Sodium in PDB 9icl: Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2, PDB code: 9icl 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 (°)	178.634, 57.763, 48.491, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / n/a

The structure of Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2 also contains other interesting chemical elements:

Manganese

(Mn)

2 atoms

The binding sites of Sodium atom in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2 (pdb code 9icl). 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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2, PDB code: 9icl:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2


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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:21.7 occ:1.00 O A:THR101 2.2 23.2 1.0 O A:VAL103 2.3 17.1 1.0 O A:ILE106 2.4 15.1 1.0 OP1 P:DG6 2.7 23.4 1.0 O A:HOH601 3.2 90.8 1.0 C A:THR101 3.3 16.9 1.0 C A:VAL103 3.3 18.0 1.0 C A:ILE106 3.4 6.9 1.0 OP2 P:DG6 3.4 29.0 1.0 N A:ILE106 3.5 11.1 1.0 P P:DG6 3.5 23.2 1.0 N A:GLY105 3.9 19.3 1.0 CA A:ILE106 3.9 7.6 1.0 N A:VAL103 4.0 24.3 1.0 CA A:THR101 4.0 13.3 1.0 CA A:SER104 4.1 17.4 1.0 N A:SER104 4.1 13.3 1.0 C A:ARG102 4.1 24.9 1.0 CA A:VAL103 4.3 23.4 1.0 N A:ARG102 4.3 15.6 1.0 C A:SER104 4.3 19.3 1.0 CB A:ILE106 4.4 12.4 1.0 N A:GLY107 4.4 6.2 1.0 O A:ARG102 4.4 32.3 1.0 C A:GLY105 4.5 16.5 1.0 CA A:ARG102 4.5 20.0 1.0 O3' P:DT5 4.6 28.2 1.0 CA A:GLY107 4.7 3.7 1.0 O A:LEU100 4.7 23.2 1.0 O5' P:DG6 4.8 20.6 1.0 CG2 A:THR101 4.8 19.9 1.0 CA A:GLY105 4.8 17.9 1.0 CB A:THR101 4.9 21.2 1.0

Sodium binding site 2 out of 2 in the Dna Polymerase Beta (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2


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 (E.C.2.7.7.7)/Dna Complex, Soaked in the Presence of Pyrophosphate and MNCL2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:44.6 occ:1.00 OP1 P:DG3 3.5 36.5 1.0 OP2 P:DG3 4.3 47.1 1.0 P P:DG3 4.4 46.4 1.0 O P:HOH615 4.7 78.6 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