Sodium in PDB 8icn: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Atp (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 Atp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8icn 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 / 2.80
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.373, 57.826, 48.227, 90.00, 90.00, 90.00
R / Rfree (%)	17.2 / 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 Atp (1 Millimolar) and MNCL2 (5 Millimolar) also contains other interesting chemical elements:

Manganese

(Mn)

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 Atp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8icn). 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 Atp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8icn:
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 Atp (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 Atp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:21.4 occ:1.00 O A:THR101 2.1 25.0 1.0 OP1 P:DT6 2.3 16.8 1.0 O A:VAL103 2.3 11.5 1.0 O P:HOH601 2.5 72.5 1.0 O A:ILE106 2.7 16.3 1.0 C A:THR101 3.2 22.5 1.0 C A:VAL103 3.3 8.9 1.0 N A:ILE106 3.5 7.7 1.0 P P:DT6 3.6 19.1 1.0 C A:ILE106 3.6 11.0 1.0 N A:VAL103 3.7 26.3 1.0 C A:ARG102 3.8 32.2 1.0 N A:GLY105 3.9 16.7 1.0 CA A:ILE106 4.0 2.3 1.0 CA A:THR101 4.1 18.9 1.0 N A:ARG102 4.1 24.6 1.0 CA A:SER104 4.1 13.7 1.0 CA A:VAL103 4.1 17.4 1.0 OP2 P:DT6 4.1 10.3 1.0 N A:SER104 4.1 9.1 1.0 CA A:ARG102 4.2 29.5 1.0 O A:ARG102 4.2 37.4 1.0 CB A:ILE106 4.2 7.3 1.0 C A:SER104 4.4 15.2 1.0 O3' P:DA5 4.5 15.6 1.0 C A:GLY105 4.5 15.1 1.0 O5' P:DT6 4.6 16.2 1.0 O A:LEU100 4.7 21.6 1.0 CA A:GLY105 4.7 17.6 1.0 N A:GLY107 4.8 14.1 1.0 CG2 A:ILE106 4.9 9.7 1.0 CB A:THR101 5.0 17.3 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 Atp (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 Atp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:57.8 occ:1.00 O A:LEU62 2.6 41.5 1.0 O A:LYS60 2.8 37.6 1.0 O A:VAL65 3.1 25.0 1.0 C A:LEU62 3.6 43.5 1.0 C A:LYS60 4.0 35.1 1.0 C A:LYS61 4.1 39.3 1.0 O A:LYS61 4.2 42.8 1.0 C A:VAL65 4.2 20.9 1.0 N A:LEU62 4.3 35.1 1.0 N A:VAL65 4.4 16.9 1.0 N A:PRO63 4.4 42.7 1.0 CA A:PRO63 4.5 40.0 1.0 CA A:LEU62 4.5 34.9 1.0 CA A:LYS61 4.6 38.8 1.0 N A:GLY64 4.6 47.0 1.0 N A:LYS61 4.7 34.1 1.0 CA A:VAL65 4.8 16.8 1.0 CG2 A:VAL65 4.8 25.2 1.0 CG A:LYS60 4.9 45.7 1.0 CE A:LYS60 4.9 62.5 1.0 C A:PRO63 4.9 44.5 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