Zinc in PDB 3hnj: Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2

The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2, PDB code: 3hnj 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)	30.70 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	48.448, 65.316, 70.773, 90.00, 104.70, 90.00
R / Rfree (%)	22.4 / 27.2

The structure of Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2 also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Zn-Induced Tetramer of the Engineered Cyt CB562 Variant Ridc-2 (pdb code 3hnj). 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-2, PDB code: 3hnj:
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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn107 b:19.2 occ:1.00 OD2 C:ASP74 2.0 18.4 1.0 NE2 A:HIS73 2.0 18.8 1.0 NE2 A:HIS77 2.0 15.8 1.0 NE2 D:HIS63 2.3 20.1 1.0 CG C:ASP74 2.7 19.2 1.0 CE1 A:HIS73 2.7 19.8 1.0 OD1 C:ASP74 2.8 22.4 1.0 CE1 A:HIS77 3.0 19.1 1.0 CD2 A:HIS77 3.0 17.2 1.0 CD2 D:HIS63 3.0 20.2 1.0 CD2 A:HIS73 3.2 19.6 1.0 CE1 D:HIS63 3.3 20.3 1.0 ND1 A:HIS73 3.9 20.4 1.0 ND1 A:HIS77 4.1 16.5 1.0 CB C:ASP74 4.2 19.4 1.0 CG A:HIS77 4.2 19.4 1.0 CG A:HIS73 4.2 19.3 1.0 CG D:HIS63 4.2 21.0 1.0 ND1 D:HIS63 4.3 21.6 1.0 O A:HOH116 4.7 26.1 1.0 CA C:ASP74 4.7 19.2 1.0 O C:ASP74 4.9 19.2 1.0 O A:HOH147 4.9 19.0 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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn107 b:14.1 occ:1.00 NE2 C:HIS63 2.0 19.8 1.0 OD2 D:ASP74 2.0 16.1 1.0 NE2 B:HIS77 2.1 17.6 1.0 NE2 B:HIS73 2.1 16.4 1.0 CE1 B:HIS77 2.9 16.4 1.0 CG D:ASP74 2.9 18.9 1.0 CD2 C:HIS63 3.0 17.4 1.0 CE1 C:HIS63 3.0 19.7 1.0 CE1 B:HIS73 3.1 19.0 1.0 CD2 B:HIS73 3.1 18.4 1.0 CD2 B:HIS77 3.2 18.8 1.0 OD1 D:ASP74 3.2 17.8 1.0 ND1 C:HIS63 4.1 18.1 1.0 ND1 B:HIS77 4.1 18.1 1.0 O D:HOH133 4.1 14.4 1.0 CG C:HIS63 4.1 18.3 1.0 ND1 B:HIS73 4.2 20.2 1.0 CG B:HIS77 4.2 19.1 1.0 CG B:HIS73 4.3 18.5 1.0 CD2 C:LEU67 4.3 16.7 1.0 CB D:ASP74 4.3 18.6 1.0 O B:HOH121 4.8 15.9 1.0 CA D:ASP74 4.9 19.0 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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn108 b:19.0 occ:1.00 O B:HOH119 1.8 15.9 1.0 O B:HOH143 2.1 9.0 1.0 OD1 B:ASP5 2.1 18.6 1.0 O B:HOH117 2.2 17.0 1.0 O B:HOH118 2.4 28.5 1.0 O B:HOH120 2.6 26.7 1.0 CG B:ASP5 3.0 21.3 1.0 OD2 B:ASP5 3.3 21.3 1.0 O B:HOH207 3.5 27.1 1.0 OD1 B:ASP2 4.1 23.0 1.0 OE1 B:GLU8 4.2 21.1 1.0 CB B:ASP5 4.3 22.1 1.0 OD2 B:ASP2 4.4 24.0 1.0 O B:HOH144 4.6 22.1 1.0 CA B:ASP5 4.6 22.6 1.0 N B:ASP5 4.7 23.0 1.0 CG B:ASP2 4.7 24.1 1.0 CD B:GLU8 4.9 22.8 1.0 OE2 B:GLU8 4.9 22.6 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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn109 b:40.0 occ:1.00 O2A B:HEM150 2.3 25.0 1.0 O B:HOH155 2.4 18.8 1.0 O1A B:HEM150 2.8 24.4 1.0 CGA B:HEM150 2.9 25.3 1.0 O2D B:HEM150 4.0 21.3 1.0 O1D B:HEM150 4.1 24.8 1.0 CGD B:HEM150 4.2 24.5 1.0 OE2 B:GLU4 4.3 24.3 1.0 CBA B:HEM150 4.3 24.6 1.0 O B:HOH157 4.4 34.9 1.0 CG B:GLU4 4.6 23.7 1.0 CD B:GLU4 4.6 24.2 1.0 CAA B:HEM150 4.9 24.1 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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn107 b:14.8 occ:1.00 OD2 A:ASP74 1.8 16.6 1.0 NE2 B:HIS63 2.0 24.3 1.0 NE2 C:HIS73 2.0 19.7 1.0 NE2 C:HIS77 2.0 12.1 1.0 CG A:ASP74 2.8 19.3 1.0 CE1 C:HIS73 2.8 22.1 1.0 CE1 B:HIS63 3.0 23.6 1.0 CD2 B:HIS63 3.0 22.9 1.0 CE1 C:HIS77 3.0 13.1 1.0 CD2 C:HIS77 3.1 11.9 1.0 OD1 A:ASP74 3.1 23.4 1.0 CD2 C:HIS73 3.1 19.7 1.0 ND1 C:HIS73 4.0 20.2 1.0 O A:HOH147 4.0 19.0 1.0 ND1 B:HIS63 4.1 23.1 1.0 CG B:HIS63 4.1 22.2 1.0 ND1 C:HIS77 4.1 13.8 1.0 CB A:ASP74 4.2 19.0 1.0 CG C:HIS73 4.2 20.0 1.0 CG C:HIS77 4.2 17.3 1.0 CD2 B:LEU67 4.6 19.0 1.0 CA A:ASP74 4.7 19.1 1.0 O A:ASP74 4.8 19.2 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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn107 b:14.6 occ:1.00 OD2 B:ASP74 1.9 17.0 1.0 NE2 A:HIS63 2.0 18.3 1.0 NE2 D:HIS73 2.0 15.2 1.0 NE2 D:HIS77 2.1 12.0 1.0 CG B:ASP74 2.8 18.6 1.0 CE1 D:HIS73 2.8 15.1 1.0 CD2 A:HIS63 3.0 17.2 1.0 CE1 A:HIS63 3.0 20.4 1.0 OD1 B:ASP74 3.0 16.9 1.0 CE1 D:HIS77 3.0 13.1 1.0 CD2 D:HIS77 3.1 12.4 1.0 CD2 D:HIS73 3.2 14.4 1.0 ND1 D:HIS73 4.0 15.0 1.0 ND1 A:HIS63 4.1 17.7 1.0 CG A:HIS63 4.1 18.7 1.0 ND1 D:HIS77 4.2 13.6 1.0 O B:HOH121 4.2 15.9 1.0 CG D:HIS73 4.2 17.6 1.0 CB B:ASP74 4.2 18.7 1.0 CG D:HIS77 4.2 16.9 1.0 CD2 A:LEU67 4.4 16.3 1.0 CA B:ASP74 4.8 18.9 1.0 O D:HOH133 4.9 14.4 1.0 O D:HOH124 5.0 30.2 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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn108 b:28.1 occ:1.00 OD1 D:ASP5 2.0 22.9 1.0 O D:HOH115 2.1 15.8 1.0 O D:HOH161 2.2 18.5 1.0 O D:HOH117 2.4 32.4 1.0 O D:HOH116 2.4 33.1 1.0 O D:HOH118 2.4 28.0 1.0 CG D:ASP5 2.9 22.0 1.0 OD2 D:ASP5 3.2 20.3 1.0 OD1 D:ASP2 4.0 22.3 1.0 OD2 D:ASP2 4.0 21.1 1.0 CB D:ASP5 4.3 22.6 1.0 OE2 D:GLU8 4.4 23.2 1.0 CG D:ASP2 4.4 23.1 1.0 N D:ASP5 4.5 23.0 1.0 CA D:ASP5 4.5 22.7 1.0 O D:HOH162 4.7 27.7 1.0 OE1 D:GLU8 4.8 23.4 1.0 CB D:GLU4 4.9 23.6 1.0 CD D:GLU8 4.9 23.5 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-2


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-2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn109 b:45.5 occ:1.00 O D:HOH165 2.3 32.9 1.0 O2A D:HEM150 2.3 27.8 1.0 O D:HOH120 2.4 25.3 1.0 O D:HOH121 2.6 25.4 1.0 CGA D:HEM150 3.1 28.6 1.0 O1A D:HEM150 3.1 28.6 1.0 O1D D:HEM150 3.7 23.5 1.0 OE2 D:GLU4 4.0 24.1 1.0 CGD D:HEM150 4.2 24.0 1.0 O2D D:HEM150 4.4 23.1 1.0 O D:HOH167 4.5 30.9 1.0 CBA D:HEM150 4.5 28.7 1.0 CD D:GLU4 4.5 23.8 1.0 O D:HOH119 4.6 23.4 1.0 CG D:GLU4 4.6 23.7 1.0 O D:HOH204 4.6 25.6 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