Calcium in PDB 8ica: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Seven Base Pairs of Dna; Soaked in the Presence of Datp (1 Millimolar) and CACL2 (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 Datp (1 Millimolar) and CACL2 (5 Millimolar), PDB code: 8ica 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 / 3.00
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	179.839, 57.719, 48.175, 90.00, 90.00, 90.00
R / Rfree (%)	15.9 / 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 Datp (1 Millimolar) and CACL2 (5 Millimolar) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Datp (1 Millimolar) and CACL2 (5 Millimolar) (pdb code 8ica). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total only one binding site of Calcium was 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 Datp (1 Millimolar) and CACL2 (5 Millimolar), PDB code: 8ica:

Calcium binding site 1 out of 1 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 Datp (1 Millimolar) and CACL2 (5 Millimolar)


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca 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 Datp (1 Millimolar) and CACL2 (5 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca339 b:30.0 occ:0.61 OD1 A:ASP190 2.9 42.2 1.0 O A:HOH655 3.0 37.0 1.0 O1G A:DTP338 3.3 62.8 0.5 O2B A:DTP338 3.3 81.5 0.5 O3A A:DTP338 3.5 74.8 0.5 CG A:ASP190 3.5 40.4 1.0 O3G A:DTP338 3.6 66.5 0.5 O A:ASP190 3.8 24.0 1.0 OD2 A:ASP190 3.8 53.6 1.0 PB A:DTP338 3.9 76.9 0.5 PG A:DTP338 3.9 66.5 0.5 O3B A:DTP338 4.0 72.5 0.5 OD1 A:ASP192 4.1 52.0 1.0 O A:HOH657 4.1 49.5 1.0 O A:HOH656 4.2 39.1 1.0 CG A:ASP192 4.2 45.7 1.0 OD2 A:ASP192 4.4 55.0 1.0 C A:ASP190 4.5 17.2 1.0 O A:HOH502 4.7 3.6 1.0 O A:HOH661 4.7 55.6 1.0 CB A:ASP190 4.7 26.0 1.0 N A:ASP190 4.8 16.2 1.0 CB A:ASP192 4.9 25.5 1.0 CA A:ASP190 4.9 17.5 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