Sodium in PDB 8ics: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dctp (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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8ics 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 (°)	178.792, 57.623, 48.419, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 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 Dctp (1 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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar) (pdb code 8ics). 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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar), PDB code: 8ics:
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 Dctp (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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:22.2 occ:1.00 O A:THR101 2.2 20.9 1.0 O A:VAL103 2.2 8.8 1.0 O P:HOH601 2.4 93.7 1.0 OP1 P:DT6 2.5 22.4 1.0 O A:ILE106 2.5 1.0 1.0 C A:VAL103 3.0 11.5 1.0 C A:THR101 3.3 16.7 1.0 N A:VAL103 3.6 19.6 1.0 C A:ILE106 3.6 1.0 1.0 C A:ARG102 3.6 20.3 1.0 N A:SER104 3.7 9.9 1.0 P P:DT6 3.7 17.7 1.0 N A:ILE106 3.8 2.1 1.0 CA A:SER104 3.8 8.2 1.0 CA A:VAL103 3.8 17.6 1.0 O A:ARG102 3.9 19.6 1.0 N A:GLY105 4.0 14.8 1.0 OP2 P:DT6 4.1 19.5 1.0 CA A:ILE106 4.1 4.2 1.0 CA A:ARG102 4.1 24.0 1.0 N A:ARG102 4.2 20.9 1.0 CA A:THR101 4.2 9.6 1.0 C A:SER104 4.3 13.8 1.0 O5' P:DT6 4.5 16.0 1.0 CB A:ILE106 4.5 5.4 1.0 N A:GLY107 4.7 1.0 1.0 C A:GLY105 4.7 8.3 1.0 O A:LEU100 4.8 21.5 1.0 CB A:VAL103 4.8 17.2 1.0 O3' P:DA5 5.0 11.8 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 Dctp (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 Dctp (1 Millimolar) and MNCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:63.3 occ:1.00 O A:LEU62 2.4 30.5 1.0 C A:LEU62 3.4 28.0 1.0 O A:LYS60 3.4 38.3 1.0 CA A:PRO63 4.0 33.2 1.0 N A:PRO63 4.0 28.5 1.0 O A:VAL65 4.1 16.4 1.0 O A:LYS61 4.3 35.3 1.0 C A:LYS61 4.3 30.8 1.0 N A:LEU62 4.5 15.7 1.0 CA A:LEU62 4.5 18.6 1.0 C A:LYS60 4.6 36.3 1.0 N A:GLY64 4.6 35.4 1.0 CD A:PRO63 4.8 29.3 1.0 N A:VAL65 4.8 12.6 1.0 C A:PRO63 4.8 31.4 1.0 C A:VAL65 4.9 14.7 1.0 CA A:LYS61 4.9 40.2 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