Chlorine in PDB 5v1o: 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;

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

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

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 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 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 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

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