Zinc in PDB 5xzj: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5, PDB code: 5xzj was solved by W.J.Song, F.A.Tezcan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	63.89 / 1.98
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.747, 63.481, 127.785, 90.00, 90.00, 90.00
R / Rfree (%)	17.7 / 21.7

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 also contains other interesting chemical elements:

Iron	(Fe)	4 atoms
Chlorine	(Cl)	1 atom

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 (pdb code 5xzj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5, PDB code: 5xzj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/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 CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:25.2 occ:1.00 OD1 C:ASP74 2.1 25.2 1.0 NE2 A:HIS73 2.1 24.6 1.0 NE2 A:HIS77 2.1 26.3 1.0 NE2 B:HIS63 2.1 20.4 1.0 CG C:ASP74 2.9 25.1 1.0 CD2 B:HIS63 3.0 22.4 1.0 CE1 A:HIS73 3.0 28.1 1.0 CE1 A:HIS77 3.0 28.4 1.0 OD2 C:ASP74 3.1 25.8 1.0 CD2 A:HIS73 3.2 25.4 1.0 CD2 A:HIS77 3.2 26.2 1.0 CE1 B:HIS63 3.2 22.7 1.0 ND1 A:HIS73 4.2 26.3 1.0 ND1 A:HIS77 4.2 25.6 1.0 CG B:HIS63 4.2 22.6 1.0 O C:HOH339 4.3 30.1 1.0 CG A:HIS73 4.3 26.2 1.0 ND1 B:HIS63 4.3 23.0 1.0 CG A:HIS77 4.3 26.3 1.0 CB C:ASP74 4.4 25.0 1.0 CD1 B:ILE67 4.6 25.6 1.0 O A:HOH350 4.7 41.6 1.0 O A:HOH341 4.9 36.8 1.0 CA C:ASP74 4.9 24.9 1.0

Zinc binding site 2 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/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 CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:43.9 occ:1.00 ND1 D:HIS100 2.0 37.0 1.0 OE2 A:GLU89 2.2 42.8 1.0 CL A:CL206 2.2 48.2 1.0 NE2 A:HIS93 2.2 45.5 1.0 CD A:GLU89 2.9 45.3 1.0 CG D:HIS100 3.0 37.0 1.0 OE1 A:GLU89 3.0 43.5 1.0 CD2 A:HIS93 3.0 42.4 1.0 CE1 D:HIS100 3.0 34.8 1.0 CB D:HIS100 3.3 36.8 1.0 CE1 A:HIS93 3.3 49.6 1.0 NE2 D:HIS100 4.1 34.9 1.0 CD2 D:HIS100 4.1 36.8 1.0 CA D:HIS100 4.2 39.5 1.0 CG A:HIS93 4.2 45.0 1.0 ND1 A:HIS93 4.4 48.4 1.0 CG A:GLU89 4.4 39.9 1.0 O A:HOH365 4.4 39.9 1.0

Zinc binding site 3 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/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 CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:26.4 occ:1.00 OD2 A:ASP12 1.9 25.6 1.0 OE1 A:GLU8 2.0 28.7 1.0 CD A:GLU8 2.7 33.0 1.0 CG A:ASP12 2.8 28.8 1.0 OE2 A:GLU8 2.9 32.0 1.0 OD1 A:ASP12 3.0 26.8 1.0 O A:HOH317 3.9 46.4 1.0 CG A:GLU8 4.2 33.5 1.0 CB A:ASP12 4.2 28.8 1.0 O A:HOH339 4.3 45.0 1.0 O A:GLU8 4.7 32.8 1.0 O A:HOH332 4.8 44.0 1.0

Zinc binding site 4 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/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 CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:98.9 occ:1.00 O A:HOH384 2.4 36.3 1.0 O A:HOH382 2.9 53.7 1.0 CD2 D:HIS93 3.7 37.8 1.0 O A:HOH378 3.8 34.3 1.0 NE2 D:HIS93 4.0 38.2 1.0 CG D:HIS93 4.0 38.0 1.0 CG A:HIS100 4.1 33.5 1.0 ND1 A:HIS100 4.3 34.7 1.0 CB A:HIS100 4.3 32.5 1.0 ND1 D:HIS93 4.4 41.4 1.0 CD2 A:HIS100 4.4 34.0 1.0 CE1 D:HIS93 4.4 40.2 1.0 CB D:HIS93 4.5 38.6 1.0 CE1 A:HIS100 4.6 36.8 1.0 O D:HOH347 4.6 46.9 1.0 NE2 A:HIS100 4.7 35.3 1.0 ZN D:ZN203 4.8 36.2 1.0

Zinc binding site 5 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/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 CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:23.0 occ:1.00 OD1 D:ASP74 1.9 25.3 1.0 NE2 A:HIS63 2.1 25.2 1.0 NE2 B:HIS77 2.1 22.6 1.0 NE2 B:HIS73 2.1 25.2 1.0 CG D:ASP74 2.8 28.6 1.0 CD2 A:HIS63 3.0 27.1 1.0 OD2 D:ASP74 3.1 26.6 1.0 CE1 B:HIS73 3.1 26.7 1.0 CD2 B:HIS77 3.1 21.3 1.0 CE1 B:HIS77 3.1 23.0 1.0 CE1 A:HIS63 3.1 26.4 1.0 CD2 B:HIS73 3.2 24.8 1.0 O D:HOH305 4.0 41.8 1.0 CG A:HIS63 4.2 26.3 1.0 ND1 A:HIS63 4.2 25.2 1.0 ND1 B:HIS73 4.2 28.5 1.0 ND1 B:HIS77 4.2 22.1 1.0 CG B:HIS77 4.2 22.0 1.0 CB D:ASP74 4.3 26.7 1.0 CG B:HIS73 4.3 25.1 1.0 CD1 A:ILE67 4.6 26.3 1.0 O B:HOH346 4.8 40.0 1.0 CA D:ASP74 4.9 26.4 1.0 O B:HOH327 4.9 29.0 1.0

Zinc binding site 6 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/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 CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:48.7 occ:1.00 ND1 C:HIS100 2.1 40.9 1.0 NE2 B:HIS93 2.1 56.1 1.0 O B:HOH358 2.1 27.4 1.0 OE1 B:GLU89 2.4 47.3 1.0 OE2 B:GLU89 2.7 50.7 1.0 CD B:GLU89 2.9 49.6 1.0 CE1 B:HIS93 3.0 58.8 1.0 CE1 C:HIS100 3.0 41.4 1.0 CG C:HIS100 3.0 40.0 1.0 CD2 B:HIS93 3.2 54.5 1.0 CB C:HIS100 3.4 35.8 1.0 NE2 C:HIS100 4.1 45.4 1.0 ND1 B:HIS93 4.1 59.4 1.0 CD2 C:HIS100 4.1 44.3 1.0 CA C:HIS100 4.2 33.1 1.0 O B:HOH353 4.2 18.2 1.0 CG B:HIS93 4.3 52.6 1.0 O C:HOH347 4.3 45.5 1.0 CG B:GLU89 4.4 45.4 1.0

Zinc binding site 7 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/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 CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:62.3 occ:1.00 O B:HOH354 2.2 27.2 1.0 O D:HOH315 2.4 29.5 1.0 OE2 B:GLU81 2.7 37.9 1.0 O D:HOH345 2.8 37.9 1.0 OE1 B:GLU81 3.1 45.2 1.0 NZ B:LYS83 3.1 56.0 1.0 CD B:GLU81 3.2 42.6 1.0 O C:HOH370 3.3 47.2 1.0 CE B:LYS83 4.0 50.5 1.0 ND2 D:ASN80 4.0 36.9 1.0 ND1 D:HIS77 4.0 22.2 1.0 CE1 D:HIS77 4.0 22.8 1.0 O D:HOH333 4.3 39.7 1.0 CG D:ASN80 4.5 35.2 1.0 CD B:LYS83 4.6 46.8 1.0 CG B:GLU81 4.6 41.9 1.0 CB D:ASN80 4.6 33.5 1.0

Zinc binding site 8 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/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 CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn205 b:0.0 occ:1.00 O B:HOH376 2.0 31.7 1.0 O C:HOH371 2.3 49.2 1.0 O B:HOH355 3.2 48.5 1.0 O B:HOH373 3.4 28.1 1.0 CG B:HIS100 4.3 25.3 1.0 CD2 C:HIS93 4.3 26.4 1.0 CB B:HIS100 4.5 25.4 1.0 ND1 B:HIS100 4.6 24.4 1.0 OG1 B:THR97 4.6 24.3 1.0 NE2 C:HIS93 4.6 27.1 1.0 CD2 B:HIS100 4.6 25.6 1.0 CG C:HIS93 4.7 26.6 1.0 CG2 B:ILE67 4.8 22.9 1.0 CA B:THR97 4.8 24.3 1.0 O B:HOH345 4.9 28.7 1.0 CE1 B:HIS100 5.0 26.5 1.0

Zinc binding site 9 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn202 b:26.6 occ:1.00 NE2 D:HIS63 2.0 30.6 1.0 NE2 C:HIS73 2.1 31.0 1.0 OD1 A:ASP74 2.1 26.9 1.0 NE2 C:HIS77 2.1 24.3 1.0 CE1 C:HIS73 2.9 35.5 1.0 CG A:ASP74 2.9 28.9 1.0 CD2 D:HIS63 3.0 31.1 1.0 CE1 D:HIS63 3.0 31.1 1.0 CE1 C:HIS77 3.1 26.9 1.0 OD2 A:ASP74 3.1 28.2 1.0 CD2 C:HIS77 3.1 25.9 1.0 CD2 C:HIS73 3.2 32.0 1.0 ND1 C:HIS73 4.1 35.2 1.0 ND1 D:HIS63 4.1 29.8 1.0 CG D:HIS63 4.2 32.2 1.0 ND1 C:HIS77 4.2 25.0 1.0 CG C:HIS73 4.3 30.9 1.0 CG C:HIS77 4.3 26.3 1.0 CB A:ASP74 4.3 26.9 1.0 O A:HOH341 4.3 36.8 1.0 O C:HOH352 4.9 38.4 1.0 CD1 D:ILE67 4.9 34.8 1.0 O C:HOH339 4.9 30.1 1.0 CA A:ASP74 4.9 25.6 1.0 O A:ASP74 5.0 25.5 1.0

Zinc binding site 10 out of 14 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, C96T/AB5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn203 b:25.5 occ:1.00 OE2 C:GLU89 1.9 28.4 1.0 ND1 B:HIS100 2.1 24.4 1.0 NE2 C:HIS93 2.2 27.1 1.0 CD C:GLU89 2.8 31.3 1.0 CE1 B:HIS100 3.1 26.5 1.0 OE1 C:GLU89 3.1 30.1 1.0 CE1 C:HIS93 3.1 28.2 1.0 CG B:HIS100 3.2 25.3 1.0 CD2 C:HIS93 3.2 26.4 1.0 CB B:HIS100 3.5 25.4 1.0 CA B:HIS100 4.2 25.4 1.0 NE2 B:HIS100 4.2 23.9 1.0 CG C:GLU89 4.2 32.4 1.0 ND1 C:HIS93 4.3 26.5 1.0 CD2 B:HIS100 4.3 25.6 1.0 CG C:HIS93 4.3 26.6 1.0

W.J.Song, J.Yu, F.A.Tezcan. Importance of Scaffold Flexibility/Rigidity in the Design and Directed Evolution of Artificial Metallo-Beta-Lactamases. J. Am. Chem. Soc. V. 139 16772 2017.
ISSN: ESSN 1520-5126
PubMed: 28992705
DOI: 10.1021/JACS.7B08981