Chlorine in PDB 5v1o: Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp

Enzymatic activity of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp

All present enzymatic activity of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp:
2.7.7.7;

Protein crystallography data

The structure of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp, PDB code: 5v1o was solved by B.D.Freudenthal, M.A.Schaich, A.M.Whitaker, M.R.Smith, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 31.80 / 1.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 50.574, 79.685, 55.416, 90.00, 107.76, 90.00
R / Rfree (%) 17.9 / 21.5

Other elements in 5v1o:

The structure of Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp also contains other interesting chemical elements:

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

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp (pdb code 5v1o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 3 binding sites of Chlorine where determined in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted Dctp, PDB code: 5v1o:
Jump to Chlorine binding site number: 1; 2; 3;

Chlorine binding site 1 out of 3 in 5v1o

Go back to Chlorine Binding Sites List in 5v1o
Chlorine binding site 1 out of 3 in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted 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 Product Complex with 8-Oxog:A and Inserted Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:51.6
occ:1.00
O A:HOH526 3.0 18.4 1.0
O A:HOH550 3.1 43.6 1.0
N A:CYS267 3.2 14.2 1.0
N A:TYR266 3.5 14.6 1.0
CA A:GLN264 3.5 17.1 1.0
C A:GLN264 3.5 19.8 1.0
CG1 A:VAL313 3.6 19.8 1.0
O A:GLN264 3.7 18.6 1.0
CB A:TYR266 3.7 15.2 1.0
SG A:CYS267 3.8 16.8 1.0
CB A:VAL313 3.8 20.6 1.0
O A:ASP263 3.9 22.7 1.0
CA A:TYR266 3.9 14.8 1.0
CB A:CYS267 4.0 14.2 1.0
N A:TYR265 4.0 14.3 1.0
C A:TYR266 4.0 16.7 1.0
CA A:CYS267 4.2 13.5 1.0
O A:TYR296 4.4 13.7 1.0
O A:VAL313 4.4 28.1 1.0
CB A:GLN264 4.4 16.0 1.0
CD2 A:TYR266 4.4 27.5 1.0
C A:TYR265 4.4 13.6 1.0
N A:GLN264 4.5 15.6 1.0
C A:ASP263 4.6 21.9 1.0
CG A:TYR266 4.6 20.0 1.0
CG2 A:VAL313 4.7 16.8 1.0
CA A:TYR265 4.8 17.8 1.0
C A:VAL313 4.9 25.0 1.0
CG A:GLN264 4.9 15.7 1.0
CA A:VAL313 5.0 23.6 1.0

Chlorine binding site 2 out of 3 in 5v1o

Go back to Chlorine Binding Sites List in 5v1o
Chlorine binding site 2 out of 3 in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted 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 Product Complex with 8-Oxog:A and Inserted Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:53.5
occ:1.00
NH1 A:ARG89 3.2 56.2 1.0
N A:LEU82 3.2 23.3 1.0
CA A:LYS81 3.7 26.0 1.0
C A:LYS81 3.9 25.9 1.0
NH2 A:ARG89 3.9 52.2 1.0
O A:LEU82 4.0 21.1 1.0
CB A:LYS81 4.0 33.1 1.0
CZ A:ARG89 4.0 48.4 1.0
CB A:LEU85 4.1 25.8 1.0
CA A:LEU82 4.2 25.8 1.0
CB A:LEU82 4.3 23.0 1.0
CD1 A:LEU85 4.4 24.8 1.0
C A:LEU82 4.5 25.6 1.0
CG A:GLU86 4.6 36.6 1.0
CG A:LYS81 4.6 41.9 1.0
O A:GLY80 4.7 26.1 1.0
N A:GLU86 4.9 27.2 1.0
CG A:LEU85 4.9 28.8 1.0
N A:LYS81 4.9 25.6 1.0

Chlorine binding site 3 out of 3 in 5v1o

Go back to Chlorine Binding Sites List in 5v1o
Chlorine binding site 3 out of 3 in the Dna Polymerase Beta Product Complex with 8-Oxog:A and Inserted 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 Product Complex with 8-Oxog:A and Inserted Dctp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:24.2
occ:1.00
NH2 A:ARG299 3.0 18.4 0.6
O A:HOH691 3.2 27.2 1.0
OG1 A:THR297 3.2 19.2 1.0
ND2 A:ASN294 3.3 18.0 1.0
NE A:ARG299 3.5 17.9 0.6
CZ A:ARG299 3.7 26.1 0.6
CB A:TYR296 3.9 17.3 1.0
CG2 A:THR297 3.9 17.1 1.0
OD1 A:ASN294 4.0 16.8 1.0
CD2 A:TYR296 4.0 15.0 1.0
CG A:ASN294 4.1 17.3 1.0
CB A:THR297 4.2 14.9 1.0
CZ A:ARG299 4.3 25.1 0.4
NE A:ARG299 4.3 20.1 0.4
CG A:TYR296 4.4 17.9 1.0
NH2 A:ARG299 4.5 21.9 0.4
O A:HOH508 4.5 38.2 1.0
NH1 A:ARG299 4.7 16.5 0.4
O T:HOH114 4.7 28.6 1.0
N A:THR297 4.7 15.8 1.0
CD A:ARG299 4.8 20.5 0.4
CD A:ARG299 4.8 20.5 0.6
O A:HOH594 4.9 14.6 1.0
NH1 A:ARG299 4.9 23.6 0.6

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 12:33:06 2020

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