Sodium in PDB 9ics: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2, PDB code: 9ics 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 (°)	178.874, 57.670, 48.476, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2 (pdb code 9ics). 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 + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2, PDB code: 9ics:
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 + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp 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 + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:31.2 occ:1.46 O A:THR101 2.0 24.1 1.0 O A:VAL103 2.6 15.8 1.0 O A:ILE106 2.6 7.7 1.0 OP1 P:DG6 2.8 22.7 1.0 C A:THR101 3.1 16.4 1.0 C A:VAL103 3.2 14.9 1.0 O A:HOH601 3.4 79.0 1.0 N A:VAL103 3.6 19.2 1.0 C A:ARG102 3.7 16.8 1.0 C A:ILE106 3.7 6.3 1.0 N A:SER104 3.8 9.3 1.0 P P:DG6 3.8 22.0 1.0 CA A:SER104 3.9 17.7 1.0 N A:ARG102 3.9 11.6 1.0 CA A:THR101 4.0 13.7 1.0 CA A:ARG102 4.0 12.1 1.0 CA A:VAL103 4.0 21.2 1.0 OP2 P:DG6 4.0 25.8 1.0 N A:ILE106 4.1 8.9 1.0 O A:ARG102 4.1 16.8 1.0 N A:GLY105 4.2 4.5 1.0 CA A:ILE106 4.4 6.3 1.0 CG2 A:THR101 4.4 24.3 1.0 C A:SER104 4.4 17.8 1.0 O A:LEU100 4.6 19.0 1.0 CB A:ILE106 4.6 11.3 1.0 N A:GLY107 4.7 8.6 1.0 CB A:THR101 4.8 24.3 1.0 O3' P:DT5 4.9 22.0 1.0 O5' P:DG6 4.9 11.6 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp 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 + 2',3'- Dideoxycytidine-5'-Triphosphate, Soaked in the Presence of Ddctp and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:40.3 occ:1.00 OP1 P:DG3 3.7 38.9 1.0 OP2 P:DG3 4.1 47.5 1.0 P P:DG3 4.4 48.7 1.0 O P:HOH615 4.9 69.4 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