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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:

Calcium (Ca) 4 atoms

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 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 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 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 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 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 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 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 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 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: Sat Jul 12 11:47:50 2025

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