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Copper in PDB 1jif: Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin

Protein crystallography data

The structure of Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin, PDB code: 1jif was solved by M.Sugiyama, T.Kumagai, M.Hayashida, M.Maruyama, Y.Matoba, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.00 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 35.730, 83.470, 43.060, 90.00, 106.20, 90.00
R / Rfree (%) 15.8 / 20.7

Other elements in 1jif:

The structure of Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin (pdb code 1jif). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 2 binding sites of Copper where determined in the Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin, PDB code: 1jif:
Jump to Copper binding site number: 1; 2;

Copper binding site 1 out of 2 in 1jif

Go back to Copper Binding Sites List in 1jif
Copper binding site 1 out of 2 in the Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu404

b:15.6
occ:1.00
NJ B:BLM402 1.9 15.5 1.0
NG B:BLM402 1.9 15.0 1.0
NH B:BLM402 2.0 12.1 1.0
NC B:BLM402 2.2 11.8 1.0
NB B:BLM402 2.3 15.1 1.0
C12 B:BLM402 2.8 11.3 1.0
C7 B:BLM402 2.8 16.4 1.0
C27 B:BLM402 2.9 18.2 1.0
C3 B:BLM402 2.9 18.6 1.0
C6 B:BLM402 2.9 15.3 1.0
C10 B:BLM402 2.9 13.2 1.0
C29 B:BLM402 2.9 14.4 1.0
C2 B:BLM402 3.0 22.5 1.0
C13 B:BLM402 3.1 13.5 1.0
CL A:CL502 3.1 24.6 1.0
C14 B:BLM402 3.3 15.2 1.0
C1 B:BLM402 3.6 34.4 1.0
OH1 B:BLM402 3.6 18.7 1.0
O1 B:BLM402 3.9 29.4 1.0
NK B:BLM402 3.9 17.8 1.0
C30 B:BLM402 4.0 15.3 1.0
NE B:BLM402 4.0 11.9 1.0
O12 B:BLM402 4.0 16.2 1.0
NI B:BLM402 4.1 16.4 1.0
C28 B:BLM402 4.1 16.5 1.0
C9 B:BLM402 4.1 12.9 1.0
NA B:BLM402 4.4 31.6 1.0
O70 B:BLM402 4.4 20.4 1.0
C5 B:BLM402 4.4 15.7 1.0
O B:HOH640 4.4 26.5 1.0
C8 B:BLM402 4.6 12.5 1.0
OH3 B:BLM402 4.8 36.2 0.6
O A:HOH613 5.0 26.5 1.0

Copper binding site 2 out of 2 in 1jif

Go back to Copper Binding Sites List in 1jif
Copper binding site 2 out of 2 in the Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Crystal Structure of Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus Complexed with Copper(II)-Bleomycin within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu403

b:15.3
occ:1.00
NG B:BLM401 1.8 14.2 1.0
NJ B:BLM401 1.9 15.9 1.0
NH B:BLM401 2.0 12.7 1.0
NC B:BLM401 2.2 11.6 1.0
NB B:BLM401 2.2 13.4 1.0
C6 B:BLM401 2.8 15.8 1.0
C12 B:BLM401 2.8 19.5 1.0
C7 B:BLM401 2.8 18.6 1.0
C27 B:BLM401 2.8 17.0 1.0
C3 B:BLM401 2.9 14.7 1.0
C10 B:BLM401 2.9 13.5 1.0
C29 B:BLM401 2.9 17.8 1.0
CL B:CL501 3.0 20.9 1.0
C2 B:BLM401 3.0 16.5 1.0
C13 B:BLM401 3.1 14.4 1.0
C14 B:BLM401 3.3 15.1 1.0
C1 B:BLM401 3.5 26.4 1.0
OH1 B:BLM401 3.6 17.0 1.0
NK B:BLM401 4.0 15.5 1.0
O12 B:BLM401 4.0 19.3 1.0
NI B:BLM401 4.0 16.8 1.0
C28 B:BLM401 4.0 16.1 1.0
O1 B:BLM401 4.0 29.3 1.0
NE B:BLM401 4.0 13.6 1.0
C30 B:BLM401 4.1 19.7 1.0
C9 B:BLM401 4.1 11.5 1.0
NA B:BLM401 4.2 24.1 1.0
C5 B:BLM401 4.3 15.6 1.0
O B:HOH618 4.4 22.8 1.0
O70 B:BLM401 4.5 16.7 1.0
C8 B:BLM401 4.6 9.9 1.0
O58 B:BLM401 5.0 20.9 1.0

Reference:

M.Sugiyama, T.Kumagai, M.Hayashida, M.Maruyama, Y.Matoba. The 1.6-A Crystal Structure of the Copper(II)-Bound Bleomycin Complexed with the Bleomycin-Binding Protein From Bleomycin-Producing Streptomyces Verticillus. J.Biol.Chem. V. 277 2311 2002.
ISSN: ISSN 0021-9258
PubMed: 11706014
DOI: 10.1074/JBC.M103278200
Page generated: Sun Dec 13 10:59:41 2020

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