Sodium in PDB 7icr: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2, PDB code: 7icr was solved by H.Pelletier, M.R.Sawaya, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.283, 57.743, 48.480, 90.00, 90.00, 90.00
R / Rfree (%)	16 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 (pdb code 7icr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2, PDB code: 7icr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:18.9 occ:1.00 O A:THR101 2.1 16.7 1.0 O A:ILE106 2.1 1.0 1.0 OP1 P:DG6 2.3 18.0 1.0 O A:HOH665 2.5 13.6 1.0 O A:VAL103 2.9 11.4 1.0 C A:ILE106 3.1 1.0 1.0 C A:THR101 3.2 16.0 1.0 P P:DG6 3.3 14.9 1.0 N A:ILE106 3.5 5.8 1.0 OP2 P:DG6 3.5 18.3 1.0 C A:VAL103 3.6 11.8 1.0 CA A:ILE106 3.8 3.2 1.0 CA A:THR101 3.9 13.9 1.0 O A:HOH601 4.0 0.0 1.0 N A:VAL103 4.1 20.7 1.0 N A:GLY105 4.1 5.4 1.0 N A:GLY107 4.1 1.0 1.0 N A:SER104 4.3 13.3 1.0 CA A:SER104 4.3 13.9 1.0 N A:ARG102 4.3 11.6 1.0 CB A:ILE106 4.3 6.8 1.0 O5' P:DG6 4.4 9.1 1.0 C A:ARG102 4.4 26.2 1.0 CA A:GLY107 4.5 1.0 1.0 CA A:VAL103 4.5 14.2 1.0 CG2 A:THR101 4.5 23.8 1.0 C A:GLY105 4.5 10.1 1.0 O3' P:DT5 4.6 11.2 1.0 C A:SER104 4.6 12.9 1.0 CA A:ARG102 4.7 12.6 1.0 CB A:THR101 4.7 24.3 1.0 O A:LEU100 4.9 17.7 1.0 CA A:GLY105 4.9 10.2 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:24.1 occ:1.00 OP1 P:DG3 3.7 41.7 1.0 OP2 P:DG3 3.9 44.6 1.0 P P:DG3 4.3 48.4 1.0 O P:HOH615 4.8 61.6 1.0

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566