
|
3.9
|
5.0
|
1.0
|
CA
|
A:PHE133
|
4.0
|
5.8
|
1.0
|
HG23
|
F:THR110
|
4.0
|
10.0
|
1.0
|
C
|
A:ASP132
|
4.0
|
5.1
|
1.0
|
C
|
F:MET152
|
4.0
|
5.9
|
1.0
|
CB
|
F:MET152
|
4.1
|
6.4
|
1.0
|
CA
|
F:GLY153
|
4.1
|
5.5
|
1.0
|
O
|
F:HOH612
|
4.1
|
32.2
|
1.0
|
OD1
|
A:ASP132
|
4.1
|
8.2
|
1.0
|
CB
|
F:THR110
|
4.2
|
7.1
|
1.0
|
O
|
A:PRO131
|
4.2
|
5.5
|
1.0
|
O
|
A:HOH461
|
4.2
|
12.4
|
1.0
|
HB
|
F:THR110
|
4.2
|
8.5
|
1.0
|
N
|
F:GLY153
|
4.2
|
5.6
|
1.0
|
HG22
|
F:THR110
|
4.3
|
10.0
|
1.0
|
HA
|
A:PHE133
|
4.4
|
7.0
|
1.0
|
HA3
|
F:GLY153
|
4.5
|
6.5
|
1.0
|
CG
|
A:ASP132
|
4.6
|
6.8
|
1.0
|
O
|
A:HOH493
|
4.6
|
17.4
|
1.0
|
O
|
F:HOH456
|
4.6
|
13.1
|
1.0
|
O
|
A:HOH425
|
4.7
|
7.8
|
1.0
|
CA
|
F:MET152
|
4.7
|
5.8
|
1.0
|
H
|
A:ASP134
|
4.7
|
7.5
|
1.0
|
H
|
F:GLY153
|
4.8
|
6.7
|
1.0
|
CB
|
A:ASP132
|
4.8
|
6.5
|
1.0
|
MG
|
A:MG305
|
4.8
|
13.7
|
0.7
|
N
|
A:ASP132
|
4.9
|
4.9
|
1.0
|
CG
|
A:PHE133
|
4.9
|
7.2
|
1.0
|
C
|
A:PRO131
|
5.0
|
4.9
|
1.0
|
HB2
|
A:ASP132
|
5.0
|
7.8
|
1.0
|
|
Chlorine binding site 4 out
of 12 in 4k6o
Go back to
Chlorine Binding Sites List in 4k6o
Chlorine binding site 4 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl301
b:19.6
occ:0.58
|
O
|
B:HOH733
|
2.2
|
29.9
|
0.7
|
H
|
B:GLY25
|
2.5
|
11.7
|
1.0
|
H
|
B:ASP26
|
2.7
|
14.1
|
1.0
|
HG3
|
B:ARG29
|
2.8
|
23.8
|
1.0
|
O
|
B:HOH543
|
3.0
|
19.9
|
1.0
|
O
|
B:HOH646
|
3.1
|
41.4
|
1.0
|
O
|
A:HOH775
|
3.1
|
41.1
|
1.0
|
HB2
|
B:PRO24
|
3.2
|
9.9
|
1.0
|
N
|
B:GLY25
|
3.2
|
9.7
|
1.0
|
HH22
|
A:ARG47
|
3.3
|
25.4
|
0.8
|
HB3
|
B:ASP26
|
3.4
|
18.6
|
1.0
|
HA2
|
B:GLY92
|
3.5
|
13.0
|
0.8
|
N
|
B:ASP26
|
3.5
|
11.8
|
1.0
|
HA2
|
B:GLY92
|
3.6
|
12.0
|
0.2
|
CG
|
B:ARG29
|
3.7
|
19.8
|
1.0
|
HA3
|
B:GLY25
|
3.7
|
12.4
|
1.0
|
HB2
|
B:ASP26
|
3.8
|
18.6
|
1.0
|
NH2
|
A:ARG47
|
3.8
|
21.2
|
0.8
|
CA
|
B:GLY25
|
3.9
|
10.3
|
1.0
|
HE
|
B:ARG29
|
3.9
|
25.9
|
1.0
|
CB
|
B:PRO24
|
4.0
|
8.3
|
1.0
|
HH21
|
A:ARG47
|
4.0
|
25.4
|
0.8
|
CB
|
B:ASP26
|
4.0
|
15.5
|
1.0
|
HA
|
B:PRO24
|
4.0
|
9.8
|
1.0
|
HB3
|
B:PRO24
|
4.1
|
9.9
|
1.0
|
C
|
B:PRO24
|
4.2
|
8.5
|
1.0
|
HG2
|
B:ARG29
|
4.2
|
23.8
|
1.0
|
O
|
B:HOH550
|
4.2
|
28.2
|
1.0
|
O
|
B:VAL91
|
4.2
|
8.9
|
1.0
|
HB2
|
B:ARG29
|
4.2
|
20.6
|
1.0
|
C
|
B:GLY25
|
4.2
|
10.4
|
1.0
|
HH21
|
A:ARG47
|
4.2
|
17.7
|
0.2
|
CA
|
B:PRO24
|
4.2
|
8.1
|
1.0
|
HD3
|
B:ARG29
|
4.3
|
25.1
|
1.0
|
HA3
|
B:GLY92
|
4.3
|
13.0
|
0.8
|
CA
|
B:GLY92
|
4.3
|
10.8
|
0.8
|
HA3
|
B:GLY92
|
4.3
|
12.0
|
0.2
|
CA
|
B:ASP26
|
4.4
|
13.3
|
1.0
|
CA
|
B:GLY92
|
4.4
|
10.0
|
0.2
|
CD
|
B:ARG29
|
4.4
|
20.9
|
1.0
|
CB
|
B:ARG29
|
4.5
|
17.1
|
1.0
|
HH12
|
A:ARG47
|
4.5
|
21.8
|
0.8
|
NE
|
B:ARG29
|
4.5
|
21.6
|
1.0
|
NH2
|
A:ARG47
|
4.6
|
14.7
|
0.2
|
HB3
|
B:ARG29
|
4.6
|
20.6
|
1.0
|
CZ
|
A:ARG47
|
4.7
|
20.0
|
0.8
|
HH22
|
A:ARG47
|
4.7
|
17.7
|
0.2
|
H
|
B:THR93
|
4.7
|
11.9
|
0.2
|
HG13
|
B:VAL91
|
4.7
|
11.3
|
1.0
|
HA2
|
B:GLY25
|
4.8
|
12.4
|
1.0
|
H
|
B:THR93
|
4.9
|
11.9
|
0.8
|
NH1
|
A:ARG47
|
4.9
|
18.1
|
0.8
|
|
Chlorine binding site 5 out
of 12 in 4k6o
Go back to
Chlorine Binding Sites List in 4k6o
Chlorine binding site 5 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl302
b:11.3
occ:1.00
|
H
|
B:ASN221
|
2.4
|
8.5
|
1.0
|
O
|
B:HOH593
|
3.0
|
31.6
|
1.0
|
HA
|
B:ILE220
|
3.0
|
8.7
|
1.0
|
HE2
|
B:LYS225
|
3.0
|
19.0
|
1.0
|
HG13
|
B:ILE220
|
3.0
|
10.3
|
1.0
|
O
|
B:HOH693
|
3.2
|
36.1
|
1.0
|
N
|
B:ASN221
|
3.2
|
7.1
|
1.0
|
HB2
|
B:GLN224
|
3.3
|
11.3
|
1.0
|
O
|
B:HOH496
|
3.4
|
17.8
|
0.8
|
HG21
|
B:VAL103
|
3.5
|
17.5
|
1.0
|
HG2
|
B:LYS225
|
3.6
|
13.1
|
1.0
|
HB3
|
B:ASN221
|
3.7
|
9.6
|
1.0
|
HG23
|
B:VAL103
|
3.8
|
17.5
|
1.0
|
CA
|
B:ILE220
|
3.8
|
7.2
|
1.0
|
HG3
|
B:GLN224
|
3.9
|
13.5
|
1.0
|
CG1
|
B:ILE220
|
3.9
|
8.6
|
1.0
|
CE
|
B:LYS225
|
3.9
|
15.8
|
1.0
|
O
|
B:ASN221
|
4.0
|
6.7
|
1.0
|
H21
|
B:EDO309
|
4.0
|
23.6
|
0.5
|
CG2
|
B:VAL103
|
4.0
|
14.6
|
1.0
|
C
|
B:ILE220
|
4.0
|
6.7
|
1.0
|
CB
|
B:GLN224
|
4.1
|
9.4
|
1.0
|
HB3
|
B:GLN224
|
4.1
|
11.3
|
1.0
|
HG12
|
B:ILE220
|
4.1
|
10.3
|
1.0
|
CA
|
B:ASN221
|
4.2
|
6.7
|
1.0
|
HG22
|
B:VAL103
|
4.2
|
17.5
|
1.0
|
HE3
|
B:LYS225
|
4.3
|
19.0
|
1.0
|
CB
|
B:ASN221
|
4.3
|
8.0
|
1.0
|
HB2
|
B:ASN221
|
4.3
|
9.6
|
1.0
|
CB
|
B:ILE220
|
4.4
|
7.6
|
1.0
|
CG
|
B:LYS225
|
4.4
|
10.9
|
1.0
|
CG
|
B:GLN224
|
4.5
|
11.3
|
1.0
|
C
|
B:ASN221
|
4.5
|
6.7
|
1.0
|
CD
|
B:LYS225
|
4.6
|
13.3
|
1.0
|
HD3
|
B:LYS225
|
4.6
|
16.0
|
1.0
|
HB
|
B:ILE220
|
4.7
|
9.1
|
1.0
|
HG3
|
B:LYS225
|
4.7
|
13.1
|
1.0
|
HZ1
|
B:LYS225
|
4.8
|
22.6
|
1.0
|
O
|
B:HOH484
|
4.8
|
24.0
|
1.0
|
NZ
|
B:LYS225
|
4.9
|
18.8
|
1.0
|
HZ3
|
B:LYS225
|
4.9
|
22.6
|
1.0
|
HG2
|
B:GLN224
|
4.9
|
13.5
|
1.0
|
O
|
B:ILE219
|
4.9
|
8.8
|
1.0
|
N
|
B:ILE220
|
5.0
|
7.3
|
1.0
|
O
|
B:HOH591
|
5.0
|
30.4
|
1.0
|
|
Chlorine binding site 6 out
of 12 in 4k6o
Go back to
Chlorine Binding Sites List in 4k6o
Chlorine binding site 6 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl301
b:15.5
occ:0.47
|
H
|
C:GLY25
|
2.4
|
11.7
|
1.0
|
H
|
C:ASP26
|
2.7
|
14.9
|
1.0
|
HD3
|
C:ARG29
|
2.8
|
31.1
|
1.0
|
O
|
C:HOH786
|
3.0
|
12.1
|
0.6
|
N
|
C:GLY25
|
3.2
|
9.7
|
1.0
|
HB2
|
C:PRO24
|
3.2
|
9.9
|
1.0
|
O
|
C:HOH572
|
3.3
|
35.1
|
1.0
|
O
|
D:HOH672
|
3.3
|
24.6
|
0.4
|
O
|
C:HOH686
|
3.3
|
36.3
|
1.0
|
N
|
C:ASP26
|
3.5
|
12.4
|
1.0
|
HA2
|
C:GLY92
|
3.5
|
11.5
|
0.7
|
HB3
|
C:ASP26
|
3.6
|
20.5
|
1.0
|
HA2
|
C:GLY92
|
3.6
|
12.1
|
0.3
|
HA3
|
C:GLY25
|
3.7
|
12.0
|
1.0
|
HB2
|
C:ASP26
|
3.8
|
20.5
|
1.0
|
CD
|
C:ARG29
|
3.8
|
25.9
|
1.0
|
CA
|
C:GLY25
|
3.9
|
10.0
|
1.0
|
CB
|
C:PRO24
|
4.0
|
8.3
|
1.0
|
HE
|
C:ARG29
|
4.0
|
32.4
|
1.0
|
HA
|
C:PRO24
|
4.0
|
9.3
|
1.0
|
CB
|
C:ASP26
|
4.1
|
17.1
|
1.0
|
HB2
|
C:ARG29
|
4.1
|
25.6
|
1.0
|
HB3
|
C:PRO24
|
4.1
|
9.9
|
1.0
|
C
|
C:PRO24
|
4.1
|
8.3
|
1.0
|
C
|
C:GLY25
|
4.2
|
10.4
|
1.0
|
HA3
|
C:GLY92
|
4.2
|
12.1
|
0.3
|
CA
|
C:PRO24
|
4.2
|
7.7
|
1.0
|
O
|
C:VAL91
|
4.2
|
8.4
|
1.0
|
HD2
|
C:ARG29
|
4.3
|
31.1
|
1.0
|
HA3
|
C:GLY92
|
4.3
|
11.5
|
0.7
|
NE
|
C:ARG29
|
4.3
|
27.0
|
1.0
|
CA
|
C:GLY92
|
4.3
|
9.6
|
0.7
|
CA
|
C:GLY92
|
4.4
|
10.1
|
0.3
|
CA
|
C:ASP26
|
4.4
|
14.3
|
1.0
|
O
|
C:HOH474
|
4.4
|
22.4
|
1.0
|
HH12
|
D:ARG47
|
4.5
|
18.0
|
0.6
|
HG3
|
C:ARG29
|
4.5
|
29.0
|
1.0
|
CG
|
C:ARG29
|
4.6
|
24.2
|
1.0
|
H
|
C:THR93
|
4.7
|
12.5
|
0.3
|
HG13
|
C:VAL91
|
4.7
|
11.1
|
1.0
|
CB
|
C:ARG29
|
4.7
|
21.4
|
1.0
|
NH1
|
D:ARG47
|
4.8
|
15.0
|
0.6
|
HA2
|
C:GLY25
|
4.8
|
12.0
|
1.0
|
HH11
|
D:ARG47
|
4.9
|
18.0
|
0.6
|
HB3
|
C:ARG29
|
4.9
|
25.6
|
1.0
|
H
|
C:THR93
|
4.9
|
11.1
|
0.7
|
|
Chlorine binding site 7 out
of 12 in 4k6o
Go back to
Chlorine Binding Sites List in 4k6o
Chlorine binding site 7 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl302
b:10.5
occ:0.96
|
H
|
C:ASN221
|
2.4
|
7.8
|
1.0
|
HE2
|
C:LYS225
|
3.0
|
19.0
|
1.0
|
HA
|
C:ILE220
|
3.0
|
8.3
|
1.0
|
O
|
C:HOH594
|
3.0
|
26.3
|
0.8
|
HG13
|
C:ILE220
|
3.0
|
11.0
|
1.0
|
O
|
C:HOH551
|
3.2
|
23.2
|
0.8
|
N
|
C:ASN221
|
3.2
|
6.5
|
1.0
|
HB2
|
C:GLN224
|
3.3
|
10.7
|
1.0
|
HG21
|
C:VAL103
|
3.5
|
16.9
|
1.0
|
O
|
C:HOH512
|
3.6
|
24.6
|
1.0
|
HG2
|
C:LYS225
|
3.6
|
12.5
|
1.0
|
HB3
|
C:ASN221
|
3.7
|
8.9
|
1.0
|
HG23
|
C:VAL103
|
3.8
|
16.9
|
1.0
|
HG3
|
C:GLN224
|
3.8
|
12.9
|
1.0
|
CA
|
C:ILE220
|
3.8
|
7.0
|
1.0
|
CG1
|
C:ILE220
|
3.9
|
9.1
|
1.0
|
CE
|
C:LYS225
|
3.9
|
15.8
|
1.0
|
O
|
C:ASN221
|
4.0
|
6.4
|
1.0
|
HB3
|
C:GLN224
|
4.0
|
10.7
|
1.0
|
CG2
|
C:VAL103
|
4.0
|
14.1
|
1.0
|
C
|
C:ILE220
|
4.0
|
6.9
|
1.0
|
CB
|
C:GLN224
|
4.0
|
8.9
|
1.0
|
HG12
|
C:ILE220
|
4.0
|
11.0
|
1.0
|
H12
|
C:EOH310
|
4.0
|
20.0
|
1.0
|
CA
|
C:ASN221
|
4.2
|
6.5
|
1.0
|
HG22
|
C:VAL103
|
4.2
|
16.9
|
1.0
|
CB
|
C:ASN221
|
4.3
|
7.5
|
1.0
|
HE3
|
C:LYS225
|
4.3
|
19.0
|
1.0
|
HB2
|
C:ASN221
|
4.4
|
8.9
|
1.0
|
CG
|
C:LYS225
|
4.4
|
10.4
|
1.0
|
CB
|
C:ILE220
|
4.4
|
7.6
|
1.0
|
CG
|
C:GLN224
|
4.4
|
10.8
|
1.0
|
C
|
C:ASN221
|
4.5
|
5.9
|
1.0
|
CD
|
C:LYS225
|
4.6
|
13.2
|
1.0
|
HD3
|
C:LYS225
|
4.7
|
15.8
|
1.0
|
HB
|
C:ILE220
|
4.7
|
9.1
|
1.0
|
HG3
|
C:LYS225
|
4.7
|
12.5
|
1.0
|
HZ3
|
C:LYS225
|
4.7
|
22.8
|
1.0
|
HZ2
|
C:LYS225
|
4.7
|
22.8
|
1.0
|
NZ
|
C:LYS225
|
4.7
|
19.0
|
1.0
|
HG2
|
C:GLN224
|
4.8
|
12.9
|
1.0
|
O
|
C:HOH502
|
4.9
|
23.7
|
1.0
|
O
|
C:ILE219
|
4.9
|
8.4
|
1.0
|
O
|
C:HOH779
|
4.9
|
49.5
|
1.0
|
N
|
C:ILE220
|
5.0
|
6.5
|
1.0
|
|
Chlorine binding site 8 out
of 12 in 4k6o
Go back to
Chlorine Binding Sites List in 4k6o
Chlorine binding site 8 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl303
b:23.4
occ:1.00
|
H
|
C:PHE133
|
2.4
|
7.3
|
1.0
|
O
|
C:HOH446
|
2.4
|
13.5
|
1.0
|
O
|
C:HOH682
|
2.7
|
30.0
|
1.0
|
HG21
|
B:THR110
|
2.8
|
11.6
|
1.0
|
HB2
|
C:PHE133
|
3.0
|
8.9
|
1.0
|
HG1
|
B:THR110
|
3.0
|
9.7
|
1.0
|
O
|
B:HOH493
|
3.1
|
10.8
|
0.5
|
HA
|
C:ASP132
|
3.1
|
7.2
|
1.0
|
N
|
C:PHE133
|
3.2
|
6.1
|
1.0
|
HA2
|
B:GLY153
|
3.2
|
8.1
|
1.0
|
HB2
|
B:MET152
|
3.7
|
9.9
|
1.0
|
CB
|
C:PHE133
|
3.7
|
7.4
|
1.0
|
CG2
|
B:THR110
|
3.7
|
9.6
|
1.0
|
HB3
|
C:PHE133
|
3.7
|
8.9
|
1.0
|
OG1
|
B:THR110
|
3.7
|
8.1
|
1.0
|
HB3
|
B:MET152
|
3.8
|
9.9
|
1.0
|
O
|
B:MET152
|
3.8
|
8.9
|
1.0
|
CA
|
C:ASP132
|
3.9
|
6.0
|
1.0
|
HG23
|
B:THR110
|
4.0
|
11.6
|
1.0
|
CA
|
C:PHE133
|
4.0
|
6.5
|
1.0
|
C
|
C:ASP132
|
4.0
|
5.8
|
1.0
|
C
|
B:MET152
|
4.0
|
7.3
|
1.0
|
CA
|
B:GLY153
|
4.1
|
6.8
|
1.0
|
CB
|
B:THR110
|
4.1
|
8.0
|
1.0
|
O
|
B:HOH600
|
4.1
|
35.3
|
1.0
|
CB
|
B:MET152
|
4.2
|
8.2
|
1.0
|
O
|
C:HOH444
|
4.2
|
12.6
|
1.0
|
O
|
C:PRO131
|
4.2
|
6.0
|
1.0
|
HB
|
B:THR110
|
4.2
|
9.6
|
1.0
|
N
|
B:GLY153
|
4.2
|
6.8
|
1.0
|
OD1
|
C:ASP132
|
4.2
|
9.8
|
1.0
|
HG22
|
B:THR110
|
4.3
|
11.6
|
1.0
|
HA
|
C:PHE133
|
4.5
|
7.8
|
1.0
|
HA3
|
B:GLY153
|
4.5
|
8.1
|
1.0
|
O
|
B:HOH460
|
4.6
|
14.4
|
1.0
|
CG
|
C:ASP132
|
4.6
|
8.3
|
1.0
|
O
|
C:HOH414
|
4.7
|
8.6
|
1.0
|
H
|
B:GLY153
|
4.7
|
8.2
|
1.0
|
CA
|
B:MET152
|
4.8
|
7.4
|
1.0
|
CB
|
C:ASP132
|
4.8
|
7.0
|
1.0
|
H
|
C:ASP134
|
4.8
|
9.2
|
1.0
|
MG
|
C:MG307
|
4.8
|
12.7
|
0.6
|
O
|
C:HOH533
|
4.9
|
12.9
|
0.6
|
N
|
C:ASP132
|
4.9
|
5.3
|
1.0
|
CG
|
C:PHE133
|
5.0
|
8.2
|
1.0
|
C
|
C:PRO131
|
5.0
|
5.3
|
1.0
|
|
Chlorine binding site 9 out
of 12 in 4k6o
Go back to
Chlorine Binding Sites List in 4k6o
Chlorine binding site 9 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 9 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl301
b:13.6
occ:0.69
|
O
|
D:HOH559
|
2.3
|
26.9
|
1.0
|
H
|
D:GLY25
|
2.6
|
9.9
|
1.0
|
H
|
D:ASP26
|
2.6
|
10.7
|
1.0
|
O
|
C:HOH523
|
2.9
|
22.0
|
1.0
|
HG3
|
D:ARG29
|
3.1
|
19.9
|
1.0
|
O
|
D:HOH564
|
3.1
|
19.3
|
0.9
|
O
|
D:HOH670
|
3.1
|
53.3
|
1.0
|
HB2
|
D:PRO24
|
3.2
|
9.4
|
1.0
|
N
|
D:GLY25
|
3.3
|
8.2
|
1.0
|
HA2
|
D:GLY92
|
3.4
|
16.2
|
0.5
|
HO1
|
C:GOL312
|
3.4
|
35.6
|
1.0
|
N
|
D:ASP26
|
3.5
|
8.9
|
1.0
|
HA2
|
D:GLY92
|
3.5
|
11.9
|
0.5
|
HB3
|
D:ASP26
|
3.5
|
13.2
|
1.0
|
HH22
|
C:ARG47
|
3.5
|
18.6
|
0.7
|
HB2
|
D:ASP26
|
3.6
|
13.2
|
1.0
|
HA3
|
D:GLY25
|
3.8
|
10.4
|
1.0
|
CB
|
D:PRO24
|
3.9
|
7.8
|
1.0
|
CB
|
D:ASP26
|
3.9
|
11.0
|
1.0
|
CA
|
D:GLY25
|
4.0
|
8.7
|
1.0
|
CG
|
D:ARG29
|
4.0
|
16.6
|
1.0
|
HA
|
D:PRO24
|
4.0
|
8.5
|
1.0
|
HB3
|
D:PRO24
|
4.1
|
9.4
|
1.0
|
HB2
|
D:ARG29
|
4.1
|
14.8
|
1.0
|
NH2
|
C:ARG47
|
4.1
|
15.5
|
0.7
|
O
|
D:HOH780
|
4.1
|
23.7
|
0.6
|
HA3
|
D:GLY92
|
4.1
|
11.9
|
0.5
|
O
|
D:VAL91
|
4.2
|
9.5
|
1.0
|
C
|
D:PRO24
|
4.2
|
7.2
|
1.0
|
C
|
D:GLY25
|
4.2
|
8.9
|
1.0
|
CA
|
D:GLY92
|
4.2
|
13.5
|
0.5
|
HA3
|
D:GLY92
|
4.3
|
16.2
|
0.5
|
CA
|
D:GLY92
|
4.3
|
9.9
|
0.5
|
CA
|
D:PRO24
|
4.3
|
7.1
|
1.0
|
HE
|
D:ARG29
|
4.3
|
23.4
|
1.0
|
O1
|
C:GOL312
|
4.3
|
29.6
|
1.0
|
H
|
D:THR93
|
4.3
|
14.5
|
0.5
|
CA
|
D:ASP26
|
4.4
|
9.6
|
1.0
|
HH21
|
C:ARG47
|
4.4
|
18.6
|
0.7
|
HG2
|
D:ARG29
|
4.4
|
19.9
|
1.0
|
HH12
|
C:ARG47
|
4.5
|
17.8
|
0.7
|
HG23
|
D:THR93
|
4.5
|
16.5
|
0.5
|
O
|
D:HOH466
|
4.5
|
24.0
|
1.0
|
CB
|
D:ARG29
|
4.5
|
12.4
|
1.0
|
HH12
|
C:ARG47
|
4.5
|
16.1
|
0.3
|
HB3
|
D:ARG29
|
4.6
|
14.8
|
1.0
|
HG13
|
D:VAL91
|
4.7
|
11.1
|
1.0
|
H
|
D:THR93
|
4.7
|
9.4
|
0.5
|
HH22
|
C:ARG47
|
4.8
|
17.0
|
0.3
|
CZ
|
C:ARG47
|
4.9
|
15.1
|
0.7
|
HA2
|
D:GLY25
|
4.9
|
10.4
|
1.0
|
O
|
D:HOH584
|
4.9
|
30.0
|
1.0
|
NH1
|
C:ARG47
|
4.9
|
14.9
|
0.7
|
N
|
D:THR93
|
4.9
|
12.1
|
0.5
|
NE
|
D:ARG29
|
4.9
|
19.5
|
1.0
|
H12
|
C:GOL312
|
5.0
|
34.3
|
1.0
|
C
|
D:VAL91
|
5.0
|
10.0
|
1.0
|
CD
|
D:ARG29
|
5.0
|
18.8
|
1.0
|
O
|
D:ASP26
|
5.0
|
8.9
|
1.0
|
|
Chlorine binding site 10 out
of 12 in 4k6o
Go back to
Chlorine Binding Sites List in 4k6o
Chlorine binding site 10 out
of 12 in the X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution
Mono view
Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 10 of X-Ray Structure Uridine Phosphorylase From Vibrio Cholerae in Complex with 6-Methyluracil at 1.17 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl301
b:10.7
occ:0.74
|
H
|
E:GLY25
|
2.5
|
8.2
|
1.0
|
HH11
|
E:ARG29
|
2.5
|
15.3
|
1.0
|
H
|
E:ASP26
|
2.6
|
9.9
|
1.0
|
HD2
|
E:ARG29
|
3.0
|
15.1
|
1.0
|
O
|
F:HOH601
|
3.1
|
31.1
|
1.0
|
HA2
|
E:GLY92
|
3.2
|
12.2
|
0.5
|
HD3
|
E:ARG29
|
3.2
|
15.1
|
1.0
|
O
|
E:HOH814
|
3.2
|
28.7
|
0.5
|
N
|
E:GLY25
|
3.2
|
6.8
|
1.0
|
HA2
|
E:GLY92
|
3.3
|
10.6
|
0.5
|
HB2
|
E:PRO24
|
3.3
|
7.4
|
1.0
|
NH1
|
E:ARG29
|
3.4
|
12.7
|
1.0
|
N
|
E:ASP26
|
3.4
|
8.3
|
1.0
|
HH21
|
F:ARG47
|
3.4
|
18.3
|
0.4
|
HB3
|
E:ASP26
|
3.5
|
12.8
|
1.0
|
CD
|
E:ARG29
|
3.5
|
12.6
|
1.0
|
HB2
|
E:ASP26
|
3.7
|
12.8
|
1.0
|
HA3
|
E:GLY25
|
3.7
|
8.9
|
1.0
|
HH12
|
E:ARG29
|
3.7
|
15.3
|
1.0
|
CA
|
E:GLY25
|
3.8
|
7.4
|
1.0
|
CB
|
E:ASP26
|
4.0
|
10.7
|
1.0
|
CB
|
E:PRO24
|
4.0
|
6.1
|
1.0
|
CA
|
E:GLY92
|
4.0
|
10.2
|
0.5
|
HA
|
E:PRO24
|
4.0
|
7.3
|
1.0
|
O
|
E:VAL91
|
4.1
|
7.7
|
1.0
|
NH2
|
F:ARG47
|
4.1
|
15.2
|
0.4
|
HA3
|
E:GLY92
|
4.1
|
12.2
|
0.5
|
HB2
|
E:ARG29
|
4.1
|
11.6
|
1.0
|
CA
|
E:GLY92
|
4.1
|
8.8
|
0.5
|
O
|
E:HOH814
|
4.2
|
24.8
|
0.5
|
C
|
E:GLY25
|
4.2
|
7.5
|
1.0
|
HB3
|
E:PRO24
|
4.2
|
7.4
|
1.0
|
H
|
E:THR93
|
4.2
|
9.9
|
0.5
|
C
|
E:PRO24
|
4.2
|
6.2
|
1.0
|
HH22
|
F:ARG47
|
4.2
|
18.3
|
0.4
|
HA3
|
E:GLY92
|
4.2
|
10.6
|
0.5
|
CA
|
E:PRO24
|
4.3
|
6.1
|
1.0
|
CZ
|
E:ARG29
|
4.3
|
11.3
|
1.0
|
H
|
E:THR93
|
4.3
|
9.9
|
0.5
|
NE
|
E:ARG29
|
4.4
|
11.9
|
1.0
|
CA
|
E:ASP26
|
4.4
|
9.2
|
1.0
|
HB3
|
E:ARG29
|
4.4
|
11.6
|
1.0
|
HH22
|
F:ARG47
|
4.5
|
15.2
|
0.6
|
O
|
E:HOH741
|
4.6
|
31.6
|
0.7
|
CB
|
E:ARG29
|
4.6
|
9.7
|
1.0
|
HG23
|
E:THR93
|
4.7
|
16.8
|
1.0
|
HG13
|
E:VAL91
|
4.7
|
10.2
|
1.0
|
CG
|
E:ARG29
|
4.7
|
11.5
|
1.0
|
HA2
|
E:GLY25
|
4.8
|
8.9
|
1.0
|
NH2
|
F:ARG47
|
4.8
|
12.7
|
0.6
|
C
|
E:VAL91
|
4.9
|
7.1
|
1.0
|
N
|
E:THR93
|
4.9
|
8.2
|
1.0
|
N
|
E:GLY92
|
4.9
|
9.4
|
0.5
|
C
|
E:GLY92
|
4.9
|
9.8
|
0.5
|
N
|
E:GLY92
|
4.9
|
8.6
|
0.5
|
|
Reference:
I.I.Prokofev,
A.A.Lashkov,
A.G.Gabdoulkhakov,
M.V.Dontsova,
T.A.Seregina,
A.S.Mironov,
C.Betzel,
A.M.Mikhailov.
Crystallization and Preliminary X-Ray Study of Vibrio Cholerae Uridine Phosphorylase in Complex with 6-Methyluracil Acta Crystallogr.,Sect.F V. 70 60 2014.
ISSN: ESSN 1744-3091
DOI: 10.1107/S2053230X13031877
Page generated: Sun Jul 21 18:01:25 2024
|