Sodium in PDB 8icm: 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), MNCL2 (5 Millimolar), and Ammonium Sulfate (75 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), MNCL2 (5 Millimolar), and Ammonium Sulfate (75 Millimolar), PDB code: 8icm 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 (°)	178.812, 57.784, 48.517, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / n/a

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), MNCL2 (5 Millimolar), and Ammonium Sulfate (75 Millimolar) (pdb code 8icm). 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), MNCL2 (5 Millimolar), and Ammonium Sulfate (75 Millimolar), PDB code: 8icm:
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), MNCL2 (5 Millimolar), and Ammonium Sulfate (75 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), MNCL2 (5 Millimolar), and Ammonium Sulfate (75 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:22.3 occ:1.00 O A:THR101 2.0 14.2 1.0 OP1 P:DT6 2.3 19.8 1.0 O A:ILE106 2.5 12.4 1.0 O A:VAL103 2.6 10.0 1.0 O A:HOH601 2.8 72.8 1.0 C A:THR101 3.2 12.2 1.0 C A:VAL103 3.2 8.7 1.0 C A:ILE106 3.4 7.0 1.0 N A:ILE106 3.5 1.0 1.0 P P:DT6 3.5 20.9 1.0 N A:VAL103 3.6 22.7 1.0 N A:SER104 3.8 9.2 1.0 CA A:ILE106 3.8 2.0 1.0 C A:ARG102 3.9 23.5 1.0 CA A:SER104 3.9 10.2 1.0 OP2 P:DT6 3.9 19.4 1.0 CA A:THR101 4.0 10.6 1.0 CA A:VAL103 4.0 16.6 1.0 N A:GLY105 4.1 18.4 1.0 N A:ARG102 4.1 15.3 1.0 CB A:ILE106 4.2 4.6 1.0 CA A:ARG102 4.2 21.3 1.0 C A:SER104 4.3 14.0 1.0 O5' P:DT6 4.4 12.8 1.0 O A:ARG102 4.5 27.1 1.0 N A:GLY107 4.5 7.9 1.0 C A:GLY105 4.5 9.9 1.0 O A:LEU100 4.5 17.2 1.0 O3' P:DA5 4.8 15.1 1.0 CG2 A:THR101 4.9 15.1 1.0 CB A:VAL103 4.9 17.7 1.0 CA A:GLY105 4.9 12.5 1.0 CA A:GLY107 5.0 5.7 1.0 CB A:THR101 5.0 15.0 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), MNCL2 (5 Millimolar), and Ammonium Sulfate (75 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), MNCL2 (5 Millimolar), and Ammonium Sulfate (75 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:69.9 occ:1.00 O A:LEU62 2.4 37.0 1.0 O A:LYS60 3.1 30.9 1.0 C A:LEU62 3.3 30.1 1.0 O A:VAL65 3.8 25.8 1.0 C A:LYS61 3.9 28.0 1.0 O A:LYS61 4.0 28.0 1.0 N A:LEU62 4.0 23.5 1.0 N A:PRO63 4.0 32.4 1.0 CA A:PRO63 4.1 31.4 1.0 CA A:LEU62 4.2 21.6 1.0 C A:LYS60 4.2 27.9 1.0 CA A:LYS61 4.5 34.8 1.0 N A:GLY64 4.7 43.8 1.0 N A:VAL65 4.7 16.3 1.0 C A:PRO63 4.8 38.7 1.0 C A:VAL65 4.8 18.2 1.0 N A:LYS61 4.9 30.8 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