Sodium in PDB 8ici: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Dgtp (1 Millimolar) and MGCL2 (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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar), PDB code: 8ici 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 (°)	179.222, 57.694, 48.229, 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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar) also contains other interesting chemical elements:

Magnesium

(Mg)

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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar) (pdb code 8ici). 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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar), PDB code: 8ici:
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 Dgtp (1 Millimolar) and MGCL2 (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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na341 b:53.5 occ:1.00 O A:THR101 2.0 13.6 1.0 O A:HOH601 2.1 74.7 1.0 OP1 P:DT6 2.2 14.4 1.0 O A:VAL103 2.4 5.0 1.0 O A:ILE106 2.5 11.2 1.0 C A:THR101 3.2 10.7 1.0 C A:VAL103 3.3 6.1 1.0 C A:ILE106 3.5 5.9 1.0 P P:DT6 3.5 13.7 1.0 N A:ILE106 3.6 3.6 1.0 C A:ARG102 3.7 26.5 1.0 N A:VAL103 3.8 24.1 1.0 CA A:SER104 3.9 5.1 1.0 N A:GLY105 3.9 12.0 1.0 N A:SER104 3.9 2.8 1.0 O A:ARG102 3.9 35.1 1.0 N A:ARG102 4.0 9.6 1.0 CA A:ARG102 4.0 18.9 1.0 CA A:ILE106 4.1 1.0 1.0 OP2 P:DT6 4.1 8.6 1.0 CA A:THR101 4.2 10.3 1.0 CA A:VAL103 4.2 13.7 1.0 CB A:ILE106 4.3 4.4 1.0 C A:SER104 4.3 11.6 1.0 O3' P:DA5 4.5 12.2 1.0 N A:GLY107 4.6 5.4 1.0 O5' P:DT6 4.6 2.3 1.0 C A:GLY105 4.7 10.2 1.0 O A:LEU100 4.8 24.1 1.0 CA A:GLY105 4.9 7.0 1.0 CG2 A:ILE106 4.9 4.5 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 Dgtp (1 Millimolar) and MGCL2 (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 Dgtp (1 Millimolar) and MGCL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na342 b:9.3 occ:1.00 O A:LEU62 2.1 36.7 1.0 O A:LYS60 2.5 39.5 1.0 O A:VAL65 3.0 23.1 1.0 C A:LEU62 3.3 33.9 1.0 C A:LYS60 3.7 40.5 1.0 C A:LYS61 3.8 29.7 1.0 O A:LYS61 3.8 26.8 1.0 C A:VAL65 3.9 19.6 1.0 N A:LEU62 4.0 24.8 1.0 N A:VAL65 4.2 19.1 1.0 CA A:LEU62 4.2 28.1 1.0 N A:PRO63 4.2 28.8 1.0 CA A:VAL65 4.3 15.4 1.0 CA A:LYS61 4.4 38.7 1.0 CA A:PRO63 4.4 26.8 1.0 N A:LYS61 4.5 38.5 1.0 CE A:LYS60 4.6 55.5 1.0 N A:GLY64 4.7 41.0 1.0 CB A:VAL65 4.8 14.7 1.0 CA A:LYS60 4.8 38.0 1.0 CG A:LYS60 4.9 38.7 1.0 C A:PRO63 4.9 35.9 1.0 N A:GLY66 5.0 19.0 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