Sodium in PDB 9icm: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Double Stranded Dna (No 5'-Phosphate)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Double Stranded Dna (No 5'-Phosphate), PDB code: 9icm 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 (°)	178.698, 57.867, 48.556, 90.00, 90.00, 90.00
R / Rfree (%)	15.5 / 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 Double Stranded Dna (No 5'-Phosphate) (pdb code 9icm). 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 Double Stranded Dna (No 5'-Phosphate), PDB code: 9icm:
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 Double Stranded Dna (No 5'-Phosphate)


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 Double Stranded Dna (No 5'-Phosphate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:26.7 occ:1.00 O A:THR101 2.2 31.8 1.0 OP1 P:DG6 2.3 28.4 1.0 O A:ILE106 2.4 8.4 1.0 O A:VAL103 2.4 17.0 1.0 C A:THR101 3.3 26.1 1.0 P P:DG6 3.4 28.0 1.0 C A:ILE106 3.4 4.5 1.0 C A:VAL103 3.5 14.8 1.0 O A:HOH601 3.5 97.8 1.0 OP2 P:DG6 3.6 30.2 1.0 N A:ILE106 3.6 16.9 1.0 N A:GLY105 3.8 17.9 1.0 CA A:SER104 4.1 13.6 1.0 CA A:ILE106 4.1 11.9 1.0 C A:ARG102 4.1 27.6 1.0 N A:VAL103 4.1 25.8 1.0 CA A:THR101 4.1 21.2 1.0 N A:SER104 4.2 5.1 1.0 N A:ARG102 4.3 27.7 1.0 C A:SER104 4.3 18.5 1.0 O A:ARG102 4.4 33.8 1.0 N A:GLY107 4.4 3.4 1.0 O3' P:DT5 4.4 27.0 1.0 CA A:VAL103 4.4 19.7 1.0 O5' P:DG6 4.5 22.2 1.0 CA A:ARG102 4.5 26.4 1.0 C A:GLY105 4.5 23.1 1.0 CB A:ILE106 4.5 11.2 1.0 CA A:GLY107 4.6 7.0 1.0 CA A:GLY105 4.8 23.7 1.0 O A:LEU100 5.0 33.5 1.0 CB A:THR101 5.0 25.3 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 Double Stranded Dna (No 5'-Phosphate)


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 Double Stranded Dna (No 5'-Phosphate) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:51.0 occ:1.00 OP2 P:DG3 3.2 44.1 1.0 OP1 P:DG3 4.0 44.6 1.0 P P:DG3 4.1 46.7 1.0 O P:HOH615 4.4 72.7 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