Cadmium in PDB 8ice: 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 CDCL2 (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 Datp (1 Millimolar) and CDCL2 (1 Millimolar), PDB code: 8ice 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 / 3.20
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	178.260, 57.756, 48.255, 90.00, 90.00, 90.00
R / Rfree (%)	17.1 / 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 CDCL2 (1 Millimolar) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Cadmium 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 CDCL2 (1 Millimolar) (pdb code 8ice). This binding sites where shown within 5.0 Angstroms radius around Cadmium atom.
In total 2 binding sites of Cadmium 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 Datp (1 Millimolar) and CDCL2 (1 Millimolar), PDB code: 8ice:
Jump to Cadmium binding site number: 1; 2;

Cadmium 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 Datp (1 Millimolar) and CDCL2 (1 Millimolar)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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 CDCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd339 b:30.0 occ:0.47 OD1 A:ASP190 2.2 54.7 1.0 O3G A:DTP338 2.3 57.9 0.5 O1G A:DTP338 2.4 49.5 0.5 OP2 P:DA8 2.5 94.5 0.5 PG A:DTP338 2.9 54.2 0.5 OD1 A:ASP192 3.1 51.8 1.0 CG A:ASP190 3.1 50.1 1.0 OD2 A:ASP190 3.5 51.6 1.0 OD2 A:ASP192 3.8 49.9 1.0 CG A:ASP192 3.9 44.4 1.0 O3B A:DTP338 3.9 63.8 0.5 P P:DA8 3.9 95.1 0.5 O2G A:DTP338 4.1 46.5 0.5 O A:ASP190 4.1 4.6 1.0 O2B A:DTP338 4.3 73.5 0.5 O A:HOH522 4.4 10.1 1.0 O A:HOH655 4.5 40.9 1.0 OP1 P:DA8 4.5 95.4 0.5 CB A:ASP190 4.5 36.1 1.0 N A:ASP190 4.6 17.6 1.0 PB A:DTP338 4.6 70.7 0.5 O5' P:DA8 4.6 96.8 0.5 O3A A:DTP338 4.8 73.7 0.5 C A:ASP190 4.8 7.4 1.0 O A:HOH502 4.8 1.0 1.0 O3' P:DG7 4.9 92.1 1.0 CA A:ASP190 5.0 17.1 1.0

Cadmium 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 Datp (1 Millimolar) and CDCL2 (1 Millimolar)


Mono view


Stereo pair view

A full contact list of Cadmium with other atoms in the Cd 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 Datp (1 Millimolar) and CDCL2 (1 Millimolar) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cd343 b:30.0 occ:0.95 ND1 A:HIS51 2.2 40.2 1.0 CE1 A:HIS51 3.1 38.5 1.0 CG A:HIS51 3.2 38.4 1.0 CB A:HIS51 3.6 32.4 1.0 O A:PRO50 4.2 46.1 1.0 NE2 A:HIS51 4.2 38.8 1.0 CD2 A:HIS51 4.3 40.0 1.0 CA A:HIS51 4.4 31.0 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