Chlorine in PDB 5lok: X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
Enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
All present enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution:
2.4.2.3;
Protein crystallography data
The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution, PDB code: 5lok
was solved by
I.I.Prokofev,
A.A.Lashkov,
A.G.Gabdoulkhakov,
M.V.Dontsova,
C.Betzel,
A.M.Mikhailov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
39.68 /
1.11
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.258,
71.772,
89.228,
69.35,
72.17,
85.78
|
|
R / Rfree (%)
|
11.4 /
13.6
|
Other elements in 5lok:
The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution
(pdb code 5lok). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the
X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution, PDB code: 5lok:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 5lok
Go back to
Chlorine Binding Sites List in 5lok
Chlorine binding site 1 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 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 of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl301
b:22.0
occ:0.64
|
O
|
B:HOH431
|
2.4
|
35.3
|
1.0
|
|
H
|
B:GLY25
|
2.5
|
13.2
|
1.0
|
|
H
|
B:ASP26
|
2.5
|
13.9
|
1.0
|
|
O
|
B:HOH610
|
2.8
|
31.2
|
1.0
|
|
HB2
|
B:PRO24
|
3.1
|
11.6
|
1.0
|
|
O
|
B:HOH611
|
3.2
|
18.5
|
0.6
|
|
N
|
B:GLY25
|
3.2
|
11.0
|
1.0
|
|
HG3
|
B:ARG29
|
3.3
|
21.9
|
0.6
|
|
N
|
B:ASP26
|
3.3
|
11.6
|
1.0
|
|
HB3
|
B:ASP26
|
3.4
|
16.5
|
1.0
|
|
O
|
A:HOH596
|
3.4
|
33.9
|
1.0
|
|
HB2
|
B:ASP26
|
3.5
|
16.5
|
1.0
|
|
HA2
|
B:GLY92
|
3.5
|
18.6
|
0.3
|
|
HA2
|
B:GLY92
|
3.6
|
19.3
|
0.7
|
|
HD2
|
B:ARG29
|
3.6
|
29.4
|
0.4
|
|
HA3
|
B:GLY25
|
3.8
|
13.0
|
1.0
|
|
CB
|
B:ASP26
|
3.8
|
13.8
|
1.0
|
|
HH22
|
A:ARG47
|
3.8
|
27.2
|
1.0
|
|
CB
|
B:PRO24
|
3.9
|
9.7
|
1.0
|
|
CA
|
B:GLY25
|
3.9
|
10.8
|
1.0
|
|
HB2
|
B:ARG29
|
4.0
|
18.2
|
0.6
|
|
HB2
|
B:ARG29
|
4.0
|
21.5
|
0.4
|
|
HA
|
B:PRO24
|
4.0
|
11.2
|
1.0
|
|
HB3
|
B:PRO24
|
4.1
|
11.6
|
1.0
|
|
C
|
B:GLY25
|
4.1
|
10.7
|
1.0
|
|
C
|
B:PRO24
|
4.1
|
9.1
|
1.0
|
|
O
|
B:HOH510
|
4.2
|
21.5
|
0.6
|
|
CG
|
B:ARG29
|
4.2
|
18.2
|
0.6
|
|
HA3
|
B:GLY92
|
4.2
|
18.6
|
0.3
|
|
O
|
B:VAL91
|
4.2
|
13.8
|
1.0
|
|
HB3
|
B:ARG29
|
4.2
|
21.5
|
0.4
|
|
CA
|
B:PRO24
|
4.2
|
9.3
|
1.0
|
|
CA
|
B:ASP26
|
4.2
|
12.7
|
1.0
|
|
CA
|
B:GLY92
|
4.3
|
15.5
|
0.3
|
|
HG2
|
B:ARG29
|
4.3
|
25.4
|
0.4
|
|
HH12
|
A:ARG47
|
4.3
|
23.3
|
1.0
|
|
NH2
|
A:ARG47
|
4.4
|
22.7
|
1.0
|
|
HE
|
B:ARG29
|
4.4
|
26.4
|
0.6
|
|
CB
|
B:ARG29
|
4.5
|
17.9
|
0.4
|
|
CD
|
B:ARG29
|
4.5
|
24.5
|
0.4
|
|
HG2
|
B:ARG29
|
4.5
|
21.9
|
0.6
|
|
CB
|
B:ARG29
|
4.5
|
15.2
|
0.6
|
|
O
|
B:HOH418
|
4.5
|
35.8
|
1.0
|
|
CA
|
B:GLY92
|
4.6
|
16.1
|
0.7
|
|
HG23
|
B:THR93
|
4.6
|
20.3
|
0.7
|
|
CG
|
B:ARG29
|
4.7
|
21.1
|
0.4
|
|
HB3
|
B:ARG29
|
4.7
|
18.2
|
0.6
|
|
H
|
B:THR93
|
4.7
|
18.5
|
0.7
|
|
HG13
|
B:VAL91
|
4.8
|
15.9
|
1.0
|
|
H
|
B:THR93
|
4.8
|
21.5
|
0.3
|
|
HH21
|
A:ARG47
|
4.8
|
27.2
|
1.0
|
|
HA2
|
B:GLY25
|
4.8
|
13.0
|
1.0
|
|
NH1
|
A:ARG47
|
4.8
|
19.4
|
1.0
|
|
O
|
B:HOH428
|
4.9
|
42.2
|
1.0
|
|
O
|
B:ASP26
|
4.9
|
12.6
|
1.0
|
|
HA3
|
B:GLY92
|
4.9
|
19.3
|
0.7
|
|
HA
|
B:ASP26
|
4.9
|
15.2
|
1.0
|
|
HE
|
B:ARG29
|
5.0
|
32.7
|
0.4
|
|
CZ
|
A:ARG47
|
5.0
|
20.2
|
1.0
|
|
Chlorine binding site 2 out
of 6 in 5lok
Go back to
Chlorine Binding Sites List in 5lok
Chlorine binding site 2 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 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 of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl302
b:32.6
occ:0.54
|
H
|
B:ASN221
|
2.0
|
24.2
|
0.5
|
|
H
|
B:ASN221
|
2.1
|
24.2
|
0.5
|
|
HG13
|
B:ILE220
|
2.4
|
28.3
|
0.5
|
|
O
|
B:HOH541
|
2.7
|
37.5
|
1.0
|
|
HA
|
B:ILE220
|
2.8
|
26.5
|
0.5
|
|
HA
|
B:ILE220
|
2.9
|
23.7
|
0.5
|
|
N
|
B:ASN221
|
2.9
|
20.2
|
1.0
|
|
HG21
|
B:VAL103
|
3.2
|
25.9
|
0.6
|
|
CG1
|
B:ILE220
|
3.2
|
23.6
|
0.5
|
|
HG12
|
B:ILE220
|
3.3
|
28.3
|
0.5
|
|
HD3
|
B:PRO228
|
3.3
|
72.2
|
1.0
|
|
O
|
B:ASN221
|
3.5
|
20.5
|
1.0
|
|
HB3
|
B:ASN221
|
3.5
|
24.9
|
1.0
|
|
CA
|
B:ILE220
|
3.5
|
22.1
|
0.5
|
|
HG23
|
B:VAL103
|
3.6
|
25.9
|
0.6
|
|
HB2
|
B:GLN224
|
3.6
|
43.6
|
1.0
|
|
CA
|
B:ILE220
|
3.6
|
19.7
|
0.5
|
|
C
|
B:ILE220
|
3.7
|
21.2
|
0.5
|
|
HB
|
B:ILE220
|
3.7
|
27.2
|
0.5
|
|
O
|
B:GLU226
|
3.7
|
56.3
|
1.0
|
|
CG2
|
B:VAL103
|
3.7
|
21.6
|
0.6
|
|
C
|
B:ILE220
|
3.7
|
19.5
|
0.5
|
|
CA
|
B:ASN221
|
3.8
|
19.9
|
1.0
|
|
HG22
|
B:VAL103
|
3.9
|
25.9
|
0.6
|
|
HG22
|
B:ILE220
|
3.9
|
28.2
|
0.5
|
|
HG21
|
B:VAL103
|
4.0
|
30.9
|
0.4
|
|
CB
|
B:ILE220
|
4.0
|
23.2
|
0.5
|
|
C
|
B:ASN221
|
4.0
|
19.4
|
1.0
|
|
CB
|
B:ASN221
|
4.0
|
20.8
|
1.0
|
|
HG23
|
B:VAL103
|
4.1
|
30.9
|
0.4
|
|
CD
|
B:PRO228
|
4.1
|
60.1
|
1.0
|
|
CB
|
B:ILE220
|
4.1
|
22.7
|
0.5
|
|
HD11
|
B:ILE220
|
4.2
|
28.9
|
0.5
|
|
HG3
|
B:PRO228
|
4.3
|
72.5
|
1.0
|
|
HD2
|
B:PRO228
|
4.3
|
72.2
|
1.0
|
|
HB2
|
B:ASN221
|
4.3
|
24.9
|
1.0
|
|
CD1
|
B:ILE220
|
4.3
|
24.1
|
0.5
|
|
CG2
|
B:VAL103
|
4.3
|
25.8
|
0.4
|
|
HG22
|
B:VAL103
|
4.3
|
30.9
|
0.4
|
|
O
|
B:GLN224
|
4.4
|
39.4
|
1.0
|
|
OE1
|
B:GLN224
|
4.4
|
39.5
|
1.0
|
|
HB
|
B:ILE220
|
4.4
|
27.9
|
0.5
|
|
CB
|
B:GLN224
|
4.5
|
36.4
|
1.0
|
|
HA
|
B:ILE227
|
4.5
|
69.5
|
1.0
|
|
HD12
|
B:ILE220
|
4.5
|
28.9
|
0.5
|
|
CG2
|
B:ILE220
|
4.6
|
23.5
|
0.5
|
|
HB3
|
B:GLN224
|
4.6
|
43.6
|
1.0
|
|
HA
|
B:ASN221
|
4.7
|
23.8
|
1.0
|
|
CG
|
B:PRO228
|
4.8
|
60.4
|
1.0
|
|
H
|
B:GLN224
|
4.8
|
37.2
|
1.0
|
|
N
|
B:ILE220
|
4.8
|
22.1
|
0.5
|
|
N
|
B:ILE220
|
4.8
|
17.9
|
0.5
|
|
O
|
B:ILE220
|
4.9
|
20.8
|
0.5
|
|
O
|
B:ILE219
|
4.9
|
22.3
|
0.5
|
|
C
|
B:GLU226
|
4.9
|
56.2
|
1.0
|
|
O
|
B:ILE219
|
4.9
|
17.6
|
0.5
|
|
O
|
B:ILE220
|
4.9
|
18.7
|
0.5
|
|
Chlorine binding site 3 out
of 6 in 5lok
Go back to
Chlorine Binding Sites List in 5lok
Chlorine binding site 3 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 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 of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl301
b:16.0
occ:0.67
|
H
|
C:GLY25
|
2.4
|
14.7
|
1.0
|
|
H
|
C:ASP26
|
2.6
|
16.8
|
1.0
|
|
HH11
|
C:ARG29
|
2.7
|
25.1
|
0.6
|
|
HD2
|
C:ARG29
|
3.0
|
24.3
|
0.6
|
|
O
|
C:HOH594
|
3.1
|
41.3
|
1.0
|
|
HH12
|
C:ARG29
|
3.2
|
32.8
|
0.4
|
|
CZ
|
C:ARG29
|
3.2
|
27.3
|
0.4
|
|
HA2
|
C:GLY92
|
3.2
|
20.4
|
1.0
|
|
N
|
C:GLY25
|
3.2
|
12.3
|
1.0
|
|
O
|
D:HOH590
|
3.2
|
27.9
|
1.0
|
|
NH1
|
C:ARG29
|
3.2
|
27.3
|
0.4
|
|
HH22
|
C:ARG29
|
3.2
|
33.2
|
0.4
|
|
NH2
|
C:ARG29
|
3.2
|
27.7
|
0.4
|
|
HB2
|
C:PRO24
|
3.3
|
14.8
|
1.0
|
|
HG3
|
C:ARG29
|
3.3
|
28.3
|
0.4
|
|
HD3
|
C:ARG29
|
3.4
|
24.3
|
0.6
|
|
N
|
C:ASP26
|
3.4
|
14.0
|
1.0
|
|
NH1
|
C:ARG29
|
3.5
|
21.0
|
0.6
|
|
HA3
|
C:GLY25
|
3.5
|
15.1
|
1.0
|
|
HH11
|
C:ARG29
|
3.6
|
32.8
|
0.4
|
|
CD
|
C:ARG29
|
3.6
|
20.3
|
0.6
|
|
HB3
|
C:ASP26
|
3.6
|
19.2
|
1.0
|
|
HH21
|
C:ARG29
|
3.6
|
33.2
|
0.4
|
|
HB2
|
C:ASP26
|
3.7
|
19.2
|
1.0
|
|
HH22
|
D:ARG47
|
3.7
|
25.6
|
1.0
|
|
CA
|
C:GLY25
|
3.8
|
12.6
|
1.0
|
|
NE
|
C:ARG29
|
3.9
|
26.7
|
0.4
|
|
HH12
|
C:ARG29
|
3.9
|
25.1
|
0.6
|
|
O
|
C:VAL91
|
4.0
|
15.0
|
1.0
|
|
CB
|
C:ASP26
|
4.0
|
16.0
|
1.0
|
|
CB
|
C:PRO24
|
4.1
|
12.3
|
1.0
|
|
HA
|
C:PRO24
|
4.1
|
14.0
|
1.0
|
|
CA
|
C:GLY92
|
4.1
|
17.0
|
1.0
|
|
C
|
C:GLY25
|
4.1
|
13.4
|
1.0
|
|
C
|
C:PRO24
|
4.2
|
11.9
|
1.0
|
|
HG23
|
C:THR93
|
4.2
|
21.9
|
1.0
|
|
CG
|
C:ARG29
|
4.2
|
23.6
|
0.4
|
|
HE
|
C:ARG29
|
4.2
|
32.0
|
0.4
|
|
HB2
|
C:ARG29
|
4.2
|
22.9
|
0.6
|
|
H
|
C:THR93
|
4.3
|
19.7
|
1.0
|
|
HB3
|
C:PRO24
|
4.3
|
14.8
|
1.0
|
|
NH2
|
D:ARG47
|
4.3
|
21.4
|
1.0
|
|
HH12
|
D:ARG47
|
4.3
|
21.9
|
1.0
|
|
HB2
|
C:ARG29
|
4.3
|
26.3
|
0.4
|
|
CA
|
C:PRO24
|
4.3
|
11.7
|
1.0
|
|
CZ
|
C:ARG29
|
4.4
|
20.6
|
0.6
|
|
CA
|
C:ASP26
|
4.4
|
14.8
|
1.0
|
|
NE
|
C:ARG29
|
4.4
|
20.6
|
0.6
|
|
HA3
|
C:GLY92
|
4.5
|
20.4
|
1.0
|
|
HB3
|
C:ARG29
|
4.5
|
22.9
|
0.6
|
|
HG13
|
C:VAL91
|
4.6
|
16.8
|
1.0
|
|
CD
|
C:ARG29
|
4.6
|
25.3
|
0.4
|
|
HH21
|
D:ARG47
|
4.7
|
25.6
|
1.0
|
|
HA2
|
C:GLY25
|
4.7
|
15.1
|
1.0
|
|
CB
|
C:ARG29
|
4.7
|
19.1
|
0.6
|
|
CB
|
C:ARG29
|
4.7
|
21.9
|
0.4
|
|
N
|
C:THR93
|
4.8
|
16.4
|
1.0
|
|
NH1
|
D:ARG47
|
4.8
|
18.3
|
1.0
|
|
CG
|
C:ARG29
|
4.8
|
19.7
|
0.6
|
|
C
|
C:GLY92
|
4.8
|
17.7
|
1.0
|
|
C
|
C:VAL91
|
4.8
|
14.0
|
1.0
|
|
CZ
|
D:ARG47
|
4.9
|
19.8
|
1.0
|
|
HB3
|
C:ARG29
|
4.9
|
26.3
|
0.4
|
|
HG2
|
C:ARG29
|
4.9
|
28.3
|
0.4
|
|
N
|
C:GLY92
|
4.9
|
15.1
|
1.0
|
|
Chlorine binding site 4 out
of 6 in 5lok
Go back to
Chlorine Binding Sites List in 5lok
Chlorine binding site 4 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 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 of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl301
b:53.9
occ:1.00
|
H
|
E:ASN221
|
2.1
|
21.0
|
0.5
|
|
H
|
E:ASN221
|
2.2
|
21.0
|
0.5
|
|
HG13
|
E:ILE220
|
2.4
|
27.9
|
0.5
|
|
O
|
E:HOH515
|
2.6
|
44.0
|
1.0
|
|
HD12
|
E:ILE220
|
2.8
|
26.0
|
0.5
|
|
HA
|
E:ILE220
|
2.8
|
25.8
|
0.5
|
|
HD12
|
E:ILE220
|
2.8
|
28.4
|
0.5
|
|
N
|
E:ASN221
|
3.0
|
17.5
|
1.0
|
|
HA
|
E:ILE220
|
3.0
|
19.2
|
0.5
|
|
HD3
|
E:PRO228
|
3.0
|
77.8
|
1.0
|
|
HG13
|
E:ILE220
|
3.1
|
24.0
|
0.5
|
|
CG1
|
E:ILE220
|
3.2
|
23.2
|
0.5
|
|
HD11
|
E:ILE220
|
3.2
|
28.4
|
0.5
|
|
CD1
|
E:ILE220
|
3.2
|
23.7
|
0.5
|
|
HG21
|
E:VAL103
|
3.2
|
31.4
|
0.7
|
|
HG21
|
E:VAL103
|
3.4
|
33.6
|
0.3
|
|
HD11
|
E:ILE220
|
3.4
|
26.0
|
0.5
|
|
CD1
|
E:ILE220
|
3.4
|
21.7
|
0.5
|
|
HB3
|
E:ASN221
|
3.5
|
21.2
|
1.0
|
|
O
|
E:ASN221
|
3.6
|
18.9
|
1.0
|
|
CA
|
E:ILE220
|
3.6
|
21.5
|
0.5
|
|
HG23
|
E:VAL103
|
3.6
|
31.4
|
0.7
|
|
HB2
|
E:GLN224
|
3.6
|
45.2
|
1.0
|
|
O
|
E:GLU226
|
3.6
|
62.3
|
1.0
|
|
CG1
|
E:ILE220
|
3.7
|
20.0
|
0.5
|
|
HG23
|
E:VAL103
|
3.7
|
33.6
|
0.3
|
|
C
|
E:ILE220
|
3.7
|
19.4
|
0.5
|
|
CG2
|
E:VAL103
|
3.8
|
26.2
|
0.7
|
|
CA
|
E:ILE220
|
3.8
|
16.0
|
0.5
|
|
CG2
|
E:VAL103
|
3.8
|
28.0
|
0.3
|
|
C
|
E:ILE220
|
3.8
|
16.2
|
0.5
|
|
HG22
|
E:VAL103
|
3.8
|
33.6
|
0.3
|
|
CD
|
E:PRO228
|
3.9
|
64.8
|
1.0
|
|
CA
|
E:ASN221
|
3.9
|
17.3
|
1.0
|
|
HG12
|
E:ILE220
|
3.9
|
27.9
|
0.5
|
|
HG22
|
E:VAL103
|
4.0
|
31.4
|
0.7
|
|
CB
|
E:ILE220
|
4.0
|
22.7
|
0.5
|
|
HG3
|
E:PRO228
|
4.0
|
78.0
|
1.0
|
|
HD2
|
E:PRO228
|
4.0
|
77.8
|
1.0
|
|
CB
|
E:ASN221
|
4.1
|
17.7
|
1.0
|
|
O
|
E:GLN224
|
4.1
|
42.3
|
1.0
|
|
C
|
E:ASN221
|
4.1
|
17.1
|
1.0
|
|
HD13
|
E:ILE220
|
4.2
|
28.4
|
0.5
|
|
HB2
|
E:ASN221
|
4.2
|
21.2
|
1.0
|
|
HD13
|
E:ILE220
|
4.3
|
26.0
|
0.5
|
|
CB
|
E:ILE220
|
4.4
|
17.9
|
0.5
|
|
OE1
|
E:GLN224
|
4.4
|
39.5
|
1.0
|
|
HG12
|
E:ILE220
|
4.5
|
24.0
|
0.5
|
|
CG
|
E:PRO228
|
4.5
|
65.0
|
1.0
|
|
CB
|
E:GLN224
|
4.5
|
37.6
|
1.0
|
|
HA
|
E:ILE227
|
4.5
|
76.6
|
1.0
|
|
HB
|
E:ILE220
|
4.6
|
27.2
|
0.5
|
|
HB3
|
E:GLN224
|
4.6
|
45.2
|
1.0
|
|
HA
|
E:ASN221
|
4.7
|
20.8
|
1.0
|
|
H
|
E:GLN224
|
4.8
|
38.0
|
1.0
|
|
HB
|
E:ILE220
|
4.8
|
21.4
|
0.5
|
|
N
|
E:ILE220
|
4.8
|
22.4
|
0.5
|
|
C
|
E:GLU226
|
4.8
|
62.3
|
1.0
|
|
O
|
E:ILE219
|
4.9
|
23.4
|
0.5
|
|
HG23
|
E:ILE220
|
4.9
|
27.4
|
0.5
|
|
C
|
E:GLN224
|
4.9
|
42.3
|
1.0
|
|
N
|
E:ILE220
|
4.9
|
14.2
|
0.5
|
|
O
|
E:ILE220
|
4.9
|
19.1
|
0.5
|
|
N
|
E:PRO228
|
5.0
|
64.8
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 5lok
Go back to
Chlorine Binding Sites List in 5lok
Chlorine binding site 5 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 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 of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Cl302
b:21.7
occ:0.70
|
O
|
E:HOH466
|
2.2
|
29.8
|
0.7
|
|
HH11
|
E:ARG29
|
2.5
|
25.6
|
0.5
|
|
H
|
E:GLY25
|
2.5
|
14.5
|
1.0
|
|
H
|
E:ASP26
|
2.5
|
16.4
|
1.0
|
|
O
|
E:HOH599
|
2.9
|
45.1
|
1.0
|
|
HD3
|
E:ARG29
|
3.0
|
25.1
|
0.5
|
|
HD2
|
E:ARG29
|
3.0
|
25.1
|
0.5
|
|
HD3
|
E:ARG29
|
3.1
|
22.8
|
0.2
|
|
HB2
|
E:PRO24
|
3.2
|
13.3
|
1.0
|
|
N
|
E:GLY25
|
3.2
|
12.1
|
1.0
|
|
HG3
|
E:ARG29
|
3.3
|
23.6
|
0.3
|
|
NH1
|
E:ARG29
|
3.3
|
21.3
|
0.5
|
|
N
|
E:ASP26
|
3.3
|
13.7
|
1.0
|
|
O
|
E:HOH591
|
3.3
|
23.2
|
0.5
|
|
HB3
|
E:ASP26
|
3.4
|
19.9
|
1.0
|
|
O
|
E:HOH591
|
3.4
|
17.3
|
0.5
|
|
CD
|
E:ARG29
|
3.4
|
20.9
|
0.5
|
|
HA2
|
E:GLY92
|
3.5
|
19.5
|
0.6
|
|
HB2
|
E:ASP26
|
3.5
|
19.9
|
1.0
|
|
HA2
|
E:GLY92
|
3.5
|
20.1
|
0.4
|
|
HA3
|
E:GLY25
|
3.7
|
15.0
|
1.0
|
|
HH12
|
E:ARG29
|
3.7
|
25.6
|
0.5
|
|
HH22
|
F:ARG47
|
3.8
|
25.9
|
1.0
|
|
CB
|
E:ASP26
|
3.8
|
16.6
|
1.0
|
|
CA
|
E:GLY25
|
3.8
|
12.5
|
1.0
|
|
CB
|
E:PRO24
|
4.0
|
11.1
|
1.0
|
|
HB2
|
E:ARG29
|
4.0
|
22.2
|
0.5
|
|
CD
|
E:ARG29
|
4.0
|
19.0
|
0.2
|
|
HA
|
E:PRO24
|
4.1
|
13.0
|
1.0
|
|
C
|
E:GLY25
|
4.1
|
12.5
|
1.0
|
|
HB2
|
E:ARG29
|
4.1
|
22.2
|
0.2
|
|
HG23
|
E:THR93
|
4.1
|
21.4
|
0.6
|
|
HB2
|
E:ARG29
|
4.1
|
22.8
|
0.3
|
|
HG3
|
E:ARG29
|
4.1
|
22.6
|
0.2
|
|
CG
|
E:ARG29
|
4.2
|
19.7
|
0.3
|
|
C
|
E:PRO24
|
4.2
|
11.2
|
1.0
|
|
HB3
|
E:PRO24
|
4.2
|
13.3
|
1.0
|
|
CA
|
E:ASP26
|
4.2
|
15.1
|
1.0
|
|
HH12
|
F:ARG47
|
4.2
|
22.9
|
1.0
|
|
O
|
E:VAL91
|
4.2
|
15.3
|
1.0
|
|
CZ
|
E:ARG29
|
4.3
|
21.4
|
0.5
|
|
CA
|
E:PRO24
|
4.3
|
10.9
|
1.0
|
|
NE
|
E:ARG29
|
4.3
|
21.6
|
0.5
|
|
NH2
|
F:ARG47
|
4.4
|
21.6
|
1.0
|
|
CA
|
E:GLY92
|
4.4
|
16.8
|
0.4
|
|
HE
|
E:ARG29
|
4.4
|
24.8
|
0.3
|
|
HB3
|
E:ARG29
|
4.4
|
22.2
|
0.5
|
|
HA3
|
E:GLY92
|
4.4
|
20.1
|
0.4
|
|
H
|
E:THR93
|
4.4
|
17.6
|
0.6
|
|
HD2
|
E:ARG29
|
4.4
|
22.8
|
0.2
|
|
CA
|
E:GLY92
|
4.5
|
16.3
|
0.6
|
|
HG2
|
E:ARG29
|
4.5
|
23.6
|
0.3
|
|
CG
|
E:ARG29
|
4.5
|
18.8
|
0.2
|
|
CB
|
E:ARG29
|
4.5
|
18.5
|
0.5
|
|
CG
|
E:ARG29
|
4.6
|
19.6
|
0.5
|
|
CB
|
E:ARG29
|
4.6
|
19.0
|
0.3
|
|
NH1
|
F:ARG47
|
4.7
|
19.1
|
1.0
|
|
H
|
E:THR93
|
4.7
|
22.5
|
0.4
|
|
HA3
|
E:GLY92
|
4.7
|
19.5
|
0.6
|
|
CB
|
E:ARG29
|
4.8
|
18.5
|
0.2
|
|
HG13
|
E:VAL91
|
4.8
|
16.6
|
1.0
|
|
HA2
|
E:GLY25
|
4.8
|
15.0
|
1.0
|
|
HH21
|
F:ARG47
|
4.8
|
25.9
|
1.0
|
|
HB3
|
E:ARG29
|
4.8
|
22.8
|
0.3
|
|
HE
|
E:ARG29
|
4.9
|
22.9
|
0.2
|
|
CZ
|
F:ARG47
|
4.9
|
19.9
|
1.0
|
|
HA
|
E:ASP26
|
4.9
|
18.1
|
1.0
|
|
O
|
E:ASP26
|
4.9
|
14.8
|
1.0
|
|
HB3
|
E:ARG29
|
5.0
|
22.2
|
0.2
|
|
NE
|
E:ARG29
|
5.0
|
19.1
|
0.2
|
|
N
|
E:THR93
|
5.0
|
14.7
|
0.6
|
|
Chlorine binding site 6 out
of 6 in 5lok
Go back to
Chlorine Binding Sites List in 5lok
Chlorine binding site 6 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 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 of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl301
b:25.6
occ:0.61
|
O
|
F:HOH429
|
2.5
|
28.1
|
0.6
|
|
H
|
F:ASP26
|
2.5
|
17.8
|
1.0
|
|
H
|
F:GLY25
|
2.5
|
16.6
|
1.0
|
|
O
|
E:HOH608
|
2.6
|
45.9
|
1.0
|
|
HB2
|
F:PRO24
|
3.0
|
16.5
|
1.0
|
|
HG3
|
F:ARG29
|
3.0
|
34.5
|
1.0
|
|
O
|
F:HOH561
|
3.2
|
34.1
|
1.0
|
|
N
|
F:GLY25
|
3.2
|
13.8
|
1.0
|
|
HB3
|
F:ASP26
|
3.3
|
21.0
|
1.0
|
|
N
|
F:ASP26
|
3.3
|
14.8
|
1.0
|
|
HB2
|
F:ASP26
|
3.5
|
21.0
|
1.0
|
|
O
|
E:HOH594
|
3.6
|
33.8
|
1.0
|
|
HA2
|
F:GLY92
|
3.6
|
25.7
|
0.7
|
|
HA2
|
F:GLY92
|
3.7
|
22.1
|
0.3
|
|
CB
|
F:PRO24
|
3.8
|
13.7
|
1.0
|
|
CB
|
F:ASP26
|
3.8
|
17.5
|
1.0
|
|
HA3
|
F:GLY25
|
3.8
|
16.4
|
1.0
|
|
CG
|
F:ARG29
|
3.9
|
28.7
|
1.0
|
|
CA
|
F:GLY25
|
3.9
|
13.7
|
1.0
|
|
HH22
|
E:ARG47
|
4.0
|
29.7
|
1.0
|
|
HB3
|
F:PRO24
|
4.0
|
16.5
|
1.0
|
|
HB2
|
F:ARG29
|
4.0
|
28.4
|
1.0
|
|
HA
|
F:PRO24
|
4.0
|
15.6
|
1.0
|
|
C
|
F:PRO24
|
4.1
|
12.4
|
1.0
|
|
C
|
F:GLY25
|
4.1
|
14.2
|
1.0
|
|
HG2
|
F:ARG29
|
4.2
|
34.5
|
1.0
|
|
O
|
F:VAL91
|
4.2
|
19.1
|
1.0
|
|
CA
|
F:PRO24
|
4.2
|
13.0
|
1.0
|
|
CA
|
F:ASP26
|
4.2
|
15.7
|
1.0
|
|
HE
|
F:ARG29
|
4.3
|
42.5
|
1.0
|
|
HA3
|
F:GLY92
|
4.3
|
22.1
|
0.3
|
|
HH12
|
E:ARG47
|
4.4
|
26.1
|
1.0
|
|
CB
|
F:ARG29
|
4.4
|
23.7
|
1.0
|
|
CA
|
F:GLY92
|
4.4
|
18.4
|
0.3
|
|
NH2
|
E:ARG47
|
4.5
|
24.7
|
1.0
|
|
HG23
|
F:THR93
|
4.5
|
26.9
|
0.7
|
|
HB3
|
F:ARG29
|
4.6
|
28.4
|
1.0
|
|
CA
|
F:GLY92
|
4.6
|
21.4
|
0.7
|
|
HG13
|
F:VAL91
|
4.7
|
21.3
|
1.0
|
|
O
|
F:HOH531
|
4.7
|
34.8
|
1.0
|
|
H
|
F:THR93
|
4.7
|
25.2
|
0.7
|
|
O
|
F:ASP26
|
4.8
|
15.7
|
1.0
|
|
HA2
|
F:GLY25
|
4.8
|
16.4
|
1.0
|
|
O
|
F:HOH430
|
4.9
|
45.8
|
1.0
|
|
HH21
|
E:ARG47
|
4.9
|
29.7
|
1.0
|
|
NH1
|
E:ARG47
|
4.9
|
21.7
|
1.0
|
|
HA
|
F:ASP26
|
4.9
|
18.9
|
1.0
|
|
CD
|
F:ARG29
|
4.9
|
32.6
|
1.0
|
|
NE
|
F:ARG29
|
5.0
|
35.5
|
1.0
|
|
HA3
|
F:GLY92
|
5.0
|
25.7
|
0.7
|
|
H
|
F:THR93
|
5.0
|
22.2
|
0.3
|
|
Reference:
I.I.Prokofev,
A.G.Gabdoulkhakov,
A.A.Lashkov,
V.V.Balaev,
C.Betzel,
A.M.Mikhailov.
X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Cytidine and Cytosine at 1.11 A Resolution To Be Published.
Page generated: Sat Dec 12 12:03:44 2020
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