Sodium in PDB 7icm: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of MNCL2 (1.0 Millimolar)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of MNCL2 (1.0 Millimolar), PDB code: 7icm 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 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.467, 57.755, 48.512, 90.00, 90.00, 90.00
R / Rfree (%)	15.2 / 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; Soaked in the Presence of MNCL2 (1.0 Millimolar) (pdb code 7icm). 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; Soaked in the Presence of MNCL2 (1.0 Millimolar), PDB code: 7icm:
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; Soaked in the Presence of MNCL2 (1.0 Millimolar)


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; Soaked in the Presence of MNCL2 (1.0 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:41.2 occ:1.00 O A:THR101 2.0 26.6 1.0 O A:ILE106 2.2 8.8 1.0 O A:VAL103 2.4 25.6 1.0 OP1 P:DG6 2.7 21.4 1.0 C A:THR101 3.1 20.9 1.0 C A:ILE106 3.4 6.7 1.0 C A:VAL103 3.5 20.5 1.0 OP2 P:DG6 3.6 27.0 1.0 P P:DG6 3.6 23.6 1.0 O A:HOH601 3.7 95.8 1.0 CA A:THR101 3.8 14.4 1.0 N A:ILE106 3.8 14.7 1.0 N A:VAL103 3.9 21.5 1.0 C A:ARG102 4.0 22.1 1.0 CA A:ILE106 4.1 11.7 1.0 N A:ARG102 4.1 16.5 1.0 N A:GLY105 4.2 15.8 1.0 O A:ARG102 4.3 23.7 1.0 CA A:VAL103 4.3 21.4 1.0 N A:SER104 4.3 14.8 1.0 CA A:SER104 4.4 14.9 1.0 CG2 A:THR101 4.4 19.6 1.0 CA A:ARG102 4.4 17.6 1.0 CB A:ILE106 4.4 17.9 1.0 N A:GLY107 4.4 5.8 1.0 CB A:THR101 4.6 18.5 1.0 O3' P:DT5 4.6 16.3 1.0 C A:SER104 4.6 17.4 1.0 O A:LEU100 4.6 23.3 1.0 CA A:GLY107 4.7 5.2 1.0 C A:GLY105 4.8 18.0 1.0 O5' P:DG6 4.8 20.9 1.0 N A:THR101 4.9 12.7 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; Soaked in the Presence of MNCL2 (1.0 Millimolar)


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; Soaked in the Presence of MNCL2 (1.0 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:38.8 occ:1.00 OP1 P:DG3 3.7 39.6 1.0 O P:HOH615 4.4 84.9 1.0 OP2 P:DG3 4.4 44.4 1.0 P P:DG3 4.5 44.3 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