Chlorine in PDB 5m2t: X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution
Enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution
All present enzymatic activity of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution:
2.4.2.3;
Protein crystallography data
The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution, PDB code: 5m2t
was solved by
I.I.Prokofev,
A.A.Lashkov,
A.G.Gabdulkhakov,
C.Betzel,
A.M.Mikhailov,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
44.46 /
1.03
|
|
Space group
|
P 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
64.323,
72.039,
89.193,
110.56,
107.53,
85.83
|
|
R / Rfree (%)
|
11.8 /
13.7
|
Other elements in 5m2t:
The structure of X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 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 Uridine at 1.03 A Resolution
(pdb code 5m2t). 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 Uridine at 1.03 A Resolution, PDB code: 5m2t:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
Chlorine binding site 1 out
of 6 in 5m2t
Go back to
Chlorine Binding Sites List in 5m2t
Chlorine binding site 1 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 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 Uridine at 1.03 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl302
b:35.8
occ:0.97
|
O
|
A:HOH601
|
2.3
|
30.3
|
1.0
|
|
HH21
|
B:ARG29
|
2.5
|
30.5
|
0.5
|
|
H
|
B:GLY25
|
2.5
|
14.7
|
1.0
|
|
H
|
B:ASP26
|
2.6
|
17.5
|
1.0
|
|
HD3
|
B:ARG29
|
3.0
|
25.3
|
0.5
|
|
HA2
|
B:GLY92
|
3.0
|
15.6
|
1.0
|
|
HD2
|
B:ARG29
|
3.1
|
25.3
|
0.5
|
|
NH2
|
B:ARG29
|
3.1
|
25.4
|
0.5
|
|
N
|
B:GLY25
|
3.3
|
12.2
|
1.0
|
|
HA3
|
B:GLY25
|
3.4
|
16.1
|
1.0
|
|
HH22
|
A:ARG47
|
3.4
|
26.4
|
1.0
|
|
N
|
B:ASP26
|
3.4
|
14.6
|
1.0
|
|
HB2
|
B:ASP26
|
3.4
|
20.6
|
1.0
|
|
CD
|
B:ARG29
|
3.4
|
21.1
|
0.5
|
|
HH22
|
B:ARG29
|
3.5
|
30.5
|
0.5
|
|
O
|
B:HOH606
|
3.6
|
27.8
|
1.0
|
|
HH12
|
A:ARG47
|
3.6
|
23.6
|
1.0
|
|
HB3
|
B:ASP26
|
3.7
|
20.6
|
1.0
|
|
CA
|
B:GLY25
|
3.7
|
13.4
|
1.0
|
|
HD2
|
B:ARG29
|
3.9
|
26.7
|
0.5
|
|
CZ
|
B:ARG29
|
3.9
|
24.7
|
0.5
|
|
HB2
|
B:PRO24
|
3.9
|
11.5
|
1.0
|
|
CB
|
B:ASP26
|
3.9
|
17.1
|
1.0
|
|
HG23
|
B:THR93
|
4.0
|
17.0
|
1.0
|
|
CA
|
B:GLY92
|
4.0
|
13.0
|
1.0
|
|
O
|
B:VAL91
|
4.0
|
10.9
|
1.0
|
|
NE
|
B:ARG29
|
4.0
|
23.2
|
0.5
|
|
H
|
B:THR93
|
4.1
|
13.2
|
1.0
|
|
C
|
B:GLY25
|
4.1
|
13.3
|
1.0
|
|
NH2
|
A:ARG47
|
4.1
|
22.0
|
1.0
|
|
HA3
|
B:GLY92
|
4.3
|
15.6
|
1.0
|
|
NH1
|
A:ARG47
|
4.3
|
19.7
|
1.0
|
|
CA
|
B:ASP26
|
4.3
|
15.4
|
1.0
|
|
HA
|
B:PRO24
|
4.3
|
11.0
|
1.0
|
|
C
|
B:PRO24
|
4.4
|
9.8
|
1.0
|
|
HH22
|
B:ARG90
|
4.5
|
12.8
|
0.5
|
|
N
|
B:THR93
|
4.5
|
11.0
|
1.0
|
|
C
|
B:GLY92
|
4.6
|
11.4
|
1.0
|
|
O
|
B:HOH422
|
4.6
|
39.0
|
1.0
|
|
CB
|
B:PRO24
|
4.6
|
9.6
|
1.0
|
|
HA2
|
B:GLY25
|
4.6
|
16.1
|
1.0
|
|
CZ
|
A:ARG47
|
4.6
|
20.1
|
1.0
|
|
HH21
|
A:ARG47
|
4.6
|
26.4
|
1.0
|
|
CA
|
B:PRO24
|
4.6
|
9.2
|
1.0
|
|
HB2
|
B:ARG29
|
4.7
|
21.1
|
0.5
|
|
CG
|
B:ARG29
|
4.7
|
18.6
|
0.5
|
|
HG3
|
B:ARG29
|
4.7
|
22.3
|
0.5
|
|
CD
|
B:ARG29
|
4.7
|
22.3
|
0.5
|
|
HE
|
B:ARG29
|
4.7
|
27.8
|
0.5
|
|
HB3
|
B:PRO24
|
4.8
|
11.5
|
1.0
|
|
HD3
|
B:ARG29
|
4.8
|
26.7
|
0.5
|
|
C
|
B:VAL91
|
4.8
|
9.2
|
1.0
|
|
OE2
|
B:GLU237
|
4.9
|
30.3
|
0.4
|
|
N
|
B:GLY92
|
4.9
|
11.0
|
1.0
|
|
CG2
|
B:THR93
|
4.9
|
14.2
|
1.0
|
|
HH22
|
B:ARG90
|
4.9
|
17.3
|
0.6
|
|
HA
|
B:ASP26
|
4.9
|
18.5
|
1.0
|
|
OE1
|
B:GLU237
|
4.9
|
30.7
|
0.6
|
|
HH11
|
A:ARG47
|
5.0
|
23.6
|
1.0
|
|
HB2
|
B:ARG29
|
5.0
|
19.7
|
0.5
|
|
NH2
|
B:ARG90
|
5.0
|
14.4
|
0.6
|
|
Chlorine binding site 2 out
of 6 in 5m2t
Go back to
Chlorine Binding Sites List in 5m2t
Chlorine binding site 2 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 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 Uridine at 1.03 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl302
b:28.8
occ:0.61
|
O
|
C:HOH471
|
2.5
|
38.1
|
1.0
|
|
H
|
C:ASP26
|
2.6
|
18.8
|
1.0
|
|
H
|
C:GLY25
|
2.6
|
17.7
|
1.0
|
|
O
|
C:HOH617
|
2.9
|
55.3
|
1.0
|
|
HG3
|
C:ARG29
|
3.0
|
31.9
|
1.0
|
|
O
|
C:HOH581
|
3.1
|
35.2
|
1.0
|
|
HB2
|
C:PRO24
|
3.1
|
17.6
|
1.0
|
|
N
|
C:GLY25
|
3.3
|
14.7
|
1.0
|
|
HB3
|
C:ASP26
|
3.4
|
20.4
|
1.0
|
|
N
|
C:ASP26
|
3.4
|
15.7
|
1.0
|
|
HA2
|
C:GLY92
|
3.6
|
19.3
|
0.4
|
|
HB2
|
C:ASP26
|
3.6
|
20.4
|
1.0
|
|
HA2
|
C:GLY92
|
3.6
|
20.2
|
0.6
|
|
CB
|
C:ASP26
|
3.8
|
17.0
|
1.0
|
|
HA3
|
C:GLY25
|
3.9
|
18.2
|
1.0
|
|
CB
|
C:PRO24
|
3.9
|
14.7
|
1.0
|
|
CG
|
C:ARG29
|
3.9
|
26.6
|
1.0
|
|
CA
|
C:GLY25
|
3.9
|
15.1
|
1.0
|
|
HH22
|
D:ARG47
|
4.0
|
34.4
|
1.0
|
|
HA
|
C:PRO24
|
4.0
|
16.9
|
1.0
|
|
HB2
|
C:ARG29
|
4.0
|
28.3
|
1.0
|
|
HB3
|
C:PRO24
|
4.1
|
17.6
|
1.0
|
|
HG2
|
C:ARG29
|
4.1
|
31.9
|
1.0
|
|
C
|
C:PRO24
|
4.2
|
13.7
|
1.0
|
|
C
|
C:GLY25
|
4.2
|
15.5
|
1.0
|
|
O
|
C:VAL91
|
4.2
|
15.1
|
1.0
|
|
CA
|
C:PRO24
|
4.2
|
14.1
|
1.0
|
|
O
|
C:HOH570
|
4.3
|
33.8
|
1.0
|
|
CA
|
C:ASP26
|
4.3
|
16.3
|
1.0
|
|
HG23
|
C:THR93
|
4.3
|
21.8
|
0.6
|
|
HA3
|
C:GLY92
|
4.3
|
19.3
|
0.4
|
|
CA
|
C:GLY92
|
4.4
|
16.1
|
0.4
|
|
HE
|
C:ARG29
|
4.4
|
37.9
|
1.0
|
|
CB
|
C:ARG29
|
4.5
|
23.6
|
1.0
|
|
O
|
C:HOH578
|
4.5
|
34.4
|
1.0
|
|
NH2
|
D:ARG47
|
4.6
|
28.7
|
1.0
|
|
CA
|
C:GLY92
|
4.6
|
16.8
|
0.6
|
|
O
|
C:HOH530
|
4.6
|
21.5
|
0.6
|
|
HB3
|
C:ARG29
|
4.6
|
28.3
|
1.0
|
|
HH12
|
D:ARG47
|
4.6
|
31.6
|
1.0
|
|
H
|
C:THR93
|
4.7
|
21.5
|
0.4
|
|
HG13
|
C:VAL91
|
4.8
|
18.6
|
1.0
|
|
O
|
C:ASP26
|
4.9
|
18.1
|
1.0
|
|
HA2
|
C:GLY25
|
4.9
|
18.2
|
1.0
|
|
HH21
|
D:ARG47
|
4.9
|
34.4
|
1.0
|
|
HA3
|
C:GLY92
|
4.9
|
20.2
|
0.6
|
|
HA
|
C:ASP26
|
5.0
|
19.6
|
1.0
|
|
CD
|
C:ARG29
|
5.0
|
29.3
|
1.0
|
|
Chlorine binding site 3 out
of 6 in 5m2t
Go back to
Chlorine Binding Sites List in 5m2t
Chlorine binding site 3 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 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 Uridine at 1.03 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl303
b:20.0
occ:0.66
|
H
|
C:PHE133
|
2.1
|
12.4
|
1.0
|
|
O
|
B:HOH540
|
2.8
|
11.3
|
1.0
|
|
HG21
|
B:THR110
|
2.8
|
11.6
|
1.0
|
|
HB2
|
C:PHE133
|
2.9
|
15.4
|
1.0
|
|
HA
|
C:ASP132
|
2.9
|
11.5
|
1.0
|
|
N
|
C:PHE133
|
2.9
|
10.3
|
1.0
|
|
O
|
C:HOH532
|
3.1
|
41.8
|
1.0
|
|
HG1
|
B:THR110
|
3.4
|
11.2
|
1.0
|
|
HB3
|
C:PHE133
|
3.4
|
15.4
|
1.0
|
|
O
|
C:HOH415
|
3.5
|
42.1
|
1.0
|
|
CB
|
C:PHE133
|
3.5
|
12.8
|
1.0
|
|
HA2
|
B:GLY153
|
3.6
|
9.5
|
1.0
|
|
CA
|
C:ASP132
|
3.7
|
9.6
|
1.0
|
|
CG2
|
B:THR110
|
3.8
|
9.7
|
1.0
|
|
C
|
C:ASP132
|
3.8
|
9.7
|
1.0
|
|
HB2
|
B:MET152
|
3.8
|
12.4
|
0.7
|
|
O
|
B:MET152
|
3.8
|
10.0
|
0.3
|
|
CA
|
C:PHE133
|
3.8
|
11.5
|
1.0
|
|
HB3
|
B:MET152
|
3.8
|
12.4
|
0.7
|
|
OD1
|
C:ASP132
|
3.8
|
13.1
|
0.8
|
|
HB3
|
B:MET152
|
4.0
|
17.8
|
0.3
|
|
HG23
|
B:THR110
|
4.1
|
11.6
|
1.0
|
|
O
|
C:HOH613
|
4.1
|
26.2
|
1.0
|
|
O
|
B:MET152
|
4.2
|
8.5
|
0.7
|
|
OG1
|
B:THR110
|
4.2
|
9.3
|
1.0
|
|
O
|
C:PRO131
|
4.2
|
8.8
|
1.0
|
|
CG
|
C:ASP132
|
4.2
|
12.9
|
1.0
|
|
HB2
|
B:MET152
|
4.3
|
17.8
|
0.3
|
|
CB
|
B:MET152
|
4.3
|
10.3
|
0.7
|
|
C
|
B:MET152
|
4.3
|
10.0
|
0.3
|
|
HG22
|
B:THR110
|
4.3
|
11.6
|
1.0
|
|
HB
|
B:THR110
|
4.4
|
10.1
|
1.0
|
|
CB
|
B:THR110
|
4.4
|
8.4
|
1.0
|
|
HA
|
C:PHE133
|
4.4
|
13.8
|
1.0
|
|
H
|
C:ASP134
|
4.4
|
15.3
|
1.0
|
|
C
|
B:MET152
|
4.4
|
8.4
|
0.7
|
|
CA
|
B:GLY153
|
4.5
|
8.0
|
1.0
|
|
CB
|
C:ASP132
|
4.5
|
11.3
|
1.0
|
|
CB
|
B:MET152
|
4.6
|
14.8
|
0.3
|
|
N
|
B:GLY153
|
4.6
|
8.3
|
1.0
|
|
O
|
C:HOH548
|
4.7
|
13.0
|
1.0
|
|
O
|
B:HOH502
|
4.7
|
21.0
|
1.0
|
|
N
|
C:ASP132
|
4.8
|
8.7
|
1.0
|
|
HB2
|
C:ASP132
|
4.8
|
13.6
|
1.0
|
|
HA3
|
B:GLY153
|
4.8
|
9.5
|
1.0
|
|
O
|
C:HOH621
|
4.8
|
58.3
|
1.0
|
|
CG
|
C:PHE133
|
4.8
|
14.4
|
1.0
|
|
OD2
|
C:ASP132
|
4.9
|
12.6
|
0.7
|
|
C
|
C:PRO131
|
4.9
|
8.4
|
1.0
|
|
C
|
C:PHE133
|
4.9
|
11.9
|
1.0
|
|
N
|
C:ASP134
|
5.0
|
12.7
|
1.0
|
|
O
|
C:ASP132
|
5.0
|
10.1
|
1.0
|
|
HE2
|
B:MET152
|
5.0
|
23.8
|
0.3
|
|
Chlorine binding site 4 out
of 6 in 5m2t
Go back to
Chlorine Binding Sites List in 5m2t
Chlorine binding site 4 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 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 Uridine at 1.03 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl302
b:19.1
occ:0.71
|
H
|
D:PHE133
|
2.1
|
8.9
|
1.0
|
|
O
|
E:HOH544
|
2.7
|
11.3
|
1.0
|
|
HG21
|
E:THR110
|
2.8
|
12.6
|
1.0
|
|
HB2
|
D:PHE133
|
2.9
|
10.8
|
1.0
|
|
N
|
D:PHE133
|
3.0
|
7.4
|
1.0
|
|
HA
|
D:ASP132
|
3.0
|
8.5
|
1.0
|
|
O
|
D:HOH541
|
3.1
|
41.4
|
1.0
|
|
HG1
|
E:THR110
|
3.3
|
11.3
|
1.0
|
|
HB3
|
D:PHE133
|
3.4
|
10.8
|
1.0
|
|
CB
|
D:PHE133
|
3.5
|
9.0
|
1.0
|
|
HA2
|
E:GLY153
|
3.5
|
9.7
|
1.0
|
|
O
|
D:HOH640
|
3.7
|
71.9
|
1.0
|
|
CG2
|
E:THR110
|
3.7
|
10.5
|
1.0
|
|
CA
|
D:ASP132
|
3.8
|
7.1
|
1.0
|
|
CA
|
D:PHE133
|
3.8
|
8.0
|
1.0
|
|
C
|
D:ASP132
|
3.8
|
6.9
|
1.0
|
|
HB2
|
E:MET152
|
3.9
|
12.4
|
1.0
|
|
HB3
|
E:MET152
|
3.9
|
12.4
|
1.0
|
|
OD1
|
D:ASP132
|
4.0
|
10.2
|
0.8
|
|
OG1
|
E:THR110
|
4.0
|
9.4
|
1.0
|
|
HG23
|
E:THR110
|
4.1
|
12.6
|
1.0
|
|
O
|
E:MET152
|
4.1
|
9.6
|
1.0
|
|
O
|
D:HOH656
|
4.2
|
20.1
|
1.0
|
|
O
|
D:PRO131
|
4.2
|
7.1
|
1.0
|
|
HB
|
E:THR110
|
4.3
|
10.8
|
1.0
|
|
CB
|
E:THR110
|
4.3
|
9.0
|
1.0
|
|
HG22
|
E:THR110
|
4.3
|
12.6
|
1.0
|
|
HA
|
D:PHE133
|
4.3
|
9.6
|
1.0
|
|
C
|
E:MET152
|
4.4
|
8.7
|
1.0
|
|
CG
|
D:ASP132
|
4.4
|
9.7
|
1.0
|
|
CA
|
E:GLY153
|
4.4
|
8.1
|
1.0
|
|
CB
|
E:MET152
|
4.4
|
10.4
|
1.0
|
|
H
|
D:ASP134
|
4.4
|
10.4
|
1.0
|
|
N
|
E:GLY153
|
4.6
|
8.4
|
1.0
|
|
O
|
D:HOH453
|
4.6
|
21.6
|
0.5
|
|
CB
|
D:ASP132
|
4.6
|
8.5
|
1.0
|
|
O
|
E:HOH514
|
4.6
|
16.0
|
1.0
|
|
O
|
D:HOH589
|
4.7
|
11.4
|
1.0
|
|
HA3
|
E:GLY153
|
4.8
|
9.7
|
1.0
|
|
MG
|
D:MG304
|
4.8
|
16.2
|
0.3
|
|
CG
|
D:PHE133
|
4.8
|
10.5
|
1.0
|
|
N
|
D:ASP132
|
4.8
|
6.4
|
1.0
|
|
HB2
|
D:ASP132
|
4.9
|
10.2
|
1.0
|
|
C
|
D:PHE133
|
5.0
|
8.0
|
1.0
|
|
C
|
D:PRO131
|
5.0
|
6.2
|
1.0
|
|
Chlorine binding site 5 out
of 6 in 5m2t
Go back to
Chlorine Binding Sites List in 5m2t
Chlorine binding site 5 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 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 Uridine at 1.03 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl303
b:32.1
occ:0.84
|
O
|
D:HOH509
|
2.4
|
33.4
|
1.0
|
|
HH21
|
D:ARG29
|
2.5
|
23.6
|
0.2
|
|
H
|
D:ASP26
|
2.5
|
17.5
|
1.0
|
|
HD2
|
D:ARG29
|
2.6
|
22.8
|
0.4
|
|
H
|
D:GLY25
|
2.6
|
16.3
|
1.0
|
|
HE
|
D:ARG29
|
2.6
|
23.1
|
0.2
|
|
O
|
C:HOH591
|
2.8
|
34.8
|
1.0
|
|
NH2
|
D:ARG29
|
2.9
|
19.7
|
0.2
|
|
HH11
|
D:ARG29
|
2.9
|
20.5
|
0.4
|
|
NE
|
D:ARG29
|
3.0
|
19.3
|
0.2
|
|
HG3
|
D:ARG29
|
3.1
|
24.1
|
0.5
|
|
CZ
|
D:ARG29
|
3.2
|
19.4
|
0.2
|
|
HB2
|
D:PRO24
|
3.2
|
15.1
|
1.0
|
|
N
|
D:GLY25
|
3.3
|
13.6
|
1.0
|
|
N
|
D:ASP26
|
3.3
|
14.6
|
1.0
|
|
HB3
|
D:ASP26
|
3.4
|
19.2
|
1.0
|
|
HH22
|
D:ARG29
|
3.4
|
23.6
|
0.2
|
|
CD
|
D:ARG29
|
3.5
|
19.0
|
0.4
|
|
HB2
|
D:ASP26
|
3.5
|
19.2
|
1.0
|
|
HD3
|
D:ARG29
|
3.6
|
22.8
|
0.4
|
|
O
|
D:HOH574
|
3.6
|
47.6
|
1.0
|
|
HA2
|
D:GLY92
|
3.6
|
13.4
|
0.5
|
|
NH1
|
D:ARG29
|
3.6
|
17.1
|
0.4
|
|
HA2
|
D:GLY92
|
3.7
|
16.7
|
0.5
|
|
HA3
|
D:GLY25
|
3.8
|
16.6
|
1.0
|
|
CB
|
D:ASP26
|
3.8
|
16.0
|
1.0
|
|
HB2
|
D:ARG29
|
3.8
|
23.1
|
0.4
|
|
CB
|
D:PRO24
|
3.9
|
12.6
|
1.0
|
|
CA
|
D:GLY25
|
3.9
|
13.9
|
1.0
|
|
HH22
|
C:ARG47
|
4.0
|
25.6
|
0.5
|
|
HB2
|
D:ARG29
|
4.0
|
23.5
|
0.2
|
|
HG3
|
D:ARG29
|
4.0
|
23.4
|
0.2
|
|
HA
|
D:PRO24
|
4.0
|
14.9
|
1.0
|
|
CG
|
D:ARG29
|
4.0
|
20.1
|
0.5
|
|
CD
|
D:ARG29
|
4.1
|
19.4
|
0.2
|
|
HB3
|
D:PRO24
|
4.1
|
15.1
|
1.0
|
|
HB2
|
D:ARG29
|
4.1
|
24.0
|
0.5
|
|
HH12
|
D:ARG29
|
4.1
|
20.5
|
0.4
|
|
HD3
|
D:ARG29
|
4.1
|
23.3
|
0.2
|
|
C
|
D:GLY25
|
4.1
|
13.9
|
1.0
|
|
C
|
D:PRO24
|
4.2
|
12.7
|
1.0
|
|
HG23
|
D:THR93
|
4.2
|
17.6
|
0.5
|
|
O
|
D:VAL91
|
4.2
|
12.4
|
1.0
|
|
CA
|
D:ASP26
|
4.2
|
15.7
|
1.0
|
|
CA
|
D:PRO24
|
4.2
|
12.4
|
1.0
|
|
NH1
|
D:ARG29
|
4.2
|
19.3
|
0.2
|
|
HE
|
D:ARG29
|
4.3
|
23.4
|
0.5
|
|
NE
|
D:ARG29
|
4.4
|
18.5
|
0.4
|
|
HB3
|
D:ARG29
|
4.4
|
23.1
|
0.4
|
|
HG2
|
D:ARG29
|
4.4
|
24.1
|
0.5
|
|
CG
|
D:ARG29
|
4.4
|
19.5
|
0.2
|
|
CB
|
D:ARG29
|
4.4
|
19.3
|
0.4
|
|
CG
|
D:ARG29
|
4.4
|
19.2
|
0.4
|
|
CA
|
D:GLY92
|
4.4
|
11.2
|
0.5
|
|
CZ
|
D:ARG29
|
4.4
|
17.8
|
0.4
|
|
O
|
D:HOH419
|
4.5
|
51.8
|
1.0
|
|
O
|
D:HOH571
|
4.5
|
22.1
|
0.5
|
|
HA3
|
D:GLY92
|
4.5
|
13.4
|
0.5
|
|
NH2
|
C:ARG47
|
4.5
|
21.4
|
0.5
|
|
CB
|
D:ARG29
|
4.5
|
20.0
|
0.5
|
|
CB
|
D:ARG29
|
4.6
|
19.6
|
0.2
|
|
HH12
|
D:ARG29
|
4.6
|
23.2
|
0.2
|
|
CA
|
D:GLY92
|
4.7
|
13.9
|
0.5
|
|
HH11
|
D:ARG29
|
4.7
|
23.2
|
0.2
|
|
HH22
|
C:ARG47
|
4.7
|
17.5
|
0.5
|
|
HB3
|
D:ARG29
|
4.7
|
24.0
|
0.5
|
|
HH12
|
C:ARG47
|
4.8
|
25.6
|
0.5
|
|
HG3
|
D:ARG29
|
4.8
|
23.1
|
0.4
|
|
HG13
|
D:VAL91
|
4.8
|
13.9
|
1.0
|
|
HB3
|
D:ARG29
|
4.8
|
23.5
|
0.2
|
|
HH21
|
C:ARG47
|
4.8
|
25.6
|
0.5
|
|
HA2
|
D:GLY25
|
4.9
|
16.6
|
1.0
|
|
O
|
D:ASP26
|
4.9
|
17.4
|
1.0
|
|
HH12
|
C:ARG47
|
4.9
|
18.8
|
0.5
|
|
H
|
D:THR93
|
4.9
|
15.2
|
0.5
|
|
HD2
|
D:ARG29
|
4.9
|
23.3
|
0.2
|
|
H
|
D:THR93
|
4.9
|
15.8
|
0.5
|
|
HA
|
D:ASP26
|
4.9
|
18.8
|
1.0
|
|
NE
|
D:ARG29
|
5.0
|
19.5
|
0.5
|
|
CD
|
D:ARG29
|
5.0
|
20.0
|
0.5
|
|
Chlorine binding site 6 out
of 6 in 5m2t
Go back to
Chlorine Binding Sites List in 5m2t
Chlorine binding site 6 out
of 6 in the X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 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 Uridine at 1.03 A Resolution within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Cl302
b:21.7
occ:0.78
|
H
|
F:GLY25
|
2.5
|
15.7
|
1.0
|
|
H
|
F:ASP26
|
2.7
|
17.0
|
1.0
|
|
HH11
|
F:ARG29
|
2.7
|
24.2
|
0.4
|
|
HD2
|
F:ARG29
|
2.8
|
23.1
|
0.4
|
|
O
|
F:HOH644
|
3.1
|
42.8
|
1.0
|
|
HH22
|
F:ARG29
|
3.1
|
21.4
|
0.3
|
|
N
|
F:GLY25
|
3.2
|
13.1
|
1.0
|
|
HD2
|
F:ARG29
|
3.2
|
25.8
|
0.3
|
|
O
|
E:HOH597
|
3.2
|
37.7
|
1.0
|
|
NH2
|
F:ARG29
|
3.3
|
17.8
|
0.3
|
|
HA2
|
F:GLY92
|
3.3
|
19.2
|
1.0
|
|
HB2
|
F:PRO24
|
3.4
|
13.7
|
1.0
|
|
NH1
|
F:ARG29
|
3.4
|
20.1
|
0.4
|
|
HG3
|
F:ARG29
|
3.4
|
22.8
|
0.3
|
|
N
|
F:ASP26
|
3.5
|
14.2
|
1.0
|
|
CZ
|
F:ARG29
|
3.6
|
18.5
|
0.3
|
|
HH21
|
F:ARG29
|
3.6
|
21.4
|
0.3
|
|
HH12
|
F:ARG29
|
3.6
|
22.0
|
0.3
|
|
HB3
|
F:ASP26
|
3.6
|
18.5
|
1.0
|
|
CD
|
F:ARG29
|
3.7
|
19.2
|
0.4
|
|
HD3
|
F:ARG29
|
3.7
|
23.1
|
0.4
|
|
HB2
|
F:ASP26
|
3.7
|
18.5
|
1.0
|
|
HA3
|
F:GLY25
|
3.7
|
16.1
|
1.0
|
|
HH22
|
E:ARG47
|
3.7
|
31.0
|
1.0
|
|
NH1
|
F:ARG29
|
3.7
|
18.4
|
0.3
|
|
HH12
|
F:ARG29
|
3.8
|
24.2
|
0.4
|
|
CA
|
F:GLY25
|
3.9
|
13.4
|
1.0
|
|
CB
|
F:ASP26
|
4.0
|
15.4
|
1.0
|
|
HA
|
F:PRO24
|
4.0
|
13.3
|
1.0
|
|
O
|
F:VAL91
|
4.1
|
11.5
|
1.0
|
|
HG23
|
F:THR93
|
4.1
|
20.9
|
1.0
|
|
CB
|
F:PRO24
|
4.1
|
11.4
|
1.0
|
|
CD
|
F:ARG29
|
4.2
|
21.5
|
0.3
|
|
C
|
F:PRO24
|
4.2
|
11.3
|
1.0
|
|
C
|
F:GLY25
|
4.2
|
13.5
|
1.0
|
|
HB2
|
F:ARG29
|
4.2
|
22.2
|
0.4
|
|
HB2
|
F:ARG29
|
4.2
|
23.7
|
0.3
|
|
HB3
|
F:PRO24
|
4.2
|
13.7
|
1.0
|
|
HH11
|
F:ARG29
|
4.3
|
22.0
|
0.3
|
|
CA
|
F:GLY92
|
4.3
|
16.0
|
1.0
|
|
HB2
|
F:ARG29
|
4.3
|
22.3
|
0.3
|
|
CZ
|
F:ARG29
|
4.3
|
20.3
|
0.4
|
|
NE
|
F:ARG29
|
4.3
|
19.3
|
0.3
|
|
NH2
|
E:ARG47
|
4.3
|
25.8
|
1.0
|
|
CA
|
F:PRO24
|
4.3
|
11.1
|
1.0
|
|
CG
|
F:ARG29
|
4.3
|
19.0
|
0.3
|
|
NE
|
F:ARG29
|
4.4
|
19.9
|
0.4
|
|
CA
|
F:ASP26
|
4.4
|
14.9
|
1.0
|
|
HH12
|
E:ARG47
|
4.5
|
29.0
|
1.0
|
|
HB3
|
F:ARG29
|
4.5
|
23.7
|
0.3
|
|
HD3
|
F:ARG29
|
4.5
|
25.8
|
0.3
|
|
H
|
F:THR93
|
4.6
|
19.1
|
1.0
|
|
HH21
|
E:ARG47
|
4.6
|
31.0
|
1.0
|
|
HG2
|
F:ARG29
|
4.6
|
24.9
|
0.3
|
|
HA3
|
F:GLY92
|
4.6
|
19.2
|
1.0
|
|
HG13
|
F:VAL91
|
4.7
|
13.8
|
1.0
|
|
HB3
|
F:ARG29
|
4.7
|
22.2
|
0.4
|
|
CB
|
F:ARG29
|
4.7
|
19.8
|
0.3
|
|
HE
|
F:ARG29
|
4.7
|
23.2
|
0.3
|
|
CB
|
F:ARG29
|
4.8
|
18.5
|
0.4
|
|
CG
|
F:ARG29
|
4.8
|
20.7
|
0.3
|
|
CB
|
F:ARG29
|
4.8
|
18.6
|
0.3
|
|
HA2
|
F:GLY25
|
4.8
|
16.1
|
1.0
|
|
CG
|
F:ARG29
|
4.8
|
18.8
|
0.4
|
|
C
|
F:GLY92
|
4.9
|
16.2
|
1.0
|
|
C
|
F:VAL91
|
4.9
|
10.2
|
1.0
|
|
CD
|
F:ARG29
|
4.9
|
19.4
|
0.3
|
|
HB3
|
F:ARG29
|
4.9
|
22.3
|
0.3
|
|
N
|
F:THR93
|
4.9
|
15.9
|
1.0
|
|
HE
|
F:ARG29
|
5.0
|
26.3
|
0.3
|
|
Reference:
I.I.Prokofev,
A.A.Lashkov,
A.G.Gabdulkhakov,
M.V.Dontsova,
C.Betzel,
A.M.Mikhailov.
X-Ray Structure of Uridine Phosphorylase From Vibrio Cholerae in Complex with Uridine at 1.03 A Resolution To Be Published.
Page generated: Sat Jul 12 05:16:24 2025
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