Sodium in PDB 9icx: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna (Non Gapped Dna Only)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna (Non Gapped Dna Only), PDB code: 9icx 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 (°)	179.010, 57.729, 48.511, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 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 (Non Gapped Dna Only) (pdb code 9icx). 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 (Non Gapped Dna Only), PDB code: 9icx:
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 (Non Gapped Dna Only)


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 (Non Gapped Dna Only) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:21.7 occ:1.00 O A:VAL103 2.1 27.2 1.0 O A:THR101 2.2 25.6 1.0 O A:ILE106 2.4 2.9 1.0 OP1 P:DG6 2.5 20.7 1.0 C A:VAL103 3.2 21.3 1.0 C A:THR101 3.3 13.2 1.0 O A:HOH601 3.3 64.3 1.0 C A:ILE106 3.5 7.7 1.0 N A:ILE106 3.6 18.1 1.0 P P:DG6 3.6 22.4 1.0 N A:VAL103 3.8 15.8 1.0 OP2 P:DG6 3.9 26.5 1.0 N A:GLY105 3.9 19.1 1.0 C A:ARG102 3.9 22.5 1.0 CA A:THR101 4.0 7.9 1.0 N A:SER104 4.0 14.5 1.0 CA A:SER104 4.0 17.7 1.0 CA A:ILE106 4.1 16.4 1.0 CA A:VAL103 4.1 23.3 1.0 N A:ARG102 4.2 12.8 1.0 O A:ARG102 4.3 29.3 1.0 CA A:ARG102 4.3 19.6 1.0 C A:SER104 4.4 23.7 1.0 CB A:ILE106 4.5 19.2 1.0 O A:LEU100 4.5 21.3 1.0 N A:GLY107 4.5 9.3 1.0 C A:GLY105 4.6 25.0 1.0 O5' P:DG6 4.7 28.8 1.0 CG2 A:THR101 4.8 9.8 1.0 CA A:GLY105 4.8 23.5 1.0 O3' P:DT5 4.8 22.1 1.0 CA A:GLY107 4.8 5.9 1.0 CB A:THR101 4.9 14.0 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 (Non Gapped Dna Only)


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 (Non Gapped Dna Only) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:45.5 occ:1.00 OP2 P:DG3 3.4 42.1 1.0 OP1 P:DG3 3.7 44.5 1.0 O P:HOH615 4.0 73.7 1.0 P P:DG3 4.0 38.9 1.0 O P:HOH570 5.0 62.3 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