Chlorine in PDB 6ba0: Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
Protein crystallography data
The structure of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis, PDB code: 6ba0
was solved by
N.Renner,
D.A.Jacques,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
61.87 /
2.03
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
83.070,
79.360,
115.990,
90.00,
99.62,
90.00
|
R / Rfree (%)
|
18.6 /
21.8
|
Other elements in 6ba0:
The structure of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
(pdb code 6ba0). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the
Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis, PDB code: 6ba0:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
Chlorine binding site 1 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 1 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl402
b:45.2
occ:1.00
|
O
|
A:HOH519
|
3.5
|
20.6
|
1.0
|
NE
|
A:ARG204
|
3.7
|
33.6
|
1.0
|
NZ
|
A:LYS309
|
3.8
|
32.1
|
1.0
|
NH2
|
A:ARG204
|
3.8
|
28.7
|
1.0
|
CZ
|
A:ARG204
|
4.2
|
26.6
|
1.0
|
CG2
|
A:ILE305
|
4.3
|
22.8
|
1.0
|
CE
|
A:LYS309
|
4.5
|
29.1
|
1.0
|
CG
|
A:ARG204
|
4.7
|
28.7
|
1.0
|
CD
|
A:ARG204
|
4.7
|
29.4
|
1.0
|
CB
|
A:ARG204
|
4.7
|
28.5
|
1.0
|
|
Chlorine binding site 2 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 2 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl403
b:38.5
occ:1.00
|
NH2
|
A:ARG257
|
3.7
|
21.9
|
1.0
|
NH1
|
A:ARG257
|
3.8
|
24.2
|
1.0
|
CZ
|
A:ARG257
|
4.2
|
22.3
|
1.0
|
|
Chlorine binding site 3 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 3 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl402
b:41.6
occ:1.00
|
O
|
B:HOH654
|
3.5
|
25.5
|
1.0
|
NH1
|
B:ARG143
|
3.5
|
34.8
|
1.0
|
NH2
|
B:ARG143
|
3.6
|
30.8
|
1.0
|
CZ
|
B:ARG143
|
4.1
|
25.9
|
1.0
|
CD
|
B:PRO116
|
4.4
|
28.0
|
1.0
|
OE1
|
B:GLU115
|
4.8
|
64.7
|
1.0
|
O
|
B:MET112
|
5.0
|
23.8
|
1.0
|
|
Chlorine binding site 4 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 4 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl403
b:51.8
occ:1.00
|
O
|
B:HOH581
|
3.1
|
29.9
|
1.0
|
NZ
|
B:LYS309
|
3.5
|
38.2
|
1.0
|
NE
|
B:ARG204
|
3.5
|
33.4
|
1.0
|
NH2
|
B:ARG204
|
3.7
|
29.6
|
1.0
|
CG2
|
B:ILE305
|
4.0
|
20.0
|
1.0
|
CZ
|
B:ARG204
|
4.1
|
31.1
|
1.0
|
CE
|
B:LYS309
|
4.4
|
27.9
|
1.0
|
CG
|
B:ARG204
|
4.5
|
28.6
|
1.0
|
CB
|
B:ARG204
|
4.5
|
21.3
|
1.0
|
CD
|
B:ARG204
|
4.6
|
28.5
|
1.0
|
CD1
|
B:ILE305
|
5.0
|
20.6
|
1.0
|
|
Chlorine binding site 5 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 5 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Cl404
b:42.9
occ:1.00
|
NH2
|
B:ARG257
|
3.6
|
24.4
|
1.0
|
NH1
|
B:ARG257
|
3.7
|
25.5
|
1.0
|
CZ
|
B:ARG257
|
4.1
|
26.4
|
1.0
|
|
Chlorine binding site 6 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 6 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 6 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl402
b:51.3
occ:1.00
|
CD
|
C:ARG72
|
3.1
|
35.7
|
1.0
|
O
|
C:LYS168
|
3.2
|
9.9
|
1.0
|
O
|
C:HOH632
|
3.3
|
27.9
|
1.0
|
O
|
C:HOH551
|
3.4
|
29.4
|
1.0
|
NH1
|
C:ARG72
|
3.9
|
55.2
|
1.0
|
CG
|
C:ARG72
|
4.1
|
31.9
|
1.0
|
NE
|
C:ARG72
|
4.2
|
38.0
|
1.0
|
CD2
|
C:LEU270
|
4.2
|
26.3
|
1.0
|
O
|
C:HOH566
|
4.3
|
18.4
|
1.0
|
C
|
C:LYS168
|
4.3
|
12.1
|
1.0
|
CD
|
C:LYS168
|
4.4
|
16.8
|
1.0
|
CZ
|
C:ARG72
|
4.5
|
30.9
|
1.0
|
O
|
C:VAL169
|
4.7
|
11.8
|
1.0
|
OE1
|
C:GLU75
|
4.7
|
47.7
|
1.0
|
O
|
C:HOH598
|
4.8
|
22.6
|
1.0
|
CB
|
C:ARG72
|
4.9
|
32.4
|
1.0
|
CD
|
C:PRO171
|
4.9
|
12.6
|
1.0
|
CG
|
C:PRO171
|
4.9
|
11.8
|
1.0
|
CA
|
C:VAL169
|
4.9
|
14.2
|
1.0
|
NZ
|
C:LYS168
|
4.9
|
14.5
|
1.0
|
C
|
C:VAL169
|
5.0
|
11.7
|
1.0
|
|
Chlorine binding site 7 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 7 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 7 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Cl403
b:48.4
occ:1.00
|
O
|
C:HOH636
|
3.1
|
37.5
|
1.0
|
O
|
C:HOH516
|
3.2
|
38.4
|
1.0
|
CG
|
C:ARG224
|
3.6
|
19.8
|
1.0
|
O
|
C:HOH530
|
3.6
|
31.8
|
1.0
|
NH1
|
C:ARG224
|
3.7
|
22.8
|
1.0
|
CD
|
C:ARG224
|
3.7
|
21.8
|
1.0
|
NE
|
C:ARG224
|
4.7
|
18.8
|
1.0
|
CZ
|
C:ARG224
|
4.7
|
20.8
|
1.0
|
O
|
C:ILE234
|
4.8
|
14.1
|
1.0
|
O
|
C:ARG224
|
4.8
|
19.9
|
1.0
|
CB
|
C:LYS228
|
4.9
|
33.4
|
1.0
|
O
|
C:HOH685
|
4.9
|
34.4
|
1.0
|
O
|
C:HOH511
|
4.9
|
31.1
|
1.0
|
CA
|
C:LYS228
|
4.9
|
24.1
|
1.0
|
|
Chlorine binding site 8 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 8 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 8 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl402
b:43.2
occ:1.00
|
O
|
D:HOH504
|
3.4
|
33.0
|
1.0
|
CG
|
D:ARG224
|
3.6
|
19.4
|
1.0
|
NH1
|
D:ARG224
|
3.6
|
24.7
|
1.0
|
O
|
D:HOH526
|
3.6
|
24.0
|
1.0
|
CD
|
D:ARG224
|
3.7
|
22.5
|
1.0
|
CZ
|
D:ARG224
|
4.5
|
26.5
|
1.0
|
NE
|
D:ARG224
|
4.6
|
22.3
|
1.0
|
O
|
D:ILE234
|
4.7
|
16.5
|
1.0
|
O
|
D:ARG224
|
5.0
|
17.2
|
1.0
|
|
Chlorine binding site 9 out
of 9 in 6ba0
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Chlorine Binding Sites List in 6ba0
Chlorine binding site 9 out
of 9 in the Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 9 of Pyrimidine-Specific Ribonucleoside Hydrolase From Gardnerella Vaginalis within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Cl403
b:38.4
occ:1.00
|
NH1
|
D:ARG257
|
3.6
|
23.3
|
1.0
|
O
|
D:HOH698
|
3.7
|
31.9
|
1.0
|
NH2
|
D:ARG257
|
3.7
|
22.2
|
1.0
|
O
|
D:HOH544
|
3.9
|
28.0
|
1.0
|
CZ
|
D:ARG257
|
4.2
|
22.3
|
1.0
|
|
Reference:
N.Renner,
D.A.Jacques.
Pyrimidine-Specific Ribonucleoside Hydrolase Rihb From Gardnerella Vaginalis To Be Published.
Page generated: Fri Jul 26 22:39:10 2024
|