Sodium in PDB 9icw: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Native Structure

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Native Structure, PDB code: 9icw 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 / 2.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.638, 57.846, 48.489, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / n/a

The binding sites of Sodium atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Native Structure (pdb code 9icw). 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 (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Native Structure, PDB code: 9icw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Native Structure


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 (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:26.1 occ:1.00 O A:THR101 2.3 25.1 1.0 O A:ILE106 2.3 14.5 1.0 O A:VAL103 2.4 24.9 1.0 OP1 P:DG6 2.5 22.9 1.0 O A:HOH601 3.3 82.0 1.0 C A:THR101 3.4 16.0 1.0 C A:VAL103 3.4 19.1 1.0 C A:ILE106 3.4 9.5 1.0 P P:DG6 3.5 25.0 1.0 OP2 P:DG6 3.6 30.4 1.0 N A:ILE106 3.8 12.2 1.0 N A:GLY105 4.0 17.4 1.0 CA A:SER104 4.0 15.5 1.0 N A:VAL103 4.1 22.1 1.0 CA A:ILE106 4.1 11.8 1.0 N A:SER104 4.1 11.7 1.0 CA A:THR101 4.1 10.4 1.0 C A:ARG102 4.2 22.7 1.0 C A:SER104 4.4 20.8 1.0 N A:ARG102 4.4 11.0 1.0 CA A:VAL103 4.4 22.7 1.0 N A:GLY107 4.4 8.4 1.0 CB A:ILE106 4.4 10.6 1.0 CA A:ARG102 4.5 16.7 1.0 O A:ARG102 4.6 30.1 1.0 O3' P:DT5 4.6 38.9 1.0 C A:GLY105 4.7 18.6 1.0 CA A:GLY107 4.7 3.0 1.0 O5' P:DG6 4.7 20.3 1.0 CG2 A:THR101 4.7 21.3 1.0 O A:LEU100 4.9 19.7 1.0 CA A:GLY105 4.9 20.3 1.0 CB A:THR101 5.0 19.9 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Native Structure


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 (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Native Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:44.8 occ:1.00 OP1 P:DG3 3.5 34.5 1.0 OP2 P:DG3 3.6 52.4 1.0 P P:DG3 4.0 43.9 1.0 O P:HOH615 4.5 83.7 1.0

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. Crystal Structures of Human Dna Polymerase Beta Complexed with Dna: Implications For Catalytic Mechanism, Processivity, and Fidelity Biochemistry V. 35 12742 1996.
ISSN: ISSN 0006-2960
PubMed: 8841118
DOI: 10.1021/BI952955D