Sodium in PDB 8icl: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar)

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar), PDB code: 8icl 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 (°)	178.721, 57.784, 48.382, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / n/a

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) also contains other interesting chemical elements:

Nickel

(Ni)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) (pdb code 8icl). 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 Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar), PDB code: 8icl:
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 Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (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 Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:2.4 occ:1.00 O A:THR101 2.1 14.8 1.0 OP1 P:DT6 2.2 13.2 1.0 O A:VAL103 2.5 5.1 1.0 O A:ILE106 2.6 8.2 1.0 O A:HOH601 2.7 99.0 1.0 C A:THR101 3.3 14.1 1.0 C A:VAL103 3.3 6.5 1.0 P P:DT6 3.3 15.0 1.0 O A:ARG102 3.3 24.5 1.0 C A:ARG102 3.5 22.5 1.0 OP2 P:DT6 3.6 17.3 1.0 C A:ILE106 3.6 1.0 1.0 N A:ILE106 3.7 1.0 1.0 N A:VAL103 3.9 21.1 1.0 N A:GLY105 3.9 6.2 1.0 N A:SER104 4.1 7.3 1.0 CA A:ARG102 4.1 21.6 1.0 CA A:ILE106 4.1 1.0 1.0 CA A:SER104 4.1 12.6 1.0 N A:ARG102 4.2 14.9 1.0 CA A:VAL103 4.2 13.5 1.0 O5' P:DT6 4.2 9.3 1.0 CA A:THR101 4.3 7.7 1.0 CB A:ILE106 4.3 5.0 1.0 C A:SER104 4.4 12.7 1.0 C A:GLY105 4.6 3.6 1.0 N A:GLY107 4.7 1.0 1.0 O3' P:DA5 4.7 7.7 1.0 O A:LEU100 4.7 16.1 1.0 CA A:GLY105 4.9 1.9 1.0 CG2 A:ILE106 5.0 8.7 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (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 Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and NICL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:37.3 occ:1.00 O A:LEU62 2.0 34.2 1.0 O A:LYS60 2.6 17.5 1.0 O A:HOH656 3.1 25.6 1.0 O A:VAL65 3.2 13.0 1.0 C A:LEU62 3.2 31.0 1.0 C A:LYS60 3.8 19.6 1.0 C A:LYS61 4.0 24.0 1.0 N A:LEU62 4.0 16.6 1.0 N A:VAL65 4.0 3.6 1.0 C A:VAL65 4.1 10.1 1.0 N A:PRO63 4.1 34.6 1.0 CG2 A:VAL65 4.1 21.5 1.0 O A:LYS61 4.1 20.5 1.0 CA A:LEU62 4.2 18.6 1.0 CA A:PRO63 4.2 32.7 1.0 CA A:VAL65 4.4 8.4 1.0 CA A:LYS61 4.5 33.2 1.0 N A:GLY64 4.6 40.5 1.0 N A:LYS61 4.6 26.2 1.0 C A:PRO63 4.7 35.6 1.0 CG A:LYS60 4.7 9.3 1.0 CA A:LYS60 4.9 20.7 1.0 CB A:VAL65 4.9 15.5 1.0 CE A:LYS60 5.0 37.7 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