Sodium in PDB 8icu: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (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 Ddatp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8icu 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 (°)	179.670, 57.593, 48.139, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 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 Ddatp (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 Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8icu). 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 Ddatp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8icu:
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 Ddatp (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 Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:17.3 occ:1.00 O A:HOH601 1.5 66.6 1.0 OP1 P:DT6 1.8 14.1 1.0 O A:ILE106 2.4 11.4 1.0 O A:THR101 2.4 28.9 1.0 O A:VAL103 2.8 3.9 1.0 P P:DT6 3.0 16.3 1.0 OP2 P:DT6 3.4 15.3 1.0 C A:ILE106 3.5 6.4 1.0 C A:THR101 3.6 21.1 1.0 N A:ILE106 3.9 12.6 1.0 C A:VAL103 3.9 5.7 1.0 N A:GLY105 3.9 20.1 1.0 O5' P:DT6 4.1 15.6 1.0 C A:ARG102 4.1 36.3 1.0 O3' P:DA5 4.1 24.7 1.0 O A:ARG102 4.2 47.7 1.0 CA A:ILE106 4.2 7.4 1.0 CA A:SER104 4.4 11.5 1.0 N A:VAL103 4.4 32.2 1.0 C A:GLY105 4.4 22.0 1.0 CA A:ARG102 4.4 25.7 1.0 N A:ARG102 4.5 20.6 1.0 N A:GLY107 4.5 2.2 1.0 N A:SER104 4.6 1.0 1.0 CA A:THR101 4.6 14.5 1.0 CB A:ILE106 4.6 5.1 1.0 C A:SER104 4.6 11.7 1.0 CA A:GLY105 4.7 26.7 1.0 CA A:VAL103 4.8 16.7 1.0 CA A:GLY107 4.8 2.3 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 Ddatp (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 Seven Base Pairs of Dna; Soaked in the Presence of Ddatp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:57.4 occ:1.00 O A:LEU62 2.3 45.7 1.0 O A:LYS60 2.9 31.5 1.0 C A:LEU62 3.3 42.2 1.0 O A:VAL65 3.4 34.2 1.0 O A:LYS61 3.7 34.1 1.0 C A:LYS61 3.8 32.5 1.0 N A:LEU62 4.0 29.9 1.0 C A:LYS60 4.0 35.8 1.0 N A:PRO63 4.1 37.0 1.0 CA A:LEU62 4.2 34.2 1.0 CA A:PRO63 4.2 29.1 1.0 CA A:LYS61 4.4 34.7 1.0 C A:VAL65 4.4 28.4 1.0 N A:VAL65 4.4 31.3 1.0 N A:LYS61 4.7 34.6 1.0 N A:GLY64 4.7 39.2 1.0 CG2 A:VAL65 4.7 28.6 1.0 CA A:VAL65 4.9 29.6 1.0 C A:PRO63 4.9 35.5 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