Sodium in PDB 7icl: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of MNCL2 (0.1 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 (0.1 Millimolar), PDB code: 7icl 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 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.387, 57.760, 48.482, 90.00, 90.00, 90.00
R / Rfree (%)	15.6 / 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 (0.1 Millimolar) (pdb code 7icl). 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 (0.1 Millimolar), PDB code: 7icl:
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 (0.1 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 (0.1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:38.4 occ:1.00 O A:VAL103 2.1 7.2 1.0 OP1 P:DG6 2.4 17.4 1.0 O A:ILE106 2.5 9.8 1.0 O A:THR101 2.7 21.9 1.0 C A:VAL103 3.1 13.7 1.0 O A:HOH601 3.3 46.5 1.0 P P:DG6 3.4 30.6 1.0 C A:ILE106 3.5 4.3 1.0 N A:ILE106 3.5 11.0 1.0 N A:GLY105 3.6 25.9 1.0 C A:THR101 3.6 19.1 1.0 OP2 P:DG6 3.7 15.4 1.0 CA A:SER104 3.8 25.4 1.0 N A:SER104 3.9 16.1 1.0 N A:VAL103 3.9 16.0 1.0 CA A:ILE106 4.0 4.7 1.0 C A:ARG102 4.1 23.5 1.0 CA A:VAL103 4.1 15.2 1.0 C A:SER104 4.1 25.8 1.0 C A:GLY105 4.3 20.3 1.0 CB A:ILE106 4.4 4.7 1.0 O5' P:DG6 4.4 24.4 1.0 O A:ARG102 4.5 30.0 1.0 N A:ARG102 4.5 19.6 1.0 CA A:GLY105 4.5 26.9 1.0 CA A:THR101 4.5 13.2 1.0 N A:GLY107 4.5 4.6 1.0 CA A:ARG102 4.6 21.8 1.0 O3' P:DT5 4.6 20.9 1.0 O A:LEU100 4.9 25.5 1.0 CA A:GLY107 4.9 4.0 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; Soaked in the Presence of MNCL2 (0.1 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 (0.1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:20.5 occ:1.00 O A:LEU62 2.2 28.1 1.0 O A:LYS60 3.0 25.5 1.0 C A:LEU62 3.1 14.1 1.0 O A:VAL65 3.1 19.2 1.0 CA A:PRO63 3.2 9.1 1.0 N A:PRO63 3.5 12.7 1.0 N A:GLY64 3.7 29.7 1.0 C A:PRO63 3.8 17.6 1.0 C A:VAL65 3.9 19.9 1.0 N A:VAL65 3.9 11.6 1.0 O A:LYS61 4.2 35.6 1.0 C A:LYS60 4.3 32.9 1.0 CA A:VAL65 4.3 10.2 1.0 CA A:LEU62 4.4 1.4 1.0 C A:LYS61 4.5 34.9 1.0 CB A:PRO63 4.5 13.0 1.0 C A:GLY64 4.6 21.8 1.0 N A:LEU62 4.6 17.4 1.0 O A:PRO63 4.8 18.2 1.0 CA A:GLY64 4.8 27.2 1.0 CD A:PRO63 4.8 17.0 1.0 N A:GLY66 4.9 19.2 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