Zinc in PDB 7dcl: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5, PDB code: 7dcl was solved by W.J.Song, J.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.53 / 2.45
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	53.408, 53.408, 251.61, 90, 90, 120
R / Rfree (%)	19.7 / 25.6

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Iron	(Fe)	2 atoms

The binding sites of Zinc atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 (pdb code 7dcl). 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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5, PDB code: 7dcl:
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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:24.3 occ:1.00 OD1 A:ASP74 1.9 24.6 1.0 CG A:ASP74 2.8 24.0 1.0 OD2 A:ASP74 3.1 22.6 1.0 O A:HOH318 4.0 31.6 1.0 CB A:ASP74 4.2 25.0 1.0 CA A:ASP74 4.7 25.2 1.0 O A:ASP74 4.9 24.2 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:38.6 occ:1.00 NE2 A:HIS93 2.2 45.7 1.0 CL A:CL207 2.3 52.0 1.0 O A:HOH338 2.6 29.6 1.0 CD2 A:HIS93 3.0 44.4 1.0 CE1 A:HIS93 3.3 43.7 1.0 OE2 A:GLU89 3.5 65.0 1.0 CG A:GLU89 4.2 60.2 1.0 CG A:HIS93 4.2 45.9 1.0 CD A:GLU89 4.2 64.2 1.0 ND1 A:HIS93 4.3 46.0 1.0 O A:GLU89 4.8 40.4 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:36.8 occ:1.00 ND1 A:HIS100 2.1 43.0 1.0 CE1 A:HIS100 3.0 43.7 1.0 CG A:HIS100 3.1 40.0 1.0 CB A:HIS100 3.4 35.8 1.0 NE2 A:HIS100 4.2 44.7 1.0 CD2 A:HIS100 4.2 42.8 1.0 CD1 A:ILE67 4.5 33.7 1.0 CA A:THR97 4.8 28.4 1.0 O A:ILE96 4.9 30.8 1.0 CG2 A:ILE96 4.9 37.3 1.0 CA A:HIS100 4.9 33.1 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:83.4 occ:1.00 NE2 A:HIS59 2.4 57.7 1.0 CD2 A:HIS59 2.9 57.9 1.0 ND2 B:ASN80 3.2 56.4 1.0 CE1 A:HIS59 3.6 55.6 1.0 CE1 B:HIS77 3.7 23.1 1.0 ND1 B:HIS77 3.8 23.0 1.0 O B:HOH342 3.8 54.8 1.0 CG A:HIS59 4.2 54.1 1.0 CG B:ASN80 4.3 51.5 1.0 ND1 A:HIS59 4.5 56.3 1.0 CD2 A:HIS63 4.8 23.6 1.0 NE2 B:HIS77 4.8 23.4 1.0 CB B:ASN80 4.9 50.4 1.0 CG B:HIS77 5.0 23.4 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:107.4 occ:1.00 OD2 A:ASP39 2.0 46.5 1.0 CG A:ASP39 2.7 44.3 1.0 OD1 A:ASP39 2.8 49.3 1.0 CA A:ALA1 2.9 46.8 1.0 O A:ALA1 2.9 44.9 1.0 O A:HOH333 3.2 50.0 1.0 C A:ALA1 3.3 41.8 1.0 N A:ALA1 3.4 48.3 1.0 CB A:ALA1 4.1 51.3 1.0 CB A:ASP39 4.2 42.6 1.0 N A:ASP2 4.7 38.0 1.0 ND2 A:ASN6 4.8 32.4 1.0 OD1 A:ASN6 4.9 31.1 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:25.6 occ:1.00 NE2 A:HIS63 2.0 21.4 1.0 NE2 B:HIS77 2.0 23.4 1.0 NE2 B:HIS73 2.0 26.0 1.0 CD2 A:HIS63 2.9 23.6 1.0 CD2 B:HIS77 2.9 23.2 1.0 CE1 A:HIS63 3.0 22.5 1.0 CE1 B:HIS73 3.0 26.2 1.0 CD2 B:HIS73 3.0 26.1 1.0 CE1 B:HIS77 3.1 23.1 1.0 CG A:HIS63 4.1 23.3 1.0 ND1 A:HIS63 4.1 22.4 1.0 CG B:HIS77 4.1 23.4 1.0 ND1 B:HIS73 4.1 26.8 1.0 ND1 B:HIS77 4.1 23.0 1.0 CG B:HIS73 4.2 25.3 1.0 O B:HOH342 4.7 54.8 1.0 O B:HOH326 4.8 46.0 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:31.1 occ:0.50 OD2 B:ASP12 2.0 28.2 1.0 OE2 B:GLU8 2.1 28.5 1.0 CG B:ASP12 2.7 30.3 1.0 OD1 B:ASP12 2.7 30.9 1.0 CD B:GLU8 2.9 30.9 1.0 CG B:GLU8 3.1 30.5 1.0 OE1 B:GLU8 4.1 31.3 1.0 CB B:ASP12 4.1 30.7 1.0 O B:GLU8 4.4 29.5 1.0 O B:HOH340 4.5 33.1 1.0 CB B:GLU8 4.5 30.2 1.0 C B:GLU8 5.0 28.3 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5


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-Directed Tetramer of the Engineered Cyt Cb 562 Variant, C96I/A38S AB5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:96.9 occ:1.00 NE2 B:HIS59 2.3 78.0 1.0 CE1 B:HIS59 3.1 78.3 1.0 O B:HOH348 3.2 48.9 1.0 CD2 B:HIS59 3.3 72.1 1.0 ND2 A:ASN80 3.4 51.2 1.0 CE1 A:HIS77 3.5 26.1 1.0 O A:HOH335 3.6 40.1 1.0 ND1 A:HIS77 3.6 27.2 1.0 ND1 B:HIS59 4.1 77.4 1.0 CG B:HIS59 4.2 67.3 1.0 CD2 B:HIS63 4.5 25.4 1.0 NE2 A:HIS77 4.5 25.3 1.0 CG A:ASN80 4.5 45.8 1.0 CG A:HIS77 4.8 27.5 1.0 CG B:HIS63 4.9 25.3 1.0

J.Yu, J.Yang, C.Seok, W.J.Song. Symmetry-Related Residues As Promising Hotspots For the Evolution of De Novo Oligomeric Enzymes Chem Sci 2021.
ISSN: ESSN 2041-6539
DOI: 10.1039/D0SC06823C