Sodium in PDB 8icj: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MGCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MGCL2, PDB code: 8icj 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 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.887, 57.755, 48.290, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / n/a

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MGCL2 (pdb code 8icj). 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 + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MGCL2, PDB code: 8icj:
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 + Thymidine- 5'-Triphosphate, 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 + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:4.9 occ:1.00 OP1 P:DT6 2.1 4.4 1.0 O A:THR101 2.1 11.0 1.0 O A:HOH601 2.2 67.3 1.0 O A:VAL103 2.5 3.5 1.0 O A:ILE106 2.8 3.1 1.0 C A:VAL103 3.2 3.1 1.0 C A:THR101 3.3 10.2 1.0 P P:DT6 3.5 4.9 1.0 N A:ILE106 3.6 1.0 1.0 C A:ILE106 3.6 1.0 1.0 N A:GLY105 3.7 4.4 1.0 CA A:SER104 3.7 10.7 1.0 C A:ARG102 3.7 10.9 1.0 N A:SER104 3.7 3.3 1.0 N A:VAL103 3.8 13.9 1.0 CA A:ILE106 3.9 1.0 1.0 O A:ARG102 4.0 11.0 1.0 OP2 P:DT6 4.0 2.1 1.0 N A:ARG102 4.1 15.5 1.0 CB A:ILE106 4.1 1.0 1.0 C A:SER104 4.1 10.2 1.0 CA A:ARG102 4.1 13.8 1.0 CA A:VAL103 4.1 9.4 1.0 CA A:THR101 4.4 2.8 1.0 C A:GLY105 4.4 1.0 1.0 O5' P:DT6 4.4 6.3 1.0 O3' P:DA5 4.5 3.8 1.0 CA A:GLY105 4.7 1.0 1.0 CG2 A:THR101 4.7 10.0 1.0 O A:LEU100 4.7 11.3 1.0 N A:GLY107 4.7 1.0 1.0 CG2 A:ILE106 4.9 1.0 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + Thymidine- 5'-Triphosphate, 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 + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MGCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:47.2 occ:1.00 OP2 P:DT3 4.9 60.5 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