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Chlorine in PDB 3cdu: Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate

Enzymatic activity of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate

All present enzymatic activity of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate:
2.7.7.48;

Protein crystallography data

The structure of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate, PDB code: 3cdu was solved by A.Gruez, B.Selisko, M.Roberts, G.Bricogne, C.Bussetta, B.Canard, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.98 / 2.10
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.405, 74.405, 285.881, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 22

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate (pdb code 3cdu). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate, PDB code: 3cdu:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 3cdu

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Chlorine binding site 1 out of 6 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl469

b:30.1
occ:1.00
 O A:HOH730 3.1 47.3 1.0
N A:GLY316 3.2 23.4 1.0
N A:LYS315 3.5 24.8 1.0
O A:HOH770 3.6 46.1 1.0
CA A:TYR314 3.7 22.1 1.0
C A:TYR314 3.7 28.0 1.0
CA A:GLY316 3.9 22.9 1.0
CB A:TYR314 4.1 22.7 1.0
C A:LYS315 4.2 27.9 1.0
CA A:LYS315 4.3 26.0 1.0
CD1 A:TYR314 4.3 20.9 1.0
O A:TYR314 4.4 29.2 1.0
C A:GLY316 4.6 28.2 1.0
CG A:TYR314 4.6 19.8 1.0
CB A:LYS315 4.7 30.9 1.0
N A:ILE317 4.7 23.9 1.0
O A:VAL313 4.9 26.9 1.0

Chlorine binding site 2 out of 6 in 3cdu

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Chlorine binding site 2 out of 6 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl470

b:31.4
occ:1.00
 NZ A:LYS220 3.0 29.3 1.0
NE2 A:HIS468 3.4 53.1 1.0
CB A:HIS466 3.6 63.3 1.0
CE1 A:HIS468 3.7 53.1 1.0
CD2 A:HIS466 3.8 69.9 1.0
CE A:LYS220 3.8 24.5 1.0
CG A:HIS466 4.0 67.7 1.0
CD2 A:LEU216 4.3 37.9 1.0
N A:HIS466 4.5 59.3 1.0
CA A:HIS466 4.6 61.6 1.0
O A:HOH809 4.6 41.1 1.0
CD2 A:HIS468 4.7 53.3 1.0
O A:HIS466 4.7 66.0 1.0
O A:HOH530 5.0 23.0 1.0

Chlorine binding site 3 out of 6 in 3cdu

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Chlorine binding site 3 out of 6 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl471

b:34.1
occ:1.00
 O A:HOH828 3.0 40.8 1.0
N A:GLU35 3.3 26.2 1.0
NZ A:LYS436 3.5 50.5 1.0
ND1 A:HIS399 3.5 23.4 1.0
CE1 A:HIS399 3.5 22.6 1.0
CA A:PHE34 3.8 21.9 1.0
CD1 A:PHE34 3.8 22.3 1.0
CB A:GLU35 4.0 27.7 1.0
CB A:PHE34 4.0 22.2 1.0
C A:PHE34 4.0 27.3 1.0
CG A:HIS399 4.1 21.1 1.0
NE2 A:HIS399 4.1 23.2 1.0
CA A:GLU35 4.2 26.3 1.0
CG A:PHE34 4.4 22.1 1.0
CD2 A:HIS399 4.4 22.6 1.0
CG A:GLU35 4.5 45.0 1.0
CE A:LYS436 4.5 54.1 1.0
O A:GLU35 4.6 25.0 1.0
OE1 A:GLU35 4.7 77.8 1.0
CD A:GLU35 4.7 80.3 1.0
CD A:LYS436 4.8 39.0 1.0
O A:VAL33 4.8 26.4 1.0
CE1 A:PHE34 4.8 22.3 1.0
CB A:HIS399 4.9 17.2 1.0
C A:GLU35 5.0 28.9 1.0

Chlorine binding site 4 out of 6 in 3cdu

Go back to Chlorine Binding Sites List in 3cdu
Chlorine binding site 4 out of 6 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl472

b:30.8
occ:1.00
 O A:HOH530 2.8 23.0 1.0
N A:ASP213 3.1 19.2 1.0
CA A:CYS212 3.6 18.5 1.0
CG A:PRO202 3.8 21.9 1.0
C A:CYS212 3.8 22.3 1.0
CB A:CYS212 3.9 15.8 1.0
CB A:PHE217 3.9 17.1 1.0
O A:ASP213 3.9 20.3 1.0
CB A:ASP213 4.0 18.9 1.0
CA A:ASP213 4.0 17.3 1.0
O A:HOH809 4.2 41.1 1.0
CD1 A:PHE217 4.3 22.5 1.0
C A:ASP213 4.4 19.7 1.0
CG A:PHE217 4.4 19.3 1.0
N A:PHE217 4.5 16.6 1.0
CA A:PHE217 4.6 16.1 1.0
CD2 A:LEU216 4.6 37.9 1.0
CB A:LEU216 4.6 19.9 1.0
CB A:PRO202 4.8 17.4 1.0
CD A:PRO202 4.9 18.6 1.0
N A:CYS212 4.9 22.8 1.0
O A:GLY211 5.0 30.8 1.0

Chlorine binding site 5 out of 6 in 3cdu

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Chlorine binding site 5 out of 6 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl473

b:48.2
occ:1.00
 N A:ASP160 3.1 18.2 1.0
O A:HOH670 3.1 58.8 1.0
CB A:ASP160 3.7 18.4 1.0
CA A:LYS159 3.9 19.8 1.0
C A:LYS159 4.0 22.7 1.0
CA A:ASP160 4.0 17.3 1.0
O A:ASP160 4.1 20.0 1.0
O A:HOH654 4.2 47.7 1.0
CD1 A:ILE176 4.2 44.1 1.0
CG A:LYS159 4.2 26.5 1.0
O A:VAL158 4.3 20.8 1.0
NZ A:LYS406 4.4 38.7 1.0
C A:ASP160 4.5 21.4 1.0
CB A:LYS159 4.6 21.0 1.0
O2 A:GOL510 4.8 57.8 1.0
N A:LYS159 5.0 20.3 1.0
C2 A:GOL510 5.0 55.6 1.0

Chlorine binding site 6 out of 6 in 3cdu

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Chlorine binding site 6 out of 6 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl474

b:91.1
occ:1.00
 O2 A:GOL502 2.8 69.6 1.0
NH2 A:ARG174 3.0 38.2 0.4
NZ A:LYS167 3.0 37.3 0.5
CZ A:ARG174 3.1 51.1 0.4
NH1 A:ARG174 3.1 47.0 0.4
C1 A:GOL502 3.6 67.5 1.0
C2 A:GOL502 3.7 68.2 1.0
O1 A:GOL502 3.7 63.7 1.0
O A:HOH774 3.7 42.0 1.0
NH1 A:ARG163 3.7 32.2 0.3
NH2 A:ARG163 3.7 28.3 0.7
NE A:ARG174 3.9 33.3 0.4
O1 A:POP482 4.1 38.7 0.5
CE A:LYS167 4.1 36.7 0.5
NH2 A:ARG163 4.1 14.8 0.3
C3 A:GOL502 4.1 69.1 1.0
O6 A:POP482 4.1 36.6 0.5
NZ A:LYS167 4.3 23.1 0.5
CZ A:ARG163 4.4 41.5 0.3
O3 A:GOL502 4.6 69.9 1.0
CZ A:ARG163 4.7 43.9 0.7
CD A:ARG174 4.7 28.6 0.4
CD A:ARG174 4.7 19.4 0.6
CD A:LYS167 4.9 29.8 0.5
NZ A:LYS61 4.9 84.5 1.0
O A:HOH610 5.0 55.1 1.0

Reference:

A.Gruez, B.Selisko, M.Roberts, G.Bricogne, C.Bussetta, I.Jabafi, B.Coutard, A.M.De Palma, J.Neyts, B.Canard. The Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase in Complex with Its Protein Primer Vpg Confirms the Existence of A Second Vpg Binding Site on Picornaviridae Polymerases J.Virol. V. 82 9577 2008.
ISSN: ISSN 0022-538X
PubMed: 18632861
DOI: 10.1128/JVI.00631-08
Page generated: Fri Jul 11 03:57:41 2025

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