Sodium in PDB 8icf: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (10 Millimolar) and MGCL2 (50 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 (10 Millimolar) and MGCL2 (50 Millimolar), PDB code: 8icf 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 (°)	178.875, 57.713, 48.385, 90.00, 90.00, 90.00
R / Rfree (%)	18.5 / 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 (10 Millimolar) and MGCL2 (50 Millimolar) (pdb code 8icf). 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 (10 Millimolar) and MGCL2 (50 Millimolar), PDB code: 8icf:
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 (10 Millimolar) and MGCL2 (50 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 (10 Millimolar) and MGCL2 (50 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:17.4 occ:1.00 O A:THR101 2.3 30.6 1.0 O A:VAL103 2.3 19.9 1.0 O A:ILE106 2.3 1.0 1.0 O A:HOH601 2.4 68.1 1.0 OP1 P:DT6 2.5 33.2 1.0 C A:VAL103 3.1 22.8 1.0 C A:THR101 3.3 19.9 1.0 C A:ILE106 3.5 2.3 1.0 N A:VAL103 3.6 17.7 1.0 N A:ILE106 3.6 6.6 1.0 C A:ARG102 3.7 20.4 1.0 P P:DT6 3.7 24.2 1.0 N A:SER104 3.9 24.8 1.0 CA A:VAL103 3.9 20.2 1.0 CA A:SER104 4.0 20.1 1.0 CA A:ILE106 4.0 7.8 1.0 N A:ARG102 4.1 16.8 1.0 CA A:ARG102 4.1 21.5 1.0 N A:GLY105 4.1 19.7 1.0 O A:ARG102 4.1 23.3 1.0 CA A:THR101 4.2 16.8 1.0 OP2 P:DT6 4.2 16.6 1.0 CB A:ILE106 4.4 12.8 1.0 C A:SER104 4.5 22.2 1.0 N A:GLY107 4.6 1.0 1.0 O5' P:DT6 4.6 23.4 1.0 O3' P:DA5 4.7 21.3 1.0 C A:GLY105 4.8 9.9 1.0 CB A:VAL103 4.9 20.8 1.0 O A:LEU100 4.9 24.9 1.0 CA A:GLY107 5.0 1.0 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 (10 Millimolar) and MGCL2 (50 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 (10 Millimolar) and MGCL2 (50 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:52.5 occ:1.00 O A:LEU62 2.4 34.6 1.0 O A:LYS60 3.0 49.3 1.0 C A:LEU62 3.5 33.7 1.0 O A:LYS61 3.7 37.1 1.0 C A:LYS61 3.9 33.7 1.0 O A:VAL65 4.1 10.1 1.0 C A:LYS60 4.2 43.6 1.0 N A:PRO63 4.2 33.3 1.0 N A:LEU62 4.3 22.0 1.0 CA A:PRO63 4.3 31.6 1.0 CA A:LYS61 4.5 44.2 1.0 CA A:LEU62 4.5 25.0 1.0 N A:LYS61 4.8 45.4 1.0 CD A:PRO63 4.9 38.6 1.0 C A:VAL65 4.9 9.2 1.0

H.Pelletier, M.R.Sawaya. Characterization of the Metal Ion Binding Helix-Hairpin-Helix Motifs in Human Dna Polymerase Beta By X-Ray Structural Analysis. Biochemistry V. 35 12778 1996.
ISSN: ISSN 0006-2960
PubMed: 8841120
DOI: 10.1021/BI960790I