Copper in PDB 2w88: Plastocyanin Variant with N-Terminal Methionine - Open Structure

The structure of Plastocyanin Variant with N-Terminal Methionine - Open Structure, PDB code: 2w88 was solved by P.B.Crowley, P.M.Matias, A.R.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	110.43 / 2.89
Space group	P 31 1 2
Cell size a, b, c (Å), α, β, γ (°)	127.700, 127.700, 94.990, 90.00, 90.00, 120.00
R / Rfree (%)	19.433 / 22.285

The structure of Plastocyanin Variant with N-Terminal Methionine - Open Structure also contains other interesting chemical elements:

Zinc

(Zn)

7 atoms

The binding sites of Copper atom in the Plastocyanin Variant with N-Terminal Methionine - Open Structure (pdb code 2w88). This binding sites where shown within 5.0 Angstroms radius around Copper atom.
In total 3 binding sites of Copper where determined in the Plastocyanin Variant with N-Terminal Methionine - Open Structure, PDB code: 2w88:
Jump to Copper binding site number: 1; 2; 3;

Copper binding site 1 out of 3 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 1 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Cu106 b:26.8 occ:1.00 ND1 A:HIS92 2.1 29.5 1.0 ND1 A:HIS39 2.1 27.2 1.0 SG A:CYS89 2.3 28.9 1.0 SD A:MET97 2.3 28.4 1.0 CE1 A:HIS92 3.0 30.7 1.0 CE1 A:HIS39 3.0 26.8 1.0 CG A:HIS92 3.1 30.2 1.0 CG A:HIS39 3.1 27.5 1.0 CE A:MET97 3.3 28.1 1.0 CB A:CYS89 3.4 29.2 1.0 CB A:HIS92 3.5 30.1 1.0 CB A:HIS39 3.5 27.8 1.0 CA A:HIS39 3.9 27.8 1.0 O A:PRO38 3.9 28.6 1.0 CG A:MET97 3.9 29.6 1.0 NE2 A:HIS92 4.1 30.5 1.0 NE2 A:HIS39 4.1 26.5 1.0 CD2 A:HIS92 4.2 30.3 1.0 CD2 A:HIS39 4.2 27.1 1.0 N A:HIS92 4.4 30.0 1.0 CB A:MET97 4.4 29.9 1.0 CA A:HIS92 4.6 30.2 1.0 C A:PRO38 4.7 28.4 1.0 N A:HIS39 4.7 28.1 1.0 CA A:CYS89 4.8 29.1 1.0

Copper binding site 2 out of 3 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 2 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Cu106 b:24.6 occ:1.00 ND1 C:HIS39 2.0 26.8 1.0 ND1 C:HIS92 2.1 29.8 1.0 SG C:CYS89 2.3 26.7 1.0 SD C:MET97 2.3 28.6 1.0 CE1 C:HIS39 2.9 28.4 1.0 CE1 C:HIS92 3.0 30.3 1.0 CG C:HIS92 3.1 29.1 1.0 CG C:HIS39 3.1 28.1 1.0 CE C:MET97 3.3 28.1 1.0 CB C:HIS92 3.4 28.6 1.0 CB C:CYS89 3.4 27.4 1.0 CB C:HIS39 3.6 28.1 1.0 CG C:MET97 3.9 29.3 1.0 CA C:HIS39 3.9 28.0 1.0 O C:PRO38 4.0 27.8 1.0 NE2 C:HIS39 4.1 29.1 1.0 NE2 C:HIS92 4.1 28.5 1.0 CD2 C:HIS92 4.2 28.5 1.0 CD2 C:HIS39 4.2 28.8 1.0 N C:HIS92 4.4 28.6 1.0 CB C:MET97 4.5 28.8 1.0 CA C:HIS92 4.5 28.9 1.0 N C:HIS39 4.7 28.1 1.0 C C:PRO38 4.7 28.1 1.0 CA C:CYS89 4.8 27.3 1.0 CB C:PRO91 4.9 27.7 1.0 CD2 C:LEU14 5.0 26.0 1.0

Copper binding site 3 out of 3 in the Plastocyanin Variant with N-Terminal Methionine - Open Structure


Mono view


Stereo pair view

A full contact list of Copper with other atoms in the Cu binding site number 3 of Plastocyanin Variant with N-Terminal Methionine - Open Structure within 5.0Å range: probe atom residue distance (Å) B Occ C:Cu106 b:23.8 occ:1.00 ND1 B:HIS39 2.1 26.3 1.0 ND1 B:HIS92 2.1 27.5 1.0 SG B:CYS89 2.3 27.1 1.0 SD B:MET97 2.3 27.1 1.0 CE1 B:HIS92 3.0 27.7 1.0 CE1 B:HIS39 3.0 25.5 1.0 CG B:HIS39 3.1 25.9 1.0 CG B:HIS92 3.1 27.3 1.0 CE B:MET97 3.3 25.9 1.0 CB B:CYS89 3.3 26.4 1.0 CB B:HIS39 3.4 26.0 1.0 CB B:HIS92 3.5 27.8 1.0 CA B:HIS39 3.8 26.4 1.0 CG B:MET97 3.9 27.0 1.0 O B:PRO38 3.9 26.0 1.0 NE2 B:HIS92 4.1 26.9 1.0 NE2 B:HIS39 4.2 24.7 1.0 CD2 B:HIS39 4.2 25.0 1.0 CD2 B:HIS92 4.2 26.3 1.0 N B:HIS92 4.4 28.2 1.0 CB B:MET97 4.4 26.4 1.0 CA B:HIS92 4.6 28.2 1.0 N B:HIS39 4.7 26.3 1.0 C B:PRO38 4.7 26.2 1.0 CA B:CYS89 4.7 26.7 1.0 CD B:PRO91 4.9 27.9 1.0

P.B.Crowley, P.M.Matias, A.R.Khan, M.Roessle, D.I.Svergun. Metal-Mediated Self-Assembly of A Beta-Sandwich Protein. Chemistry V. 15 12672 2009.
ISSN: ISSN 0947-6539
PubMed: 19834935
DOI: 10.1002/CHEM.200901410