Sodium in PDB 1zqt: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (0.01 Millimolar) and ZNCL2 (0.02 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 (0.01 Millimolar) and ZNCL2 (0.02 Millimolar), PDB code: 1zqt 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 / 3.40
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.561, 57.365, 47.857, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 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 (0.01 Millimolar) and ZNCL2 (0.02 Millimolar) also contains other interesting chemical elements:

Zinc

(Zn)

1 atom

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 (0.01 Millimolar) and ZNCL2 (0.02 Millimolar) (pdb code 1zqt). 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 (0.01 Millimolar) and ZNCL2 (0.02 Millimolar), PDB code: 1zqt:
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 (0.01 Millimolar) and ZNCL2 (0.02 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 (0.01 Millimolar) and ZNCL2 (0.02 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:11.4 occ:1.00 O A:THR101 2.1 4.8 1.0 OP1 P:DT6 2.4 5.3 1.0 O P:HOH588 2.6 94.3 1.0 O A:VAL103 2.6 1.0 1.0 O A:ILE106 3.1 5.2 1.0 C A:THR101 3.2 4.2 1.0 C A:VAL103 3.4 7.5 1.0 P P:DT6 3.7 1.0 1.0 C A:ARG102 3.7 30.1 1.0 N A:VAL103 3.8 28.6 1.0 CA A:ARG102 3.9 21.6 1.0 N A:ARG102 3.9 5.2 1.0 O A:ARG102 4.0 33.7 1.0 OP2 P:DT6 4.0 23.0 1.0 CA A:SER104 4.0 6.9 1.0 N A:SER104 4.1 9.2 1.0 C A:ILE106 4.3 4.5 1.0 N A:GLY105 4.3 1.0 1.0 CA A:VAL103 4.3 15.0 1.0 CA A:THR101 4.3 3.9 1.0 O5' P:DT6 4.5 1.0 1.0 N A:ILE106 4.6 7.2 1.0 CG2 A:THR101 4.6 12.0 1.0 C A:SER104 4.6 1.9 1.0 CA A:ILE106 4.8 7.2 1.0 O3' P:DA5 4.8 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 (0.01 Millimolar) and ZNCL2 (0.02 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 (0.01 Millimolar) and ZNCL2 (0.02 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:38.9 occ:1.00 O A:LEU62 1.7 35.1 1.0 C A:LEU62 2.9 36.4 1.0 O A:LYS60 3.2 1.2 1.0 O A:LYS61 3.5 24.6 1.0 N A:PRO63 3.7 36.6 1.0 O A:VAL65 3.7 25.8 1.0 CA A:PRO63 3.7 33.2 1.0 C A:LYS61 3.9 26.9 1.0 CA A:LEU62 4.0 27.4 1.0 N A:LEU62 4.1 23.1 1.0 N A:VAL65 4.2 19.8 1.0 N A:GLY64 4.2 37.5 1.0 C A:LYS60 4.4 14.6 1.0 C A:PRO63 4.4 29.8 1.0 CD A:PRO63 4.5 34.3 1.0 C A:VAL65 4.5 23.1 1.0 CA A:VAL65 4.7 19.7 1.0 CA A:LYS61 4.8 36.5 1.0 CB A:VAL65 4.8 27.8 1.0 CB A:PRO63 4.9 29.9 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