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

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

The structure of Regulation of Protein Function: Crystal Packing Interfaces and Conformational Dimerization also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

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 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 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 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

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