Sodium in PDB 8icy: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MNCL2, PDB code: 8icy 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 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.792, 57.617, 48.188, 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 + Thymidine- 5'-Triphosphate, Soaked in the Presence of Dttp and MNCL2 also contains other interesting chemical elements:

Manganese

(Mn)

1 atom

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 MNCL2 (pdb code 8icy). 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 MNCL2, PDB code: 8icy:
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 MNCL2


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 MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:8.6 occ:1.00 O A:HOH601 1.8 45.0 1.0 OP1 P:DT6 2.1 12.7 1.0 O A:ILE106 2.2 1.4 1.0 O A:THR101 2.5 18.1 1.0 O A:VAL103 2.5 12.5 1.0 C A:ILE106 3.0 1.0 1.0 N A:ILE106 3.0 2.5 1.0 P P:DT6 3.3 8.7 1.0 CA A:ILE106 3.4 1.0 1.0 C A:THR101 3.4 11.2 1.0 C A:VAL103 3.6 7.7 1.0 N A:GLY105 3.6 7.5 1.0 CB A:ILE106 3.8 1.0 1.0 OP2 P:DT6 3.8 1.0 1.0 C A:GLY105 3.8 7.5 1.0 N A:GLY107 4.0 1.5 1.0 CA A:THR101 4.1 11.5 1.0 N A:VAL103 4.1 25.0 1.0 CA A:SER104 4.1 6.6 1.0 C A:SER104 4.2 13.1 1.0 O3' P:DA5 4.2 12.4 1.0 N A:SER104 4.3 1.0 1.0 CA A:GLY105 4.3 3.7 1.0 OG1 A:THR101 4.4 23.1 1.0 N A:ARG102 4.4 14.3 1.0 CG2 A:ILE106 4.4 1.0 1.0 C A:ARG102 4.4 28.4 1.0 O5' P:DT6 4.4 5.8 1.0 CA A:VAL103 4.5 15.5 1.0 CA A:GLY107 4.5 1.0 1.0 CA A:ARG102 4.6 20.5 1.0 O A:GLY105 4.7 13.6 1.0 CB A:THR101 4.8 16.2 1.0 O A:LEU100 4.8 16.9 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 MNCL2


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 MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:50.1 occ:1.00 OP1 P:DT3 4.1 53.5 1.0 OP2 P:DT3 4.1 52.1 1.0 O P:HOH615 4.4 48.3 1.0 P P:DT3 4.6 57.1 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