Sodium in PDB 7icn: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2, PDB code: 7icn 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 (°)	178.573, 57.754, 48.512, 90.00, 90.00, 90.00
R / Rfree (%)	16.2 / n/a

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of NICL2 (pdb code 7icn). 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 NICL2, PDB code: 7icn:
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 NICL2


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 NICL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:23.6 occ:1.00 O A:THR101 2.1 11.3 1.0 O A:VAL103 2.4 15.7 1.0 O A:ILE106 2.5 12.7 1.0 OP1 P:DG6 2.7 13.1 1.0 C A:VAL103 3.2 14.7 1.0 O A:HOH601 3.3 82.4 1.0 C A:THR101 3.3 10.6 1.0 OP2 P:DG6 3.4 26.5 1.0 C A:ILE106 3.4 4.5 1.0 P P:DG6 3.5 17.9 1.0 N A:ILE106 3.5 4.0 1.0 CA A:ILE106 3.8 4.2 1.0 N A:VAL103 3.8 20.7 1.0 N A:SER104 3.9 12.6 1.0 CA A:SER104 4.0 14.2 1.0 C A:ARG102 4.0 16.9 1.0 CA A:VAL103 4.0 21.2 1.0 N A:GLY105 4.1 10.0 1.0 CA A:THR101 4.1 7.0 1.0 CB A:ILE106 4.1 8.8 1.0 N A:ARG102 4.3 12.1 1.0 O A:ARG102 4.3 20.2 1.0 C A:SER104 4.3 13.8 1.0 N A:GLY107 4.4 1.5 1.0 CG2 A:THR101 4.4 22.4 1.0 O3' P:DT5 4.5 11.6 1.0 CA A:ARG102 4.5 12.0 1.0 C A:GLY105 4.6 13.4 1.0 CA A:GLY107 4.7 8.2 1.0 O A:LEU100 4.8 12.9 1.0 O5' P:DG6 4.8 11.2 1.0 CB A:THR101 4.9 19.2 1.0 CB A:VAL103 4.9 19.0 1.0 CA A:GLY105 5.0 11.2 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 NICL2


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 NICL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:20.2 occ:1.00 OP1 P:DG3 3.6 32.1 1.0 OP2 P:DG3 3.8 48.2 1.0 P P:DG3 4.2 43.6 1.0 O P:HOH615 4.4 72.3 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