Zinc in PDB 2w8c: Plastocyanin Variant with N-Terminal Methionine - Closed Structure

The structure of Plastocyanin Variant with N-Terminal Methionine - Closed Structure, PDB code: 2w8c 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)	65.94 / 1.80
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	55.740, 55.740, 197.850, 90.00, 90.00, 120.00
R / Rfree (%)	17.3 / 22.4

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

Copper

(Cu)

2 atoms

The binding sites of Zinc atom in the Plastocyanin Variant with N-Terminal Methionine - Closed Structure (pdb code 2w8c). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Plastocyanin Variant with N-Terminal Methionine - Closed Structure, PDB code: 2w8c:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Plastocyanin Variant with N-Terminal Methionine - Closed Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Plastocyanin Variant with N-Terminal Methionine - Closed Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:19.2 occ:1.00 O A:HOH2070 2.0 17.3 1.0 O A:HOH2071 2.0 12.7 1.0 OD1 A:ASP44 2.0 15.7 1.0 OD1 A:ASP45 2.0 15.6 1.0 CG A:ASP44 2.8 18.0 1.0 OD2 A:ASP44 2.9 18.5 1.0 CG A:ASP45 3.1 12.8 1.0 OD2 A:ASP45 3.5 17.2 1.0 O A:HOH2023 3.9 24.1 1.0 N A:ASP45 4.1 15.6 1.0 CB A:ASP44 4.2 16.1 1.0 CB A:ASP45 4.4 17.6 1.0 CA A:ASP44 4.8 16.6 1.0 N A:LYS46 4.8 20.8 1.0 CA A:ASP45 4.8 17.7 1.0 C A:ASP44 4.8 17.1 1.0 O A:HOH2056 5.0 31.6 1.0

Zinc binding site 2 out of 4 in the Plastocyanin Variant with N-Terminal Methionine - Closed Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Plastocyanin Variant with N-Terminal Methionine - Closed Structure within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn108 b:39.2 occ:1.00 OE2 A:GLU1 2.0 33.5 1.0 OD2 A:ASP27 2.1 23.1 1.0 ND1 A:HIS24 2.2 30.9 1.0 CG A:ASP27 2.8 21.1 1.0 OD1 A:ASP27 2.9 18.4 1.0 CD A:GLU1 2.9 31.7 1.0 CE1 A:HIS24 3.0 30.0 1.0 CG A:GLU1 3.2 30.1 1.0 CG A:HIS24 3.2 29.5 1.0 CB A:HIS24 3.7 26.4 1.0 CB A:GLU1 4.1 26.1 1.0 N A:HIS24 4.1 24.0 1.0 OE1 A:GLU1 4.1 33.1 1.0 NE2 A:HIS24 4.2 30.9 1.0 CB A:ASP27 4.3 17.6 1.0 CD2 A:HIS24 4.3 29.6 1.0 N A:GLU1 4.4 27.5 1.0 CZ A:PHE3 4.5 23.3 1.0 CA A:HIS24 4.5 25.4 1.0 CE2 A:PHE3 4.5 24.4 1.0 O A:HIS24 4.9 22.9 1.0 CA A:GLU1 4.9 25.9 1.0 O A:HOH2002 4.9 36.7 1.0

Zinc binding site 3 out of 4 in the Plastocyanin Variant with N-Terminal Methionine - Closed Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Plastocyanin Variant with N-Terminal Methionine - Closed Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:16.9 occ:1.00 OD1 B:ASP44 2.0 9.4 1.0 O B:HOH2087 2.0 10.2 1.0 O B:HOH2088 2.0 14.2 1.0 OD1 B:ASP45 2.0 11.1 1.0 CG B:ASP44 2.8 18.0 1.0 OD2 B:ASP44 2.9 12.1 1.0 CG B:ASP45 3.1 6.0 1.0 OD2 B:ASP45 3.5 10.4 1.0 O B:HOH2036 4.0 19.9 1.0 N B:ASP45 4.1 9.8 1.0 O B:HOH2034 4.1 38.7 1.0 CB B:ASP44 4.2 12.1 1.0 CB B:ASP45 4.4 16.4 1.0 CA B:ASP44 4.8 14.6 1.0 CA B:ASP45 4.8 18.2 1.0 N B:LYS46 4.8 16.4 1.0 C B:ASP44 4.9 16.1 1.0

Zinc binding site 4 out of 4 in the Plastocyanin Variant with N-Terminal Methionine - Closed Structure


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Plastocyanin Variant with N-Terminal Methionine - Closed Structure within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn108 b:23.3 occ:1.00 OD2 A:ASP79 1.9 18.8 1.0 NE2 B:HIS24 2.1 16.0 1.0 O B:HOH2089 2.2 21.7 1.0 CD2 B:HIS24 3.0 16.1 1.0 CG A:ASP79 3.0 23.2 1.0 CE1 B:HIS24 3.2 23.4 1.0 OD1 A:ASP79 3.5 23.1 1.0 CB B:GLU104 3.9 11.6 1.0 CG B:HIS24 4.2 16.9 1.0 O A:HOH2047 4.2 10.3 1.0 ND1 B:HIS24 4.2 12.1 1.0 CG B:GLU104 4.3 23.6 1.0 CB A:ASP79 4.3 21.8 1.0 O B:GLY105 4.4 17.7 1.0 O A:HOH2032 4.5 28.7 1.0 NZ A:LYS58 4.5 39.7 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