Sodium in PDB 7ict: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 and MGCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 and MGCL2, PDB code: 7ict 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 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.784, 57.741, 48.480, 90.00, 90.00, 90.00
R / Rfree (%)	16.8 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of ZNCL2 and MGCL2 also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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 and MGCL2 (pdb code 7ict). 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 and MGCL2, PDB code: 7ict:
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 and MGCL2


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 and MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:31.1 occ:1.00 O A:ILE106 2.1 10.4 1.0 O A:THR101 2.3 28.8 1.0 O A:VAL103 2.5 19.9 1.0 OP1 P:DG6 2.8 27.4 1.0 O A:HOH601 3.2 99.9 1.0 C A:ILE106 3.2 6.7 1.0 C A:THR101 3.3 18.4 1.0 N A:ILE106 3.4 15.6 1.0 OP2 P:DG6 3.5 26.4 1.0 C A:VAL103 3.5 19.1 1.0 P P:DG6 3.6 23.0 1.0 CA A:ILE106 3.8 13.8 1.0 CA A:THR101 3.9 17.0 1.0 N A:GLY105 4.0 18.5 1.0 N A:VAL103 4.1 19.2 1.0 C A:ARG102 4.2 22.1 1.0 N A:GLY107 4.3 2.6 1.0 N A:SER104 4.3 16.8 1.0 CB A:ILE106 4.3 16.0 1.0 CA A:SER104 4.3 19.6 1.0 N A:ARG102 4.4 11.8 1.0 CA A:VAL103 4.4 22.3 1.0 O A:ARG102 4.4 28.7 1.0 C A:GLY105 4.5 16.2 1.0 CA A:ARG102 4.6 18.4 1.0 CA A:GLY107 4.6 1.0 1.0 C A:SER104 4.7 21.9 1.0 O3' P:DT5 4.7 28.1 1.0 CG2 A:THR101 4.7 17.3 1.0 CB A:THR101 4.7 19.6 1.0 O A:LEU100 4.7 18.4 1.0 O5' P:DG6 4.8 27.0 1.0 CA A:GLY105 4.9 15.1 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 and MGCL2


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 and MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:46.2 occ:1.00 OP1 P:DG3 3.2 36.8 1.0 O P:HOH615 4.0 60.4 1.0 OP2 P:DG3 4.0 44.4 1.0 P P:DG3 4.1 47.8 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