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Copper in PDB 3cvd: Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization

Protein crystallography data

The structure of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization, PDB code: 3cvd was solved by P.B.Crowley, P.M.Matias, H.Mi, S.J.Firbank, M.J.Banfield, C.Dennison, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.77 / 1.50
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 85.843, 85.843, 90.282, 90.00, 90.00, 90.00
R / Rfree (%) 15.3 / 18.4

Copper Binding Sites:

The binding sites of Copper atom in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization (pdb code 3cvd). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization, PDB code: 3cvd:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in 3cvd

Go back to Copper Binding Sites List in 3cvd
Copper binding site 1 out of 3 in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cu106

b:20.5
occ:1.00
ND1 A:HIS39 2.0 14.7 1.0
SG A:CYS89 2.2 14.2 1.0
ND1 A:HIS92 2.3 9.4 0.5
SD A:MET97 2.5 14.1 1.0
CE1 A:HIS39 2.9 12.0 1.0
CD2 A:HIS92 2.9 18.5 0.5
CG A:HIS39 3.1 13.0 1.0
CG A:HIS92 3.2 13.4 0.5
CB A:CYS89 3.2 13.0 1.0
CE1 A:HIS92 3.3 13.0 0.5
CE A:MET97 3.3 16.7 1.0
CB A:HIS92 3.5 13.8 0.5
CB A:HIS39 3.5 12.7 1.0
CG A:HIS92 3.5 17.9 0.5
CB A:HIS92 3.6 15.7 0.5
O A:PRO38 3.7 16.0 1.0
CA A:HIS39 3.7 12.8 1.0
CG A:MET97 3.8 13.6 1.0
NE2 A:HIS39 4.1 15.4 1.0
NE2 A:HIS92 4.1 20.1 0.5
CD2 A:HIS39 4.2 13.7 1.0
CD2 A:HIS92 4.4 12.3 0.5
NE2 A:HIS92 4.4 13.9 0.5
CB A:MET97 4.4 13.0 1.0
N A:HIS92 4.4 13.6 1.0
C A:PRO38 4.5 15.3 1.0
N A:HIS39 4.5 13.8 1.0
CA A:HIS92 4.6 13.3 0.5
CA A:HIS92 4.6 14.2 0.5
CA A:CYS89 4.6 12.3 1.0
N A:ASN40 4.8 12.6 1.0
ND1 A:HIS92 4.8 19.3 0.5
C A:HIS39 4.8 12.9 1.0

Copper binding site 2 out of 3 in 3cvd

Go back to Copper Binding Sites List in 3cvd
Copper binding site 2 out of 3 in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cu106

b:14.9
occ:1.00
ND1 B:HIS39 2.0 11.9 1.0
SG B:CYS89 2.2 12.3 1.0
ND1 B:HIS92 2.4 12.4 0.5
SD B:MET97 2.4 12.5 1.0
CE1 B:HIS39 3.0 13.7 1.0
CG B:HIS39 3.0 11.6 1.0
CB B:CYS89 3.2 12.0 1.0
CE B:MET97 3.2 13.7 1.0
CE1 B:HIS92 3.3 14.9 0.5
CG B:HIS92 3.4 13.2 0.5
CB B:HIS39 3.4 12.1 1.0
CD2 B:HIS92 3.6 17.7 0.5
CB B:HIS92 3.6 13.2 0.5
CG B:MET97 3.7 13.3 1.0
CA B:HIS39 3.7 11.1 1.0
CB B:HIS92 3.8 14.2 0.5
CG B:HIS92 4.0 16.1 0.5
O B:PRO38 4.1 12.8 1.0
NE2 B:HIS39 4.1 12.1 1.0
CD2 B:HIS39 4.1 11.9 1.0
CB B:MET97 4.3 12.2 1.0
NE2 B:HIS92 4.4 14.9 0.5
N B:HIS92 4.5 13.2 1.0
CD2 B:HIS92 4.5 13.7 0.5
CA B:CYS89 4.6 11.3 1.0
CA B:HIS92 4.7 13.0 0.5
N B:HIS39 4.7 10.7 1.0
CG B:PRO91 4.7 15.7 0.6
CA B:HIS92 4.7 13.5 0.5
N B:ASN40 4.7 11.1 1.0
C B:PRO38 4.8 11.6 1.0
C B:HIS39 4.8 10.9 1.0
NE2 B:HIS92 4.8 17.4 0.5
CB B:PRO91 4.8 14.2 0.4

Copper binding site 3 out of 3 in 3cvd

Go back to Copper Binding Sites List in 3cvd
Copper binding site 3 out of 3 in the Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cu107

b:21.6
occ:1.00
ND1 C:HIS39 2.0 16.6 1.0
SG C:CYS89 2.2 17.1 1.0
ND1 C:HIS92 2.2 14.1 0.5
SD C:MET97 2.5 18.3 1.0
CE1 C:HIS39 2.9 16.3 1.0
CD2 C:HIS92 3.1 22.1 0.5
CG C:HIS39 3.1 16.1 1.0
CE1 C:HIS92 3.2 15.3 0.5
CE C:MET97 3.2 20.3 1.0
CB C:CYS89 3.2 16.2 1.0
CG C:HIS92 3.2 16.2 0.5
CB C:HIS39 3.5 16.9 1.0
CB C:HIS92 3.5 16.7 0.5
CG C:HIS92 3.7 20.5 0.5
CB C:HIS92 3.7 18.5 0.5
CG C:MET97 3.8 17.9 1.0
CA C:HIS39 3.8 16.0 1.0
O C:PRO38 3.8 18.6 1.0
NE2 C:HIS39 4.1 17.3 1.0
CD2 C:HIS39 4.2 16.8 1.0
NE2 C:HIS92 4.3 22.7 0.5
NE2 C:HIS92 4.3 16.4 0.5
CB C:MET97 4.3 18.3 1.0
CD2 C:HIS92 4.3 16.5 0.5
N C:HIS92 4.4 17.7 1.0
CA C:HIS92 4.6 17.2 0.5
C C:PRO38 4.6 18.5 1.0
CA C:CYS89 4.6 15.2 1.0
N C:HIS39 4.7 16.3 1.0
CA C:HIS92 4.7 18.0 0.5
N C:ASN40 4.8 14.9 1.0
C C:HIS39 4.9 16.0 1.0
ND1 C:HIS92 5.0 22.9 0.5
CB C:PRO91 5.0 17.6 1.0

Reference:

P.B.Crowley, P.M.Matias, H.Mi, S.J.Firbank, M.J.Banfield, C.Dennison. Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization. Biochemistry V. 47 6583 2008.
ISSN: ISSN 0006-2960
PubMed: 18479147
DOI: 10.1021/BI800125H
Page generated: Thu Sep 3 17:10:37 2020
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