Sodium in PDB 7ico: 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: 7ico 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 / 3.30
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.143, 57.535, 48.490, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 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 7ico). 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: 7ico:
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:23.9 occ:1.00 O A:THR101 2.2 28.2 1.0 O A:VAL103 2.3 29.1 1.0 O A:ILE106 2.4 5.2 1.0 OP1 P:DG6 2.9 19.7 1.0 C A:ILE106 3.2 8.4 1.0 O A:HOH601 3.3 80.1 1.0 C A:THR101 3.3 21.9 1.0 OP2 P:DG6 3.4 15.4 1.0 C A:VAL103 3.5 31.4 1.0 P P:DG6 3.5 20.2 1.0 N A:ILE106 3.8 16.0 1.0 CA A:ILE106 3.9 15.5 1.0 CA A:THR101 3.9 16.9 1.0 N A:VAL103 4.0 32.8 1.0 N A:GLY107 4.2 4.7 1.0 CA A:VAL103 4.3 32.1 1.0 C A:ARG102 4.3 27.7 1.0 N A:ARG102 4.4 20.0 1.0 CG2 A:THR101 4.5 17.8 1.0 CA A:GLY107 4.5 1.0 1.0 O5' P:DG6 4.5 30.3 1.0 N A:SER104 4.5 30.8 1.0 N A:GLY105 4.5 19.1 1.0 CB A:ILE106 4.6 15.1 1.0 CB A:THR101 4.7 23.9 1.0 CA A:ARG102 4.7 21.7 1.0 CA A:SER104 4.7 30.6 1.0 O3' P:DT5 4.8 13.4 1.0 O A:LEU100 4.8 12.0 1.0 C A:GLY105 4.8 9.4 1.0 O A:ARG102 4.8 31.5 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:44.0 occ:1.00 OP2 P:DG3 3.7 50.7 1.0 O P:HOH615 3.9 32.6 1.0 OP1 P:DG3 3.9 42.2 1.0 P P:DG3 4.3 45.2 1.0 O P:HOH570 4.8 50.6 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