Sodium in PDB 9ici: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dttp (1 Millimolar) and ZNCL2 (1 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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9ici 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 / 3.10
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	180.932, 57.542, 48.216, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar) also contains other interesting chemical elements:

Zinc

(Zn)

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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar) (pdb code 9ici). 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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar), PDB code: 9ici:
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 Dttp (1 Millimolar) and ZNCL2 (1 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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:3.9 occ:1.00 O P:HOH601 1.6 85.7 1.0 O A:THR101 2.0 10.0 1.0 OP1 P:DT6 2.0 20.8 1.0 O A:VAL103 2.3 4.3 1.0 O A:ILE106 2.6 19.5 1.0 C A:THR101 3.2 13.0 1.0 C A:VAL103 3.3 14.2 1.0 P P:DT6 3.4 23.9 1.0 C A:ILE106 3.5 12.4 1.0 N A:ILE106 3.6 15.8 1.0 N A:VAL103 3.8 27.9 1.0 C A:ARG102 3.9 25.1 1.0 CA A:ILE106 3.9 12.2 1.0 OP2 P:DT6 4.0 36.6 1.0 N A:GLY105 4.0 22.2 1.0 N A:SER104 4.1 19.4 1.0 CA A:SER104 4.1 25.4 1.0 CG2 A:THR101 4.1 19.0 1.0 N A:ARG102 4.1 12.7 1.0 CB A:ILE106 4.2 16.8 1.0 CA A:THR101 4.2 12.5 1.0 CA A:VAL103 4.2 18.9 1.0 CA A:ARG102 4.2 19.8 1.0 O A:ARG102 4.3 23.7 1.0 O5' P:DT6 4.3 10.3 1.0 C A:SER104 4.4 23.6 1.0 N A:GLY107 4.5 13.5 1.0 O3' P:DA5 4.5 20.7 1.0 C A:GLY105 4.6 19.1 1.0 CB A:THR101 4.8 15.3 1.0 CG2 A:ILE106 4.9 14.8 1.0 CA A:GLY107 4.9 15.0 1.0 CA A:GLY105 4.9 24.3 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 Dttp (1 Millimolar) and ZNCL2 (1 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 Dttp (1 Millimolar) and ZNCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:57.6 occ:1.00 O A:LEU62 2.2 31.1 1.0 O A:LYS60 2.6 15.4 1.0 O A:VAL65 3.2 29.0 1.0 C A:LEU62 3.3 25.7 1.0 C A:LYS60 3.8 24.8 1.0 O A:LYS61 3.8 24.5 1.0 C A:LYS61 3.8 29.7 1.0 N A:LEU62 4.0 20.9 1.0 CA A:LEU62 4.1 19.9 1.0 CG2 A:VAL65 4.2 21.5 1.0 N A:PRO63 4.2 30.9 1.0 C A:VAL65 4.3 28.2 1.0 CA A:PRO63 4.4 38.0 1.0 CG A:LYS60 4.4 27.8 1.0 CE A:LYS60 4.5 49.9 1.0 N A:VAL65 4.5 19.6 1.0 CA A:LYS61 4.5 41.6 1.0 N A:LYS61 4.6 34.6 1.0 CA A:VAL65 4.8 19.9 1.0 CA A:LYS60 4.8 25.1 1.0 N A:GLY64 4.8 47.8 1.0 C A:PRO63 5.0 48.0 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