Sodium in PDB 6ph5: Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base

All present enzymatic activity of Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base:
2.7.7.7;

The structure of Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base, PDB code: 6ph5 was solved by V.K.Batra, S.H.Wilson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	22.60 / 2.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.132, 79.116, 55.203, 90.00, 106.61, 90.00
R / Rfree (%)	20.5 / 27.9

The binding sites of Sodium atom in the Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base (pdb code 6ph5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base, PDB code: 6ph5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:38.9 occ:1.00 O A:HOH522 2.3 37.0 1.0 O A:HOH533 2.3 38.0 1.0 O A:LEU62 2.5 42.9 1.0 O A:LYS60 2.5 46.4 1.0 OP1 D:DC3 2.5 39.1 1.0 O A:VAL65 2.6 46.7 1.0 C A:LEU62 3.5 40.7 1.0 P D:DC3 3.6 33.5 1.0 C A:VAL65 3.7 39.3 1.0 C A:LYS60 3.7 49.3 1.0 OP2 D:DC3 3.7 32.8 1.0 N A:VAL65 4.0 35.9 1.0 CA A:PRO63 4.1 37.3 1.0 N A:LEU62 4.1 44.0 1.0 C A:LYS61 4.1 42.1 1.0 N A:PRO63 4.2 41.9 1.0 N A:GLY64 4.3 42.5 1.0 CA A:VAL65 4.3 39.4 1.0 O A:LYS61 4.4 43.7 1.0 CA A:LEU62 4.4 42.9 1.0 CA A:LYS60 4.5 46.0 1.0 O3' D:DT2 4.6 38.2 1.0 C A:PRO63 4.6 42.8 1.0 CG A:LYS60 4.6 45.2 1.0 CA A:LYS61 4.6 45.6 1.0 N A:LYS61 4.6 48.0 1.0 CB A:VAL65 4.7 41.5 1.0 O5' D:DC3 4.7 33.1 1.0 N A:GLY66 4.7 35.5 1.0 C A:GLY64 5.0 41.9 1.0 CA A:GLY66 5.0 32.3 1.0

Sodium binding site 2 out of 2 in the Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Binary Product Complex Crystal Structure of Dna Polymerase Beta with An Extra-Helical Template Base within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:35.9 occ:1.00 O A:THR101 2.2 33.3 1.0 O A:ILE106 2.2 29.9 1.0 OP1 P:DG9 2.3 36.0 1.0 O A:VAL103 2.8 32.6 1.0 O P:HOH106 2.8 29.9 1.0 C A:ILE106 3.1 33.7 1.0 C A:THR101 3.3 32.1 1.0 P P:DG9 3.3 32.1 1.0 OP2 P:DG9 3.5 33.2 1.0 C A:VAL103 3.6 30.9 1.0 N A:ILE106 3.7 25.7 1.0 CA A:THR101 3.8 30.4 1.0 N A:GLY107 3.9 32.7 1.0 CA A:ILE106 4.0 30.4 1.0 CA A:SER104 4.1 31.1 1.0 N A:SER104 4.2 34.5 1.0 N A:GLY105 4.2 37.0 1.0 CA A:GLY107 4.2 30.8 1.0 CB A:THR101 4.2 34.2 1.0 N A:VAL103 4.3 32.3 1.0 O5' P:DG9 4.4 36.1 1.0 N A:ARG102 4.4 31.4 1.0 O3' P:DC8 4.4 39.4 1.0 C A:ARG102 4.5 35.4 1.0 CB A:ILE106 4.5 32.2 1.0 C A:SER104 4.5 34.7 1.0 CA A:VAL103 4.6 31.4 1.0 C A:GLY105 4.7 28.8 1.0 CA A:ARG102 4.7 29.4 1.0 O A:LEU100 4.9 31.3 1.0 O A:ARG102 4.9 35.8 1.0

M.J.Howard, N.A.Cavanaugh, V.K.Batra, D.D.Shock, W.A.Beard, S.H.Wilson. Dna Polymerase Beta Nucleotide-Stabilized Template Misalignment Fidelity Depends on Local Sequence Context. J.Biol.Chem. 2019.
ISSN: ESSN 1083-351X
PubMed: 31801827
DOI: 10.1074/JBC.RA119.010594