Chlorine in PDB 5v1r: Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp

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

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

Protein crystallography data

The structure of Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp, PDB code: 5v1r 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) 24.98 / 2.08
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.596, 79.730, 55.647, 90.00, 107.53, 90.00
R / Rfree (%) 18 / 23.7

Other elements in 5v1r:

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

Magnesium (Mg) 3 atoms
Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp (pdb code 5v1r). 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 Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp, PDB code: 5v1r:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5v1r

Go back to Chlorine Binding Sites List in 5v1r
Chlorine binding site 1 out of 4 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp


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 Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:41.1
occ:1.00
 O A:HOH524 3.1 30.8 1.0
N A:CYS267 3.3 28.8 1.0
N A:TYR266 3.5 29.1 1.0
CG1 A:VAL313 3.5 27.7 1.0
C A:GLN264 3.6 25.9 1.0
CA A:GLN264 3.6 23.8 1.0
CB A:TYR266 3.7 29.3 1.0
SG A:CYS267 3.8 29.4 1.0
CB A:VAL313 3.8 30.1 1.0
O A:GLN264 3.8 27.1 1.0
O A:ASP263 3.9 32.9 1.0
CA A:TYR266 3.9 26.9 1.0
CB A:CYS267 4.0 24.8 1.0
C A:TYR266 4.0 31.1 1.0
N A:TYR265 4.0 27.3 1.0
CA A:CYS267 4.3 21.4 1.0
O A:VAL313 4.4 35.9 1.0
CD1 A:TYR266 4.4 39.5 1.0
C A:TYR265 4.4 26.0 1.0
CG A:TYR266 4.5 33.8 1.0
O A:TYR296 4.5 22.3 1.0
N A:GLN264 4.5 26.7 1.0
CB A:GLN264 4.6 25.0 1.0
C A:ASP263 4.6 31.4 1.0
CG2 A:VAL313 4.6 28.6 1.0
C A:VAL313 4.8 33.3 1.0
CA A:TYR265 4.9 26.8 1.0
CA A:VAL313 4.9 38.2 1.0

Chlorine binding site 2 out of 4 in 5v1r

Go back to Chlorine Binding Sites List in 5v1r
Chlorine binding site 2 out of 4 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp


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 Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:52.2
occ:1.00
 N A:HIS34 3.3 35.8 1.0
C A:ALA32 3.4 35.7 1.0
CA A:ALA32 3.4 38.8 1.0
N A:ILE33 3.5 34.2 1.0
CB A:ALA32 3.5 35.2 1.0
CB A:HIS34 3.7 40.6 1.0
N A:LYS35 3.7 34.0 1.0
ND1 A:HIS34 3.9 50.9 1.0
O A:ALA32 3.9 36.8 1.0
CA A:HIS34 3.9 38.9 1.0
CG A:LYS35 4.2 35.3 1.0
CG A:HIS34 4.2 48.7 1.0
C A:ILE33 4.3 37.1 1.0
O A:HOH513 4.3 42.6 1.0
C A:HIS34 4.3 34.4 1.0
CA A:ILE33 4.5 40.5 1.0
CB A:LYS35 4.7 34.8 1.0
O6 D:DG1 4.8 46.2 1.0
CA A:LYS35 4.8 31.4 1.0
CG2 A:ILE33 4.8 41.7 1.0
N A:ALA32 4.9 35.1 1.0

Chlorine binding site 3 out of 4 in 5v1r

Go back to Chlorine Binding Sites List in 5v1r
Chlorine binding site 3 out of 4 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp


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 Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:57.5
occ:1.00
 N A:LEU82 3.3 40.0 1.0
OE1 A:GLU86 3.7 70.2 1.0
CA A:LYS81 3.9 44.1 1.0
C A:LYS81 4.0 42.1 1.0
O A:LEU82 4.1 37.4 1.0
CB A:LEU82 4.1 37.6 1.0
CB A:LEU85 4.1 34.9 1.0
CA A:LEU82 4.2 35.9 1.0
CD1 A:LEU85 4.2 36.1 1.0
NH2 A:ARG89 4.3 40.8 1.0
CB A:LYS81 4.3 43.4 1.0
CZ A:ARG89 4.6 56.1 1.0
CD A:GLU86 4.6 67.6 1.0
C A:LEU82 4.6 37.5 1.0
CG A:GLU86 4.7 55.2 1.0
CG A:LEU85 4.8 35.5 1.0
O A:GLY80 4.8 41.1 1.0
NE A:ARG89 4.9 47.0 1.0

Chlorine binding site 4 out of 4 in 5v1r

Go back to Chlorine Binding Sites List in 5v1r
Chlorine binding site 4 out of 4 in the Dna Polymerase Beta Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp


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 Reactant Complex with 8-Oxog:C at the Primer Terminus and Incoming Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:36.9
occ:1.00
 NH2 A:ARG299 3.0 36.2 1.0
O A:HOH639 3.1 32.2 1.0
OG1 A:THR297 3.2 29.0 1.0
NE A:ARG299 3.4 35.6 1.0
ND2 A:ASN294 3.4 28.1 1.0
CZ A:ARG299 3.6 45.4 1.0
CG2 A:THR297 3.9 19.9 1.0
OD1 A:ASN294 4.0 27.4 1.0
CB A:TYR296 4.0 33.4 1.0
CG A:ASN294 4.1 26.0 1.0
CB A:THR297 4.2 25.9 1.0
CD2 A:TYR296 4.3 27.5 1.0
CG A:TYR296 4.6 25.2 1.0
O T:HOH117 4.6 33.8 1.0
CD A:ARG299 4.7 26.3 1.0
N A:THR297 4.8 24.0 1.0
NH1 A:ARG299 4.9 43.5 1.0
O A:HOH575 4.9 26.7 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 12:33:08 2020

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