Chlorine in PDB 5v1n: Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp

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

The structure of Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp, PDB code: 5v1n 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)	39.61 / 2.01
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	50.546, 79.225, 55.536, 90.00, 107.32, 90.00
R / Rfree (%)	18.1 / 23.7

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

Calcium	(Ca)	2 atoms
Sodium	(Na)	1 atom

The binding sites of Chlorine atom in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp (pdb code 5v1n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp, PDB code: 5v1n:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A 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 Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:56.0 occ:1.00 N A:LEU82 3.0 29.4 1.0 CB A:LYS81 3.4 41.5 1.0 CA A:LYS81 3.5 30.7 1.0 O A:LEU82 3.7 28.2 1.0 C A:LYS81 3.7 32.3 1.0 CA A:LEU82 4.0 27.8 1.0 CB A:LEU85 4.1 35.0 1.0 CB A:LEU82 4.2 26.8 1.0 C A:LEU82 4.2 29.1 1.0 CG A:GLU86 4.3 39.9 1.0 OE1 A:GLU86 4.4 51.4 1.0 CD1 A:LEU85 4.5 34.0 1.0 CD A:GLU86 4.6 57.7 1.0 N A:GLU86 4.7 28.5 1.0 CZ A:ARG89 4.7 41.3 1.0 CG A:LYS81 4.8 49.6 1.0 NH2 A:ARG89 4.8 42.8 1.0 N A:LYS81 4.9 25.4 1.0 O A:GLY80 4.9 31.3 1.0 CG A:LEU85 4.9 34.4 1.0 NH1 A:ARG89 4.9 43.2 1.0 O A:LYS81 4.9 26.6 1.0 NE A:ARG89 5.0 39.5 1.0

Chlorine binding site 2 out of 2 in the Dna Polymerase Beta Substrate Complex with 8-Oxog:A 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 Substrate Complex with 8-Oxog:A at the Primer Terminus and Incoming Dctp within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:37.0 occ:1.00 NH2 A:ARG299 2.9 19.0 0.5 OG1 A:THR297 3.2 20.0 1.0 O A:HOH685 3.2 34.2 1.0 ND2 A:ASN294 3.3 18.2 1.0 NE A:ARG299 3.4 21.1 0.5 CZ A:ARG299 3.6 23.1 0.5 CG2 A:THR297 3.8 22.1 1.0 OD1 A:ASN294 3.9 19.1 1.0 CB A:TYR296 4.0 26.2 1.0 CG A:ASN294 4.1 20.6 1.0 CB A:THR297 4.1 25.8 1.0 CD2 A:TYR296 4.1 19.1 1.0 NE A:ARG299 4.2 20.2 0.5 CZ A:ARG299 4.2 24.0 0.5 NH2 A:ARG299 4.4 19.5 0.5 CG A:TYR296 4.4 22.7 1.0 O T:HOH127 4.6 32.5 1.0 CD A:ARG299 4.7 21.1 0.5 NH1 A:ARG299 4.7 27.2 0.5 CD A:ARG299 4.7 21.1 0.5 N A:THR297 4.8 17.9 1.0 NH1 A:ARG299 4.8 21.0 0.5 O A:HOH579 4.9 21.7 1.0

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