Sodium in PDB 9ico: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Dttp and MGCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Dttp and MGCL2, PDB code: 9ico 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 / 2.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.631, 57.708, 48.502, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 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 Dttp and MGCL2 (pdb code 9ico). 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 Dttp and MGCL2, PDB code: 9ico:
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 Dttp 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 Dttp and MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:24.7 occ:1.00 O A:VAL103 2.2 16.2 1.0 O A:ILE106 2.3 6.8 1.0 O A:THR101 2.5 17.4 1.0 OP1 P:DG6 2.6 24.3 1.0 O A:HOH601 3.2 96.1 1.0 OP2 P:DG6 3.3 28.0 1.0 C A:VAL103 3.3 15.5 1.0 C A:ILE106 3.3 4.7 1.0 P P:DG6 3.4 22.6 1.0 C A:THR101 3.5 15.2 1.0 N A:ILE106 3.5 7.7 1.0 N A:GLY105 3.8 11.1 1.0 CA A:ILE106 3.9 6.3 1.0 CA A:SER104 3.9 15.5 1.0 N A:SER104 4.0 13.1 1.0 N A:VAL103 4.1 22.3 1.0 C A:ARG102 4.2 27.6 1.0 C A:SER104 4.2 16.4 1.0 CA A:THR101 4.2 12.3 1.0 CA A:VAL103 4.3 20.0 1.0 O3' P:DT5 4.4 25.5 1.0 CB A:ILE106 4.4 9.3 1.0 N A:GLY107 4.4 2.6 1.0 N A:ARG102 4.4 19.2 1.0 C A:GLY105 4.4 16.9 1.0 O A:ARG102 4.5 31.0 1.0 CA A:ARG102 4.6 24.3 1.0 O5' P:DG6 4.7 19.3 1.0 CA A:GLY107 4.7 1.0 1.0 CA A:GLY105 4.7 14.5 1.0 O A:LEU100 4.9 24.9 1.0 CG2 A:THR101 5.0 24.4 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 Dttp 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 Dttp and MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:47.9 occ:1.00 OP1 P:DG3 3.6 38.1 1.0 OP2 P:DG3 3.7 49.2 1.0 O P:HOH615 4.2 91.2 1.0 P P:DG3 4.2 46.0 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