Chlorine in PDB 5v1p: Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog

Enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog

All present enzymatic activity of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog, PDB code: 5v1p was solved by B.D.Freudenthal, M.R.Smith, A.M.Whitaker, M.A.Schaich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.68 / 1.99
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.676, 79.990, 55.706, 90.00, 107.50, 90.00
R / Rfree (%) 17.5 / 23.1

Other elements in 5v1p:

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog (pdb code 5v1p). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog, PDB code: 5v1p:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5v1p

Go back to Chlorine Binding Sites List in 5v1p
Chlorine binding site 1 out of 4 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:38.3
occ:1.00
 O A:HOH524 3.0 23.9 1.0
N A:CYS267 3.1 17.1 1.0
N A:TYR266 3.5 21.1 1.0
C A:GLN264 3.5 16.9 1.0
CA A:GLN264 3.5 19.6 1.0
CG1 A:VAL313 3.5 26.0 1.0
O A:GLN264 3.7 18.7 1.0
SG A:CYS267 3.7 21.5 1.0
CB A:TYR266 3.8 21.4 1.0
CB A:VAL313 3.8 25.1 1.0
CB A:CYS267 3.8 21.4 1.0
O A:ASP263 3.9 25.4 1.0
CA A:TYR266 3.9 20.2 1.0
N A:TYR265 3.9 18.3 1.0
C A:TYR266 4.0 17.8 1.0
CA A:CYS267 4.1 14.5 1.0
O A:TYR296 4.3 17.3 1.0
C A:TYR265 4.4 23.8 1.0
CB A:GLN264 4.4 18.2 1.0
O A:VAL313 4.4 27.6 1.0
N A:GLN264 4.5 20.9 1.0
CD2 A:TYR266 4.5 29.0 1.0
C A:ASP263 4.6 24.0 1.0
CG2 A:VAL313 4.7 21.8 1.0
CG A:TYR266 4.7 29.6 1.0
CA A:TYR265 4.8 20.9 1.0
CG A:GLN264 4.9 16.2 1.0
C A:VAL313 4.9 25.8 1.0
CA A:VAL313 5.0 28.7 1.0

Chlorine binding site 2 out of 4 in 5v1p

Go back to Chlorine Binding Sites List in 5v1p
Chlorine binding site 2 out of 4 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:37.6
occ:1.00
 N A:HIS34 3.2 26.2 1.0
C A:ALA32 3.4 29.9 1.0
CB A:ALA32 3.5 26.8 1.0
CB A:HIS34 3.5 30.8 1.0
CA A:ALA32 3.5 36.0 1.0
N A:ILE33 3.6 26.2 1.0
N A:LYS35 3.7 25.9 1.0
CA A:HIS34 3.8 27.1 1.0
CD2 A:HIS34 3.9 37.6 1.0
O A:ALA32 3.9 28.4 1.0
CG A:HIS34 4.0 42.7 1.0
C A:HIS34 4.2 24.5 1.0
O A:HOH558 4.2 31.7 1.0
C A:ILE33 4.3 27.7 1.0
CG A:LYS35 4.4 31.5 1.0
CA A:ILE33 4.5 36.6 1.0
CB A:LYS35 4.8 20.0 1.0
CA A:LYS35 4.8 23.8 1.0
O6 D:DG1 4.9 33.7 1.0
N A:ALA32 4.9 27.2 1.0
CG2 A:ILE33 5.0 30.5 1.0

Chlorine binding site 3 out of 4 in 5v1p

Go back to Chlorine Binding Sites List in 5v1p
Chlorine binding site 3 out of 4 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:53.0
occ:1.00
 N A:LEU82 3.3 20.0 1.0
OE2 A:GLU86 3.8 61.7 1.0
CA A:LYS81 3.8 26.9 1.0
O A:LEU82 4.0 24.8 1.0
C A:LYS81 4.0 26.1 1.0
CB A:LEU85 4.1 27.8 1.0
CD1 A:LEU85 4.1 22.9 1.0
CA A:LEU82 4.2 26.8 1.0
CB A:LYS81 4.3 28.5 1.0
CB A:LEU82 4.3 23.6 1.0
NH1 A:ARG89 4.3 47.2 1.0
CZ A:ARG89 4.4 49.4 1.0
C A:LEU82 4.5 27.1 1.0
CG A:GLU86 4.5 43.6 1.0
CD A:GLU86 4.6 61.7 1.0
NH2 A:ARG89 4.7 51.7 1.0
CG A:LEU85 4.8 28.4 1.0
NE A:ARG89 4.8 44.2 1.0
O A:GLY80 4.8 28.0 1.0
N A:GLU86 4.9 27.6 1.0

Chlorine binding site 4 out of 4 in 5v1p

Go back to Chlorine Binding Sites List in 5v1p
Chlorine binding site 4 out of 4 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dna Polymerase Beta Substrate Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp Analog within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:30.0
occ:1.00
 NH2 A:ARG299 3.0 19.4 0.6
O A:HOH674 3.3 33.7 1.0
OG1 A:THR297 3.3 20.7 1.0
ND2 A:ASN294 3.4 21.4 1.0
NE A:ARG299 3.4 24.1 0.6
CZ A:ARG299 3.6 26.6 0.6
OD1 A:ASN294 3.9 18.9 1.0
CG2 A:THR297 3.9 18.3 1.0
CB A:TYR296 4.0 21.8 1.0
CG A:ASN294 4.1 18.9 1.0
CD2 A:TYR296 4.2 19.0 1.0
CZ A:ARG299 4.2 27.9 0.4
CB A:THR297 4.2 21.0 1.0
NE A:ARG299 4.2 25.2 0.4
NH2 A:ARG299 4.3 25.6 0.4
CG A:TYR296 4.5 23.4 1.0
NH1 A:ARG299 4.6 25.2 0.4
CD A:ARG299 4.7 24.7 0.6
N A:THR297 4.7 18.0 1.0
CD A:ARG299 4.8 24.9 0.4
NH1 A:ARG299 4.8 24.1 0.6
O T:HOH108 4.9 35.5 1.0

Reference:

A.M.Whitaker, M.R.Smith, M.A.Schaich, B.D.Freudenthal. Capturing A Mammalian Dna Polymerase Extending From An Oxidized Nucleotide. Nucleic Acids Res. V. 45 6934 2017.
ISSN: ESSN 1362-4962
PubMed: 28449123
DOI: 10.1093/NAR/GKX293
Page generated: Sat Dec 12 12:33:07 2020

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