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Cadmium in PDB 7icf: Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (0.1 Millimolar) (Four-Day Soak)

Protein crystallography data

The structure of Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (0.1 Millimolar) (Four-Day Soak), PDB code: 7icf 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 (°) 177.179, 57.710, 48.519, 90.00, 90.00, 90.00
R / Rfree (%) 15.8 / n/a

Cadmium Binding Sites:

The binding sites of Cadmium atom in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (0.1 Millimolar) (Four-Day Soak) (pdb code 7icf). 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 Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (0.1 Millimolar) (Four-Day Soak), PDB code: 7icf:
Jump to Cadmium binding site number: 1; 2;

Cadmium binding site 1 out of 2 in 7icf

Go back to Cadmium Binding Sites List in 7icf
Cadmium binding site 1 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (0.1 Millimolar) (Four-Day Soak)


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 Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (0.1 Millimolar) (Four-Day Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd340

b:94.8
occ:1.00
OD2 A:ASP192 2.9 46.6 1.0
OD2 A:ASP190 3.5 34.5 1.0
O A:HOH660 3.5 32.3 1.0
CG A:ASP190 3.5 30.8 1.0
OD1 A:ASP190 3.7 32.5 1.0
CG A:ASP192 3.7 46.6 1.0
O A:HOH549 3.8 89.1 1.0
OD1 A:ASP192 4.0 60.6 1.0
CB A:ASP190 4.4 25.2 1.0
OD2 A:ASP256 4.4 36.9 1.0
O A:HOH671 4.5 26.4 1.0
CB A:ASP192 4.6 33.4 1.0
O A:ASP190 4.8 25.5 1.0
CG A:ASP256 5.0 30.7 1.0

Cadmium binding site 2 out of 2 in 7icf

Go back to Cadmium Binding Sites List in 7icf
Cadmium binding site 2 out of 2 in the Dna Polymerase Beta (Pol B) (E.C.2.7.7.7) Complexed with Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (0.1 Millimolar) (Four-Day Soak)


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 Six Base Pairs of Dna; Soaked in the Presence of CDCL2 (0.1 Millimolar) (Four-Day Soak) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cd343

b:48.5
occ:1.00
ND1 A:HIS51 2.7 39.6 1.0
CE1 A:HIS51 3.5 32.3 1.0
CG A:HIS51 3.8 37.0 1.0
CB A:HIS51 4.2 31.0 1.0
O A:PRO50 4.4 30.0 1.0
NE2 A:HIS51 4.7 26.6 1.0
CD2 A:HIS51 4.8 31.1 1.0
CA A:HIS51 4.8 25.0 1.0

Reference:

H.Pelletier, M.R.Sawaya, W.Wolfle, S.H.Wilson, J.Kraut. A Structural Basis For Metal Ion Mutagenicity and Nucleotide Selectivity in Human Dna Polymerase Beta Biochemistry V. 35 12762 1996.
ISSN: ISSN 0006-2960
PubMed: 8841119
DOI: 10.1021/BI9529566
Page generated: Fri Aug 28 15:55:58 2020
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