Sodium in PDB 8icr: 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 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 Datp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8icr 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 (°)	179.614, 57.629, 48.284, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 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 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 Datp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8icr). 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 MNCL2 (5 Millimolar), PDB code: 8icr:
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 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 Datp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:9.1 occ:1.00 O A:THR101 2.1 23.4 1.0 OP1 P:DT6 2.3 19.5 1.0 O A:VAL103 2.5 15.9 1.0 O A:ILE106 2.7 6.9 1.0 O A:HOH601 2.9 56.5 1.0 C A:VAL103 3.2 11.1 1.0 C A:THR101 3.3 9.6 1.0 C A:ARG102 3.6 19.8 1.0 N A:VAL103 3.7 20.6 1.0 P P:DT6 3.7 12.2 1.0 C A:ILE106 3.8 1.0 1.0 N A:ILE106 3.8 1.0 1.0 N A:SER104 3.9 4.4 1.0 CA A:SER104 4.0 5.2 1.0 O A:ARG102 4.0 27.4 1.0 CA A:ARG102 4.0 11.7 1.0 N A:ARG102 4.1 2.9 1.0 CA A:VAL103 4.1 13.3 1.0 N A:GLY105 4.1 14.7 1.0 CA A:ILE106 4.2 1.0 1.0 CA A:THR101 4.3 7.0 1.0 OP2 P:DT6 4.3 4.8 1.0 CB A:ILE106 4.4 1.9 1.0 C A:SER104 4.4 10.2 1.0 O5' P:DT6 4.6 8.9 1.0 O3' P:DA5 4.6 13.3 1.0 N A:GLY107 4.9 1.0 1.0 C A:GLY105 4.9 8.8 1.0 O A:LEU100 4.9 7.4 1.0 CG2 A:ILE106 4.9 2.7 1.0 CG2 A:THR101 5.0 1.0 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven 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 Seven 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:47.0 occ:1.00 OP2 P:DT3 4.1 49.2 1.0 OP1 P:DT3 4.4 62.6 1.0 P P:DT3 4.8 59.5 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