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Chlorine in PDB 3cdw: Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and A Pyrophosphate

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

All present enzymatic activity of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and 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 Protein Primer Vpg and A Pyrophosphate, PDB code: 3cdw 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) 27.45 / 2.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 74.213, 74.213, 285.591, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 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 Protein Primer Vpg and A Pyrophosphate (pdb code 3cdw). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 7 binding sites of Chlorine where determined in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and A Pyrophosphate, PDB code: 3cdw:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7;

Chlorine binding site 1 out of 7 in 3cdw

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Chlorine binding site 1 out of 7 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and 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 Protein Primer Vpg and A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl469

b:43.1
occ:1.00
 O A:HOH726 3.1 69.1 1.0
N A:GLY316 3.2 43.0 1.0
N A:LYS315 3.5 41.4 1.0
CA A:TYR314 3.7 34.3 1.0
C A:TYR314 3.7 42.3 1.0
O A:HOH765 3.8 50.0 1.0
CA A:GLY316 3.9 42.4 1.0
CB A:TYR314 4.0 32.2 1.0
C A:LYS315 4.2 46.2 1.0
CD1 A:TYR314 4.3 28.8 1.0
CA A:LYS315 4.3 41.9 1.0
O A:TYR314 4.4 42.2 1.0
CG A:TYR314 4.6 28.5 1.0
C A:GLY316 4.6 47.4 1.0
CB A:LYS315 4.7 45.0 1.0
N A:ILE317 4.7 41.5 1.0
O A:VAL313 4.8 40.9 1.0
N A:TYR314 5.0 37.3 1.0

Chlorine binding site 2 out of 7 in 3cdw

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Chlorine binding site 2 out of 7 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and 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 Protein Primer Vpg and A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl470

b:45.9
occ:1.00
 NZ A:LYS220 3.0 48.2 1.0
NE2 A:HIS468 3.5 85.6 1.0
CB A:HIS466 3.6 83.6 1.0
CD2 A:HIS466 3.8 90.4 1.0
CE A:LYS220 3.8 39.1 1.0
CE1 A:HIS468 3.9 85.4 1.0
CG A:HIS466 4.0 87.8 1.0
CD2 A:LEU216 4.2 51.4 1.0
N A:HIS466 4.5 79.5 1.0
O A:HOH803 4.5 78.5 1.0
CA A:HIS466 4.6 82.1 1.0
O A:HIS466 4.7 87.9 1.0
CD2 A:HIS468 4.8 86.0 1.0
O A:HOH527 4.9 28.5 1.0

Chlorine binding site 3 out of 7 in 3cdw

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Chlorine binding site 3 out of 7 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and 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 Protein Primer Vpg and A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl471

b:50.5
occ:1.00
 O A:HOH822 3.1 64.5 1.0
N A:GLU35 3.3 42.5 1.0
NZ A:LYS436 3.5 77.0 1.0
ND1 A:HIS399 3.5 36.5 1.0
CE1 A:HIS399 3.5 35.9 1.0
CA A:PHE34 3.8 40.1 1.0
CD1 A:PHE34 3.9 42.0 1.0
CB A:GLU35 4.0 42.7 1.0
CB A:PHE34 4.0 41.4 1.0
C A:PHE34 4.0 44.6 1.0
NE2 A:HIS399 4.1 36.6 1.0
CG A:HIS399 4.1 34.1 1.0
CA A:GLU35 4.2 41.7 1.0
CG A:PHE34 4.4 41.1 1.0
CD2 A:HIS399 4.5 36.5 1.0
CG A:GLU35 4.5 57.2 1.0
CE A:LYS436 4.5 79.5 1.0
O A:GLU35 4.6 42.2 1.0
CD A:GLU35 4.7 99.7 1.0
OE1 A:GLU35 4.7 0.5 1.0
CD A:LYS436 4.8 57.8 1.0
O A:VAL33 4.8 42.6 1.0
CE1 A:PHE34 4.9 42.0 1.0
CB A:HIS399 4.9 30.4 1.0
C A:GLU35 4.9 44.1 1.0

Chlorine binding site 4 out of 7 in 3cdw

Go back to Chlorine Binding Sites List in 3cdw
Chlorine binding site 4 out of 7 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and 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 Protein Primer Vpg and A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl472

b:49.5
occ:1.00
 O A:HOH527 2.8 28.5 1.0
N A:ASP213 3.1 27.1 1.0
CA A:CYS212 3.6 29.5 1.0
CB A:CYS212 3.8 27.5 1.0
C A:CYS212 3.8 31.4 1.0
CG A:PRO202 3.8 35.0 1.0
O A:ASP213 3.9 28.3 1.0
CB A:PHE217 3.9 28.2 1.0
CB A:ASP213 4.0 25.3 1.0
CA A:ASP213 4.0 24.4 1.0
O A:HOH803 4.2 78.5 1.0
CD1 A:PHE217 4.2 32.1 1.0
C A:ASP213 4.3 29.6 1.0
CG A:PHE217 4.3 29.2 1.0
N A:PHE217 4.4 30.9 1.0
CA A:PHE217 4.5 27.4 1.0
CB A:LEU216 4.6 34.9 1.0
CD2 A:LEU216 4.7 51.4 1.0
CB A:PRO202 4.8 31.9 1.0
N A:CYS212 4.9 33.8 1.0
CD A:PRO202 4.9 31.2 1.0
O A:GLY211 5.0 41.2 1.0
O A:CYS212 5.0 30.7 1.0

Chlorine binding site 5 out of 7 in 3cdw

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Chlorine binding site 5 out of 7 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and 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 Protein Primer Vpg and A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl473

b:83.1
occ:1.00
 NE2 A:HIS463 3.1 58.3 1.0
O A:LEU459 3.9 38.6 1.0
CD2 A:HIS463 4.0 58.1 1.0
CE1 A:HIS463 4.1 58.1 1.0
CE1 A:TYR385 4.4 48.3 1.0
CD1 A:TYR385 4.6 44.2 1.0
C A:LEU459 4.6 36.5 1.0
CD1 A:LEU388 4.7 31.8 1.0
CB A:LEU459 4.7 29.2 1.0
CA A:LEU459 4.9 29.9 1.0

Chlorine binding site 6 out of 7 in 3cdw

Go back to Chlorine Binding Sites List in 3cdw
Chlorine binding site 6 out of 7 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and 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 Protein Primer Vpg and A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl474

b:62.5
occ:1.00
 N A:ASP160 3.2 30.8 1.0
O A:HOH666 3.2 60.3 1.0
CB A:ASP160 3.7 29.7 1.0
CA A:LYS159 3.9 35.6 1.0
CA A:ASP160 4.0 28.9 1.0
C A:LYS159 4.0 36.7 1.0
O A:ASP160 4.0 34.4 1.0
O A:HOH650 4.1 60.3 1.0
CD1 A:ILE176 4.2 49.3 1.0
CG A:LYS159 4.2 41.5 1.0
O A:VAL158 4.3 33.1 1.0
NZ A:LYS406 4.3 53.7 1.0
C A:ASP160 4.5 33.5 1.0
CB A:LYS159 4.6 37.3 1.0
O2 A:GOL506 4.7 82.4 1.0
N A:LYS159 5.0 36.5 1.0

Chlorine binding site 7 out of 7 in 3cdw

Go back to Chlorine Binding Sites List in 3cdw
Chlorine binding site 7 out of 7 in the Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and A Pyrophosphate


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of Coxsackievirus B3 Rna-Dependent Rna Polymerase (3DPOL) in Complex with Protein Primer Vpg and A Pyrophosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl475

b:0.1
occ:1.00
 O2 A:GOL498 2.9 87.4 1.0
NH2 A:ARG174 3.0 49.0 0.4
NH1 A:ARG174 3.0 57.1 0.4
CZ A:ARG174 3.1 66.9 0.4
NZ A:LYS167 3.1 50.4 0.5
NH1 A:ARG163 3.4 49.9 0.3
NH2 A:ARG163 3.7 38.8 0.7
C1 A:GOL498 3.7 85.0 1.0
O A:HOH769 3.7 60.5 1.0
C2 A:GOL498 3.7 85.7 1.0
O1 A:GOL498 3.7 81.1 1.0
CE A:LYS167 3.9 47.5 0.5
NE A:ARG174 3.9 54.3 0.4
O1 A:POP482 4.0 58.8 0.5
O6 A:POP482 4.0 55.8 0.5
NH2 A:ARG163 4.0 47.2 0.3
C3 A:GOL498 4.1 86.2 1.0
CZ A:ARG163 4.2 60.9 0.3
CD A:LYS167 4.5 38.6 0.5
O3 A:GOL498 4.6 86.3 1.0
CZ A:ARG163 4.7 49.6 0.7
CD A:ARG174 4.7 36.5 0.6
NZ A:LYS167 4.7 49.0 0.5
CD A:ARG174 4.7 47.4 0.4
CE A:LYS167 4.8 42.6 0.5
NZ A:LYS61 4.9 0.5 1.0
NE A:ARG163 5.0 28.5 0.7
O A:HOH606 5.0 63.0 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 03:58:20 2025

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