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Copper in PDB 3de8: Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination

Protein crystallography data

The structure of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination, PDB code: 3de8 was solved by E.N.Salgado, R.A.Lewis, A.L.Rheingold, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.92 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 47.566, 89.504, 52.019, 90.00, 111.01, 90.00
R / Rfree (%) 19.4 / 24.4

Other elements in 3de8:

The structure of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination also contains other interesting chemical elements:

Iron (Fe) 4 atoms
Calcium (Ca) 6 atoms

Copper Binding Sites:

The binding sites of Copper atom in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination (pdb code 3de8). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 4 binding sites of Copper where determined in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination, PDB code: 3de8:
Jump to Copper binding site number: 1; 2; 3; 4;

Copper binding site 1 out of 4 in 3de8

Go back to Copper Binding Sites List in 3de8
Copper binding site 1 out of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


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 A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu107

b:16.4
occ:1.00
NE2 A:HIS59 2.0 18.8 1.0
NE2 D:HIS73 2.1 19.1 1.0
NE2 A:HIS63 2.1 22.2 1.0
NE2 D:HIS77 2.1 20.8 1.0
O D:HOH151 2.6 22.4 1.0
CE1 A:HIS59 2.9 20.9 1.0
CD2 D:HIS73 3.0 21.0 1.0
CE1 D:HIS77 3.0 23.1 1.0
CD2 A:HIS63 3.0 23.1 1.0
CD2 A:HIS59 3.1 20.5 1.0
CE1 D:HIS73 3.1 25.1 1.0
CE1 A:HIS63 3.1 25.3 1.0
CD2 D:HIS77 3.1 21.9 1.0
O D:HOH161 3.6 14.5 1.0
O A:HOH341 4.0 27.6 1.0
ND1 A:HIS59 4.1 20.9 1.0
CG A:HIS59 4.2 19.8 1.0
CG D:HIS73 4.2 22.8 1.0
ND1 D:HIS77 4.2 20.7 1.0
ND1 D:HIS73 4.2 23.6 1.0
ND1 A:HIS63 4.2 23.3 1.0
CG A:HIS63 4.2 21.9 1.0
CG D:HIS77 4.2 19.8 1.0
O A:HOH196 4.3 23.7 1.0
O A:HOH340 4.9 41.9 1.0

Copper binding site 2 out of 4 in 3de8

Go back to Copper Binding Sites List in 3de8
Copper binding site 2 out of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


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 A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu108

b:21.4
occ:1.00
NE2 A:HIS73 2.1 18.7 1.0
NE2 A:HIS77 2.1 23.6 1.0
NE2 D:HIS59 2.1 21.6 1.0
NE2 D:HIS63 2.1 17.8 1.0
O D:HOH152 2.7 19.7 1.0
CD2 D:HIS59 2.9 22.1 1.0
CE1 A:HIS73 3.0 22.4 1.0
CE1 D:HIS63 3.0 19.6 1.0
CE1 A:HIS77 3.0 25.5 1.0
CD2 A:HIS73 3.1 22.7 1.0
CD2 A:HIS77 3.1 24.5 1.0
CD2 D:HIS63 3.2 19.3 1.0
CE1 D:HIS59 3.2 23.0 1.0
O A:HOH166 3.5 34.5 1.0
ND1 A:HIS73 4.1 21.6 1.0
CG D:HIS59 4.1 22.2 1.0
ND1 A:HIS77 4.1 22.6 1.0
ND1 D:HIS63 4.1 20.5 1.0
CG A:HIS73 4.2 19.8 1.0
ND1 D:HIS59 4.2 23.5 1.0
CG A:HIS77 4.2 22.2 1.0
CG D:HIS63 4.3 19.6 1.0
O A:HOH290 4.4 24.2 1.0
O D:HOH186 4.8 23.2 1.0
O C:HOH324 4.9 14.4 1.0

Copper binding site 3 out of 4 in 3de8

Go back to Copper Binding Sites List in 3de8
Copper binding site 3 out of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu107

b:15.1
occ:1.00
NE2 C:HIS73 2.0 19.1 1.0
NE2 B:HIS63 2.1 19.2 1.0
NE2 B:HIS59 2.1 20.3 1.0
NE2 C:HIS77 2.1 18.4 1.0
O C:HOH312 2.5 14.4 1.0
CD2 B:HIS59 2.9 21.1 1.0
CE1 C:HIS73 3.0 20.6 1.0
CD2 C:HIS77 3.0 21.4 1.0
CD2 C:HIS73 3.0 19.7 1.0
CE1 B:HIS63 3.1 23.5 1.0
CD2 B:HIS63 3.1 21.9 1.0
CE1 C:HIS77 3.1 19.2 1.0
CE1 B:HIS59 3.2 23.2 1.0
O B:HOH300 3.5 25.8 1.0
ND1 C:HIS73 4.1 18.9 1.0
CG B:HIS59 4.1 20.6 1.0
CG C:HIS73 4.2 20.0 1.0
ND1 B:HIS63 4.2 21.8 1.0
ND1 B:HIS59 4.2 20.9 1.0
CG C:HIS77 4.2 18.9 1.0
ND1 C:HIS77 4.2 17.0 1.0
CG B:HIS63 4.2 20.2 1.0
O C:HOH369 4.3 21.5 1.0
O C:HOH386 4.4 25.3 1.0
O A:HOH239 4.5 28.5 1.0
O A:HOH160 4.7 12.9 1.0
O A:HOH203 4.9 19.5 1.0

Copper binding site 4 out of 4 in 3de8

Go back to Copper Binding Sites List in 3de8
Copper binding site 4 out of 4 in the Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 4 of Crystal Structure of A Dimeric Cytochrome CB562 Assembly Induced By Copper Coordination within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu108

b:21.6
occ:1.00
NE2 B:HIS73 2.0 18.7 1.0
NE2 C:HIS59 2.0 20.8 1.0
NE2 C:HIS63 2.1 20.7 1.0
NE2 B:HIS77 2.1 23.4 1.0
O B:HOH253 2.5 26.0 1.0
CD2 C:HIS59 2.9 21.7 1.0
CE1 B:HIS73 3.0 20.8 1.0
CE1 B:HIS77 3.1 26.9 1.0
CD2 B:HIS73 3.1 21.1 1.0
CE1 C:HIS63 3.1 22.2 1.0
CD2 C:HIS63 3.1 21.9 1.0
CE1 C:HIS59 3.1 22.7 1.0
CD2 B:HIS77 3.2 27.1 1.0
O C:HOH325 3.4 22.0 1.0
O C:HOH400 3.5 35.5 1.0
CG C:HIS59 4.1 21.8 1.0
ND1 B:HIS73 4.1 21.4 1.0
ND1 C:HIS59 4.1 22.4 1.0
CG B:HIS73 4.2 20.1 1.0
ND1 B:HIS77 4.2 26.8 1.0
ND1 C:HIS63 4.2 21.6 1.0
CG C:HIS63 4.2 21.3 1.0
CG B:HIS77 4.3 25.1 1.0

Reference:

E.N.Salgado, R.A.Lewis, S.Mossin, A.L.Rheingold, F.A.Tezcan. Control of Protein Oligomerization Symmetry By Metal Coordination: C2 and C3 Symmetrical Assemblies Through Cu(II) and Ni(II) Coordination. Inorg.Chem. V. 48 2726 2009.
ISSN: ISSN 0020-1669
PubMed: 19267481
DOI: 10.1021/IC9001237
Page generated: Sun Dec 13 11:09:22 2020

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