Zinc in PDB 3iq6: Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces

The structure of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces, PDB code: 3iq6 was solved by J.N.Brodin, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	63.265, 76.770, 177.566, 90.00, 90.00, 90.00
R / Rfree (%)	22.8 / 29.6

The structure of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces (pdb code 3iq6). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces, PDB code: 3iq6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn201 b:30.4 occ:1.00 NE2 A:HIS77 2.0 28.0 1.0 NE2 B:HIS63 2.0 29.9 1.0 NE2 A:HIS73 2.0 36.1 1.0 OD1 C:ASP74 2.2 24.1 1.0 OD2 C:ASP74 2.6 35.0 1.0 CG C:ASP74 2.7 31.1 1.0 CE1 A:HIS73 2.8 42.8 1.0 CE1 B:HIS63 3.0 27.5 1.0 CE1 A:HIS77 3.0 28.4 1.0 CD2 A:HIS77 3.0 26.9 1.0 CD2 B:HIS63 3.0 32.3 1.0 CD2 A:HIS73 3.2 38.5 1.0 ND1 A:HIS73 4.0 43.8 1.0 ND1 B:HIS63 4.1 29.5 1.0 ND1 A:HIS77 4.1 34.7 1.0 CG B:HIS63 4.1 32.5 1.0 CG A:HIS77 4.1 31.8 1.0 CG A:HIS73 4.2 38.8 1.0 CB C:ASP74 4.2 25.2 1.0 CD1 B:ILE67 4.8 26.2 1.0 O C:ASP74 4.8 26.9 1.0 CA C:ASP74 4.9 26.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn201 b:33.4 occ:1.00 NE2 B:HIS77 1.9 37.5 1.0 NE2 B:HIS73 2.0 30.0 1.0 NE2 A:HIS63 2.0 39.1 1.0 OD1 D:ASP74 2.1 41.7 1.0 OD2 D:ASP74 2.6 39.3 1.0 CG D:ASP74 2.6 39.7 1.0 CE1 B:HIS73 2.7 29.1 1.0 CE1 B:HIS77 2.8 39.6 1.0 CD2 A:HIS63 3.0 37.5 1.0 CE1 A:HIS63 3.0 35.0 1.0 CD2 B:HIS77 3.0 32.0 1.0 CD2 B:HIS73 3.2 32.4 1.0 ND1 B:HIS73 3.9 28.5 1.0 ND1 B:HIS77 4.0 38.6 1.0 CB D:ASP74 4.1 38.1 1.0 CG B:HIS77 4.1 38.0 1.0 ND1 A:HIS63 4.1 40.4 1.0 CG A:HIS63 4.1 37.4 1.0 CG B:HIS73 4.2 30.4 1.0 CD1 A:ILE67 4.4 39.8 1.0 CA D:ASP74 4.7 38.1 1.0 O D:ASP74 5.0 40.0 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn201 b:33.4 occ:1.00 NE2 D:HIS63 2.0 33.6 1.0 NE2 C:HIS73 2.0 30.7 1.0 NE2 C:HIS77 2.1 25.7 1.0 OD1 A:ASP74 2.3 44.2 1.0 OD2 A:ASP74 2.3 39.6 1.0 CG A:ASP74 2.6 43.0 1.0 CD2 D:HIS63 2.9 35.4 1.0 CE1 C:HIS73 2.9 28.2 1.0 CD2 C:HIS77 3.0 27.4 1.0 CE1 D:HIS63 3.1 23.8 1.0 CD2 C:HIS73 3.1 26.1 1.0 CE1 C:HIS77 3.2 28.3 1.0 CG D:HIS63 4.1 35.2 1.0 ND1 C:HIS73 4.1 26.5 1.0 ND1 D:HIS63 4.1 37.3 1.0 CB A:ASP74 4.1 38.5 1.0 CG C:HIS77 4.2 27.6 1.0 CG C:HIS73 4.2 25.1 1.0 ND1 C:HIS77 4.2 27.7 1.0 O A:ASP74 4.7 40.5 1.0 CA A:ASP74 4.8 38.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn201 b:34.4 occ:1.00 NE2 D:HIS73 2.0 33.4 1.0 OD1 B:ASP74 2.0 26.2 1.0 NE2 C:HIS63 2.0 27.4 1.0 NE2 D:HIS77 2.1 34.2 1.0 CE1 D:HIS73 2.8 32.4 1.0 CD2 C:HIS63 2.9 31.3 1.0 CE1 D:HIS77 2.9 26.8 1.0 CG B:ASP74 3.0 34.1 1.0 CE1 C:HIS63 3.0 26.8 1.0 CD2 D:HIS73 3.1 31.8 1.0 CD2 D:HIS77 3.2 29.6 1.0 OD2 B:ASP74 3.3 35.5 1.0 O B:HOH110 3.6 31.9 1.0 ND1 D:HIS73 3.9 34.7 1.0 CG C:HIS63 4.1 33.5 1.0 ND1 C:HIS63 4.1 31.6 1.0 ND1 D:HIS77 4.1 33.2 1.0 CG D:HIS73 4.1 29.4 1.0 CG D:HIS77 4.3 33.4 1.0 CB B:ASP74 4.3 30.4 1.0 CA B:ASP74 4.9 32.7 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn201 b:32.5 occ:1.00 NE2 E:HIS73 2.0 32.4 1.0 NE2 H:HIS63 2.1 35.4 1.0 OD2 G:ASP74 2.1 43.5 1.0 NE2 E:HIS77 2.1 33.7 1.0 OD1 G:ASP74 2.3 37.4 1.0 CG G:ASP74 2.5 42.4 1.0 CE1 E:HIS73 2.8 31.5 1.0 CE1 H:HIS63 3.0 32.2 1.0 CD2 E:HIS77 3.0 39.2 1.0 CD2 H:HIS63 3.1 36.5 1.0 CD2 E:HIS73 3.2 32.6 1.0 CE1 E:HIS77 3.2 36.6 1.0 ND1 E:HIS73 4.0 25.7 1.0 CB G:ASP74 4.1 34.9 1.0 ND1 H:HIS63 4.1 36.4 1.0 CG E:HIS73 4.2 30.0 1.0 CG H:HIS63 4.2 37.2 1.0 CG E:HIS77 4.2 35.1 1.0 ND1 E:HIS77 4.3 31.2 1.0 CD1 H:ILE67 4.6 31.5 1.0 O G:ASP74 4.7 36.5 1.0 CA G:ASP74 4.8 36.4 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn201 b:37.8 occ:1.00 NE2 F:HIS77 2.0 35.1 1.0 NE2 G:HIS63 2.1 37.4 1.0 NE2 F:HIS73 2.1 41.1 1.0 OD1 H:ASP74 2.3 42.9 1.0 OD2 H:ASP74 2.7 40.8 1.0 CG H:ASP74 2.8 40.7 1.0 CE1 F:HIS73 2.8 42.5 1.0 CE1 F:HIS77 2.9 34.5 1.0 CE1 G:HIS63 3.0 40.3 1.0 CD2 F:HIS77 3.0 37.1 1.0 CD2 G:HIS63 3.1 40.5 1.0 CD2 F:HIS73 3.3 42.6 1.0 ND1 F:HIS73 4.1 41.2 1.0 ND1 F:HIS77 4.1 36.5 1.0 ND1 G:HIS63 4.1 40.6 1.0 CG F:HIS77 4.2 36.0 1.0 CG G:HIS63 4.2 37.5 1.0 CB H:ASP74 4.3 37.7 1.0 CG F:HIS73 4.3 39.9 1.0 CD1 G:ILE67 4.8 34.7 1.0 CA H:ASP74 4.9 36.4 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn201 b:35.2 occ:1.00 NE2 G:HIS73 1.9 32.6 1.0 NE2 F:HIS63 2.0 36.0 1.0 NE2 G:HIS77 2.1 29.5 1.0 OD1 E:ASP74 2.2 31.3 1.0 CE1 G:HIS73 2.7 37.4 1.0 CG E:ASP74 2.8 30.4 1.0 OD2 E:ASP74 2.8 32.3 1.0 CE1 F:HIS63 2.9 36.2 1.0 CE1 G:HIS77 3.0 24.3 1.0 CD2 F:HIS63 3.1 36.8 1.0 CD2 G:HIS77 3.1 27.0 1.0 CD2 G:HIS73 3.1 34.3 1.0 ND1 G:HIS73 3.9 36.2 1.0 ND1 F:HIS63 4.0 35.0 1.0 CG G:HIS73 4.1 32.8 1.0 ND1 G:HIS77 4.1 28.2 1.0 CG F:HIS63 4.2 35.4 1.0 CG G:HIS77 4.2 29.5 1.0 CB E:ASP74 4.3 27.9 1.0 O E:ASP74 4.8 31.4 1.0 CA E:ASP74 4.9 31.9 1.0 CD1 F:TRP66 5.0 68.1 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of A Tetrameric Zn-Bound Cytochrome CB562 Complex with Covalently and Non-Covalently Stabilized Interfaces within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn201 b:38.2 occ:1.00 NE2 H:HIS77 2.0 39.1 1.0 NE2 H:HIS73 2.0 37.5 1.0 OD1 F:ASP74 2.1 37.5 1.0 NE2 E:HIS63 2.1 25.6 1.0 CE1 H:HIS77 2.8 35.6 1.0 CE1 H:HIS73 2.8 39.1 1.0 CG F:ASP74 2.8 32.6 1.0 OD2 F:ASP74 2.9 39.3 1.0 CD2 E:HIS63 3.0 34.3 1.0 CD2 H:HIS77 3.1 33.2 1.0 CD2 H:HIS73 3.2 39.2 1.0 CE1 E:HIS63 3.2 33.0 1.0 ND1 H:HIS77 4.0 38.9 1.0 ND1 H:HIS73 4.0 36.1 1.0 CD1 E:ILE67 4.1 35.9 1.0 CG H:HIS77 4.1 33.6 1.0 CG E:HIS63 4.2 34.7 1.0 CG H:HIS73 4.2 39.3 1.0 ND1 E:HIS63 4.3 29.8 1.0 CB F:ASP74 4.3 30.8 1.0 CA F:ASP74 4.9 33.2 1.0

J.D.Brodin, A.Medina-Morales, T.Ni, E.N.Salgado, X.I.Ambroggio, F.A.Tezcan. Evolution of Metal Selectivity in Templated Protein Interfaces. J.Am.Chem.Soc. V. 132 8610 2010.
ISSN: ISSN 0002-7863
PubMed: 20515031
DOI: 10.1021/JA910844N