Sodium in PDB 9icq: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and MNCL2 (5 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 Datp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 9icq 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 (°)	178.676, 57.705, 48.482, 90.00, 90.00, 90.00
R / Rfree (%)	16.5 / n/a

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 Datp (1 Millimolar) and MNCL2 (5 Millimolar) also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

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 Datp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 9icq). 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 Datp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 9icq:
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 Datp (1 Millimolar) and MNCL2 (5 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 Datp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:36.8 occ:1.00 O A:VAL103 2.3 16.5 1.0 O A:THR101 2.3 23.8 1.0 O A:ILE106 2.4 12.1 1.0 OP1 P:DG6 2.6 24.1 1.0 O A:HOH601 3.0 86.3 1.0 C A:VAL103 3.3 17.5 1.0 C A:THR101 3.4 23.8 1.0 OP2 P:DG6 3.4 26.8 1.0 C A:ILE106 3.4 6.6 1.0 P P:DG6 3.4 24.7 1.0 N A:ILE106 3.6 10.6 1.0 N A:GLY105 3.8 1.4 1.0 CA A:SER104 3.9 12.2 1.0 CA A:ILE106 4.0 8.3 1.0 N A:VAL103 4.0 22.3 1.0 N A:SER104 4.1 15.4 1.0 CA A:THR101 4.1 19.9 1.0 C A:ARG102 4.2 23.8 1.0 C A:SER104 4.3 8.0 1.0 CA A:VAL103 4.3 23.0 1.0 N A:ARG102 4.4 21.7 1.0 N A:GLY107 4.5 3.2 1.0 CB A:ILE106 4.5 11.3 1.0 C A:GLY105 4.5 15.5 1.0 O5' P:DG6 4.5 21.7 1.0 CA A:ARG102 4.6 22.8 1.0 O A:ARG102 4.6 24.3 1.0 O3' P:DT5 4.7 20.3 1.0 CA A:GLY105 4.8 11.1 1.0 CA A:GLY107 4.9 1.0 1.0 O A:LEU100 4.9 30.2 1.0 CG2 A:THR101 5.0 23.5 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 Datp (1 Millimolar) and MNCL2 (5 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 Datp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:30.0 occ:1.00 O A:LEU62 2.1 43.9 1.0 O A:LYS60 2.6 30.1 1.0 C A:LEU62 3.1 35.0 1.0 O A:VAL65 3.3 28.6 1.0 CA A:PRO63 3.6 25.5 1.0 N A:PRO63 3.7 30.8 1.0 C A:LYS60 3.8 32.9 1.0 N A:LEU62 4.0 28.4 1.0 N A:VAL65 4.1 20.3 1.0 C A:VAL65 4.1 24.1 1.0 C A:LYS61 4.1 37.8 1.0 CA A:LEU62 4.2 26.7 1.0 C A:PRO63 4.3 26.7 1.0 N A:GLY64 4.3 28.5 1.0 O A:LYS61 4.4 43.2 1.0 CA A:VAL65 4.5 16.5 1.0 N A:LYS61 4.7 36.8 1.0 CA A:LYS61 4.7 43.7 1.0 CB A:VAL65 4.7 18.2 1.0 CA A:LYS60 4.9 29.6 1.0 CB A:PRO63 4.9 22.9 1.0 CD A:PRO63 5.0 29.4 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