Sodium in PDB 8ick: 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), MGCL2 (5 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), MGCL2 (5 Millimolar), and MNCL2 (5 Millimolar), PDB code: 8ick 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 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.494, 57.636, 48.187, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 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), MGCL2 (5 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), MGCL2 (5 Millimolar), and MNCL2 (5 Millimolar) (pdb code 8ick). 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), MGCL2 (5 Millimolar), and MNCL2 (5 Millimolar), PDB code: 8ick:
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), MGCL2 (5 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), MGCL2 (5 Millimolar), and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:23.3 occ:1.00 O A:VAL103 2.1 19.9 1.0 O A:THR101 2.1 23.9 1.0 OP1 P:DT6 2.2 20.3 1.0 O A:ILE106 2.5 18.1 1.0 O A:HOH601 2.5 56.1 1.0 C A:VAL103 3.0 13.7 1.0 C A:THR101 3.3 18.2 1.0 C A:ARG102 3.5 24.9 1.0 C A:ILE106 3.6 10.3 1.0 P P:DT6 3.6 21.2 1.0 N A:ILE106 3.6 11.9 1.0 N A:GLY105 3.6 15.1 1.0 N A:VAL103 3.7 21.9 1.0 O A:ARG102 3.7 34.2 1.0 CA A:SER104 3.7 11.4 1.0 N A:SER104 3.7 6.8 1.0 CA A:VAL103 4.0 18.1 1.0 CA A:ARG102 4.0 22.9 1.0 C A:SER104 4.0 11.5 1.0 CA A:ILE106 4.1 6.1 1.0 N A:ARG102 4.1 18.9 1.0 CA A:THR101 4.3 16.5 1.0 CB A:ILE106 4.3 8.8 1.0 O A:HOH666 4.3 69.7 1.0 OP2 P:DT6 4.3 12.6 1.0 O3' P:DA5 4.5 27.9 1.0 C A:GLY105 4.5 15.8 1.0 O5' P:DT6 4.6 14.6 1.0 O A:LEU100 4.6 23.6 1.0 CA A:GLY105 4.6 15.7 1.0 N A:GLY107 4.7 12.0 1.0 CB A:VAL103 4.8 14.0 1.0 CG2 A:THR101 5.0 20.9 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), MGCL2 (5 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), MGCL2 (5 Millimolar), and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:50.4 occ:1.00 O A:LEU62 2.4 44.5 1.0 O A:LYS60 2.7 40.1 1.0 O A:VAL65 2.9 23.8 1.0 C A:LEU62 3.4 40.5 1.0 O A:LYS61 3.9 36.4 1.0 C A:LYS60 3.9 39.0 1.0 C A:LYS61 3.9 33.0 1.0 C A:VAL65 4.0 19.5 1.0 N A:PRO63 4.1 35.2 1.0 N A:LEU62 4.1 31.1 1.0 CA A:PRO63 4.2 30.5 1.0 N A:VAL65 4.3 24.2 1.0 CA A:LEU62 4.3 32.4 1.0 N A:GLY64 4.5 45.7 1.0 CA A:LYS61 4.5 36.0 1.0 CA A:VAL65 4.6 16.1 1.0 CG2 A:VAL65 4.6 27.2 1.0 N A:LYS61 4.6 37.8 1.0 CE A:LYS60 4.7 71.1 1.0 C A:PRO63 4.7 41.7 1.0 CG A:LYS60 4.8 54.0 1.0 CA A:LYS60 5.0 37.8 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