Zinc in PDB 3hni: Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1

The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1, PDB code: 3hni was solved by E.N.Salgado, R.A.Lewis, J.Brodin, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.74 / 2.35
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	57.208, 87.935, 152.174, 90.00, 90.00, 90.00
R / Rfree (%)	22.6 / 27.8

The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Zinc atom in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 (pdb code 3hni). 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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1, PDB code: 3hni:
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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:24.1 occ:1.00 NE2 A:HIS73 2.0 26.7 1.0 NE2 D:HIS63 2.0 23.9 1.0 NE2 A:HIS77 2.0 24.2 1.0 OD2 C:ASP74 2.0 22.8 1.0 CD2 A:HIS77 2.8 24.7 1.0 CE1 A:HIS73 2.9 26.6 1.0 CD2 D:HIS63 2.9 24.8 1.0 CE1 D:HIS63 3.0 25.9 1.0 CD2 A:HIS73 3.0 27.9 1.0 CG C:ASP74 3.0 24.5 1.0 CE1 A:HIS77 3.1 24.6 1.0 OD1 C:ASP74 3.4 24.2 1.0 ND1 A:HIS73 4.0 29.0 1.0 CG A:HIS77 4.0 24.7 1.0 CG D:HIS63 4.1 25.8 1.0 ND1 D:HIS63 4.1 26.1 1.0 ND1 A:HIS77 4.1 23.5 1.0 CG A:HIS73 4.1 26.8 1.0 CB C:ASP74 4.3 24.3 1.0 CD1 D:ILE67 4.5 27.1 1.0 CA C:ASP74 4.9 25.3 1.0 O C:ASP74 4.9 25.1 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:15.6 occ:1.00 NE2 C:HIS63 2.0 22.1 1.0 OD1 D:ASP74 2.0 24.4 1.0 NE2 B:HIS77 2.0 16.2 1.0 NE2 B:HIS73 2.2 30.6 1.0 OD2 D:ASP74 2.5 25.8 1.0 CG D:ASP74 2.6 25.7 1.0 CE1 C:HIS63 3.0 22.2 1.0 CD2 B:HIS77 3.0 18.9 1.0 CE1 B:HIS73 3.0 30.7 1.0 CD2 C:HIS63 3.0 23.2 1.0 CE1 B:HIS77 3.1 17.7 1.0 CD2 B:HIS73 3.3 28.7 1.0 ND1 C:HIS63 4.1 23.1 1.0 CB D:ASP74 4.1 24.7 1.0 CG C:HIS63 4.1 24.4 1.0 ND1 B:HIS77 4.2 17.8 1.0 CG B:HIS77 4.2 21.2 1.0 ND1 B:HIS73 4.2 28.6 1.0 CG B:HIS73 4.4 27.8 1.0 CD1 C:ILE67 4.7 24.3 1.0 O D:ASP74 4.8 24.9 1.0 CA D:ASP74 4.8 25.3 1.0 CD2 D:LEU78 4.9 24.3 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn107 b:24.9 occ:1.00 NE2 B:HIS63 1.9 23.9 1.0 NE2 C:HIS77 2.0 22.7 1.0 NE2 C:HIS73 2.0 30.6 1.0 OD2 A:ASP74 2.1 25.6 1.0 OD1 A:ASP74 2.6 24.8 1.0 CE1 C:HIS73 2.6 30.0 1.0 CG A:ASP74 2.7 25.4 1.0 CE1 B:HIS63 2.9 24.7 1.0 CE1 C:HIS77 2.9 22.9 1.0 CD2 B:HIS63 3.0 25.1 1.0 CD2 C:HIS77 3.1 24.5 1.0 CD2 C:HIS73 3.3 29.9 1.0 ND1 C:HIS73 3.9 30.8 1.0 CD1 B:TRP66 4.0 29.1 0.5 ND1 B:HIS63 4.0 25.1 1.0 NE1 B:TRP66 4.1 29.5 0.5 CG B:HIS63 4.1 25.3 1.0 ND1 C:HIS77 4.1 23.9 1.0 CB A:ASP74 4.1 25.2 1.0 CG C:HIS77 4.2 24.7 1.0 CG C:HIS73 4.2 28.2 1.0 O A:ASP74 4.6 24.9 1.0 CA A:ASP74 4.8 25.4 1.0 CD1 B:ILE67 4.8 22.3 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn107 b:16.1 occ:1.00 OD2 B:ASP74 1.9 30.8 1.0 NE2 D:HIS77 2.0 22.1 1.0 NE2 D:HIS73 2.1 21.7 1.0 NE2 A:HIS63 2.2 18.2 1.0 CG B:ASP74 2.7 29.1 1.0 CD2 D:HIS77 2.8 23.1 1.0 OD1 B:ASP74 2.9 34.1 1.0 CE1 D:HIS73 2.9 22.4 1.0 CE1 D:HIS77 3.1 22.1 1.0 CD2 A:HIS63 3.1 20.8 1.0 CD2 D:HIS73 3.2 24.7 1.0 CE1 A:HIS63 3.3 19.8 1.0 CG D:HIS77 4.0 24.6 1.0 ND1 D:HIS77 4.1 24.6 1.0 ND1 D:HIS73 4.1 22.9 1.0 CB B:ASP74 4.2 26.4 1.0 CG D:HIS73 4.2 24.4 1.0 CG A:HIS63 4.3 23.6 1.0 ND1 A:HIS63 4.3 21.1 1.0 CD1 A:ILE67 4.6 26.7 1.0 O B:HOH117 4.7 20.4 1.0 O B:ASP74 4.8 25.1 1.0 CA B:ASP74 4.8 25.5 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn107 b:25.0 occ:1.00 NE2 F:HIS63 2.0 21.7 1.0 OD2 G:ASP74 2.0 25.4 1.0 NE2 E:HIS77 2.0 24.5 1.0 CE1 E:HIS73 2.2 26.9 1.0 CE1 F:HIS63 2.8 21.8 1.0 CG G:ASP74 2.8 25.3 1.0 NE2 E:HIS73 2.9 28.0 1.0 CD2 E:HIS77 3.0 24.8 1.0 OD1 G:ASP74 3.0 26.6 1.0 CE1 E:HIS77 3.0 24.3 1.0 CD2 F:HIS63 3.1 22.1 1.0 ND1 E:HIS73 3.3 28.4 1.0 ND1 F:HIS63 3.9 22.6 1.0 CG F:HIS63 4.1 23.4 1.0 ND1 E:HIS77 4.1 25.4 1.0 CD2 E:HIS73 4.1 27.8 1.0 CG E:HIS77 4.1 24.4 1.0 CB G:ASP74 4.2 25.2 1.0 CG E:HIS73 4.4 27.2 1.0 CD1 F:ILE67 4.4 24.1 1.0 O E:HOH117 4.5 27.9 1.0 CA G:ASP74 4.8 25.5 1.0 O G:ASP74 4.9 25.0 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range: probe atom residue distance (Å) B Occ F:Zn107 b:17.0 occ:1.00 OD2 H:ASP74 2.0 31.1 1.0 NE2 E:HIS63 2.0 18.9 1.0 CE1 F:HIS73 2.1 26.9 1.0 NE2 F:HIS77 2.1 20.8 1.0 NE2 F:HIS73 2.7 28.4 1.0 CG H:ASP74 2.7 28.6 1.0 OD1 H:ASP74 2.8 30.5 1.0 CE1 E:HIS63 2.9 17.9 1.0 CD2 F:HIS77 3.0 22.9 1.0 CE1 F:HIS77 3.1 22.5 1.0 CD2 E:HIS63 3.1 21.4 1.0 ND1 F:HIS73 3.3 28.1 1.0 CD2 F:HIS73 4.0 27.7 1.0 ND1 E:HIS63 4.0 21.8 1.0 CG E:HIS63 4.1 22.9 1.0 ND1 F:HIS77 4.2 22.5 1.0 CG F:HIS77 4.2 23.7 1.0 CB H:ASP74 4.2 26.1 1.0 CG F:HIS73 4.3 26.2 1.0 O F:HOH130 4.6 26.7 1.0 CA H:ASP74 4.8 25.4 1.0 O H:ASP74 4.8 25.0 1.0 CD2 H:LEU78 5.0 25.6 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn107 b:21.0 occ:1.00 OD2 E:ASP74 2.0 27.4 1.0 NE2 H:HIS63 2.0 22.1 1.0 NE2 G:HIS77 2.1 22.3 1.0 NE2 G:HIS73 2.1 26.1 1.0 CG E:ASP74 2.9 27.1 1.0 CE1 H:HIS63 2.9 21.7 1.0 CE1 G:HIS73 2.9 26.8 1.0 CD2 G:HIS77 3.0 22.8 1.0 CD2 H:HIS63 3.0 23.2 1.0 OD1 E:ASP74 3.1 27.4 1.0 CE1 G:HIS77 3.2 21.9 1.0 CD2 G:HIS73 3.2 26.5 1.0 ND1 H:HIS63 4.1 22.9 1.0 ND1 G:HIS73 4.1 28.5 1.0 CG H:HIS63 4.1 24.6 1.0 CG G:HIS77 4.2 24.1 1.0 ND1 G:HIS77 4.2 22.9 1.0 CG G:HIS73 4.3 27.2 1.0 CB E:ASP74 4.3 25.6 1.0 CD1 H:ILE67 4.8 24.2 1.0 CA E:ASP74 4.8 25.4 1.0 O E:ASP74 4.9 25.3 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1


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 the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-1 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn107 b:17.1 occ:1.00 OD1 F:ASP74 1.8 26.6 1.0 NE2 H:HIS77 2.0 16.8 1.0 NE2 H:HIS73 2.0 24.7 1.0 NE2 G:HIS63 2.1 20.1 1.0 CG F:ASP74 2.6 25.3 1.0 OD2 F:ASP74 2.8 25.2 1.0 CE1 H:HIS77 2.9 18.2 1.0 CE1 H:HIS73 2.9 27.5 1.0 CE1 G:HIS63 2.9 20.9 1.0 CD2 H:HIS77 3.1 18.3 1.0 CD2 H:HIS73 3.1 25.8 1.0 CD2 G:HIS63 3.1 21.3 1.0 O F:HOH130 3.8 26.7 1.0 ND1 H:HIS77 4.0 18.7 1.0 ND1 H:HIS73 4.0 26.5 1.0 CB F:ASP74 4.1 24.4 1.0 ND1 G:HIS63 4.1 21.0 1.0 CG H:HIS77 4.1 22.6 1.0 CG H:HIS73 4.2 26.5 1.0 CG G:HIS63 4.2 23.6 1.0 CD1 G:ILE67 4.5 22.3 1.0 CA F:ASP74 4.7 25.2 1.0 O G:HOH110 4.8 21.0 1.0 O F:ASP74 4.8 25.2 1.0

E.N.Salgado, X.I.Ambroggio, J.D.Brodin, R.A.Lewis, B.Kuhlman, F.A.Tezcan. Metal Templated Design of Protein Interfaces. Proc.Natl.Acad.Sci.Usa V. 107 1827 2010.
ISSN: ISSN 0027-8424
PubMed: 20080561
DOI: 10.1073/PNAS.0906852107