Zinc in PDB 4u9d: Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3, PDB code: 4u9d was solved by F.A.Tezcan, W.J.Song, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.48 / 2.50
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	54.830, 54.830, 237.820, 90.00, 90.00, 120.00
R / Rfree (%)	23.8 / 29.6

The structure of Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 also contains other interesting chemical elements:

Iron

(Fe)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3 (pdb code 4u9d). 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 CB562 Variant, AB3, PDB code: 4u9d:
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 CB562 Variant, AB3


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, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:56.1 occ:1.00 OE1 A:GLU86 2.0 49.0 1.0 ND1 A:HIS89 2.2 52.7 1.0 NE2 C:HIS100 2.4 56.6 1.0 NZ C:LYS104 2.6 76.6 1.0 CD A:GLU86 2.8 49.5 1.0 OE2 A:GLU86 2.9 49.7 1.0 CE C:LYS104 3.1 77.0 1.0 CE1 A:HIS89 3.1 52.5 1.0 CG A:HIS89 3.1 51.7 1.0 CE1 C:HIS100 3.3 57.2 1.0 CD2 C:HIS100 3.3 56.6 1.0 CB A:HIS89 3.4 50.8 1.0 CG A:GLU86 4.2 49.1 1.0 NE2 A:HIS89 4.2 52.8 1.0 CD2 A:HIS89 4.2 52.5 1.0 CA A:GLU86 4.3 48.2 1.0 ND1 C:HIS100 4.4 57.5 1.0 CG C:HIS100 4.4 56.6 1.0 CD C:LYS104 4.5 77.2 1.0 CB A:GLU86 4.6 49.0 1.0 CA A:HIS89 5.0 50.3 1.0

Zinc binding site 2 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:53.5 occ:1.00 OD1 B:ASP74 2.0 49.4 1.0 NE2 A:HIS73 2.0 49.0 1.0 NE2 A:HIS77 2.3 42.3 1.0 NE2 D:HIS63 2.3 71.4 1.0 CE1 A:HIS73 2.7 48.6 1.0 CG B:ASP74 2.7 48.2 1.0 OD2 B:ASP74 2.8 47.6 1.0 CD2 D:HIS63 2.9 71.8 1.0 CD2 A:HIS77 3.2 42.5 1.0 CD2 A:HIS73 3.2 48.5 1.0 CE1 D:HIS63 3.3 71.2 1.0 CE1 A:HIS77 3.3 42.1 1.0 ND1 A:HIS73 3.9 48.8 1.0 CG D:HIS63 4.1 72.6 1.0 CG A:HIS73 4.2 47.6 1.0 CB B:ASP74 4.2 47.2 1.0 ND1 D:HIS63 4.2 71.7 1.0 O B:HOH307 4.3 50.8 1.0 CG A:HIS77 4.4 42.1 1.0 ND1 A:HIS77 4.4 41.4 1.0 CD1 D:ILE67 4.6 72.1 1.0 O B:ASP74 4.8 47.6 1.0 CA B:ASP74 4.9 47.2 1.0

Zinc binding site 3 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:45.2 occ:1.00 OD1 A:ASP74 2.0 46.2 1.0 NE2 B:HIS77 2.1 45.6 1.0 NE2 C:HIS63 2.2 44.5 1.0 NE2 B:HIS73 2.2 47.0 1.0 CG A:ASP74 2.7 44.9 1.0 OD2 A:ASP74 2.7 45.4 1.0 CE1 B:HIS73 3.0 47.1 1.0 CE1 B:HIS77 3.0 45.7 1.0 CE1 C:HIS63 3.1 45.0 1.0 CD2 C:HIS63 3.2 44.5 1.0 CD2 B:HIS77 3.2 45.9 1.0 CD2 B:HIS73 3.3 47.0 1.0 ND1 B:HIS73 4.1 47.1 1.0 CB A:ASP74 4.1 45.0 1.0 ND1 B:HIS77 4.2 44.9 1.0 ND1 C:HIS63 4.2 44.6 1.0 CG C:HIS63 4.2 45.1 1.0 CG B:HIS77 4.3 45.7 1.0 O B:HOH307 4.3 50.8 1.0 CG B:HIS73 4.3 47.1 1.0 O A:ASP74 4.6 44.6 1.0 CD1 C:ILE67 4.6 46.7 1.0 CA A:ASP74 4.7 45.1 1.0 C A:ASP74 5.0 45.2 1.0

Zinc binding site 4 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn205 b:70.5 occ:1.00 ND1 C:HIS89 1.7 57.5 1.0 OE2 C:GLU86 2.3 61.9 1.0 NE2 A:HIS100 2.4 58.2 1.0 CE1 C:HIS89 2.4 58.5 1.0 OE1 C:GLU86 2.6 61.1 1.0 CD C:GLU86 2.8 61.1 1.0 NZ A:LYS104 2.9 66.9 1.0 CD2 A:HIS100 2.9 58.0 1.0 CG C:HIS89 2.9 58.0 1.0 CE A:LYS104 3.1 66.6 1.0 CE1 A:HIS100 3.5 57.7 1.0 NE2 C:HIS89 3.6 58.6 1.0 CB C:HIS89 3.6 58.3 1.0 CD2 C:HIS89 3.9 58.6 1.0 OD2 A:ASP60 4.0 57.2 1.0 CD A:LYS104 4.1 66.9 1.0 CG A:HIS100 4.2 57.9 1.0 CG C:GLU86 4.3 60.5 1.0 OD1 A:ASP60 4.4 60.0 1.0 ND1 A:HIS100 4.4 58.4 1.0 CG A:ASP60 4.6 58.1 1.0 CA C:GLU86 4.6 58.6 1.0 O A:HOH301 4.9 40.5 1.0 CB C:GLU86 4.9 59.5 1.0 O A:HIS100 5.0 57.6 1.0

Zinc binding site 5 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn206 b:51.7 occ:1.00 OD1 C:ASP74 2.0 49.0 1.0 NE2 D:HIS73 2.1 66.6 1.0 NE2 D:HIS77 2.1 58.3 1.0 NE2 A:HIS63 2.4 51.3 1.0 CE1 D:HIS73 2.5 67.2 1.0 OD2 C:ASP74 2.6 47.2 1.0 CG C:ASP74 2.6 47.1 1.0 CE1 D:HIS77 3.0 57.5 1.0 CD2 A:HIS63 3.2 50.7 1.0 CD2 D:HIS77 3.2 58.2 1.0 CD2 D:HIS73 3.3 66.5 1.0 CE1 A:HIS63 3.5 51.4 1.0 ND1 D:HIS73 3.7 67.8 1.0 CG D:HIS73 4.1 67.2 1.0 CB C:ASP74 4.1 46.8 1.0 ND1 D:HIS77 4.2 57.3 1.0 O C:HOH312 4.2 44.5 1.0 CG D:HIS77 4.3 58.0 1.0 O C:HOH308 4.3 47.5 1.0 CG A:HIS63 4.4 51.4 1.0 ND1 A:HIS63 4.5 51.9 1.0 CD1 A:ILE67 4.6 48.2 1.0 CA C:ASP74 4.8 46.6 1.0 O C:ASP74 4.9 47.3 1.0

Zinc binding site 6 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn202 b:0.0 occ:1.00 OE2 B:GLU86 1.8 81.8 1.0 NE2 D:HIS100 2.3 98.6 1.0 CE1 D:HIS100 2.5 98.7 1.0 CD B:GLU86 2.5 81.0 1.0 ND1 B:HIS89 2.6 74.3 1.0 OE1 B:GLU86 2.7 81.3 1.0 NZ D:LYS104 2.8 94.3 1.0 CE1 B:HIS89 3.4 74.3 1.0 CD2 D:HIS100 3.5 99.1 1.0 CG B:HIS89 3.7 73.4 1.0 ND1 D:HIS100 3.7 0.0 1.0 CG B:GLU86 3.9 79.7 1.0 CE D:LYS104 4.0 95.2 1.0 CB B:HIS89 4.0 71.8 1.0 CG D:HIS100 4.2 0.0 1.0 NE2 B:HIS89 4.6 74.3 1.0 CD2 B:HIS89 4.7 74.0 1.0 CB B:GLU86 4.8 78.1 1.0 CA B:GLU86 4.8 76.1 1.0

Zinc binding site 7 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn203 b:47.7 occ:1.00 OD1 D:ASP74 1.9 61.5 1.0 NE2 C:HIS77 2.1 47.1 1.0 NE2 C:HIS73 2.2 45.1 1.0 NE2 B:HIS63 2.3 56.7 1.0 CG D:ASP74 2.5 62.0 1.0 OD2 D:ASP74 2.6 60.0 1.0 CE1 C:HIS73 2.7 44.6 1.0 CE1 C:HIS77 3.0 46.9 1.0 CD2 B:HIS63 3.1 56.3 1.0 CD2 C:HIS77 3.2 46.6 1.0 CE1 B:HIS63 3.3 56.3 1.0 CD2 C:HIS73 3.5 44.6 1.0 ND1 C:HIS73 4.0 44.6 1.0 CB D:ASP74 4.0 63.0 1.0 ND1 C:HIS77 4.2 46.3 1.0 CG B:HIS63 4.2 56.0 1.0 ND1 B:HIS63 4.3 57.1 1.0 CG C:HIS77 4.3 46.8 1.0 CG C:HIS73 4.3 44.3 1.0 O C:HOH312 4.4 44.5 1.0 CA D:ASP74 4.7 63.8 1.0 O D:ASP74 4.7 62.7 1.0 CD1 B:ILE67 4.7 50.4 1.0

Zinc binding site 8 out of 8 in the Crystal Structure of the Zn-Directed Tetramer of the Engineered Cyt CB562 Variant, AB3


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, AB3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn204 b:0.0 occ:1.00 ND1 D:HIS89 1.5 91.8 1.0 OE2 D:GLU86 1.5 81.8 1.0 CE1 D:HIS89 2.1 91.4 1.0 NZ B:LYS104 2.2 70.6 1.0 NE2 B:HIS100 2.5 71.2 1.0 CD D:GLU86 2.7 82.8 1.0 CG D:HIS89 2.8 90.5 1.0 CE1 B:HIS100 3.1 71.6 1.0 NE2 D:HIS89 3.3 91.6 1.0 CE B:LYS104 3.4 71.3 1.0 CG D:GLU86 3.6 82.9 1.0 CB D:HIS89 3.6 88.5 1.0 CD2 D:HIS89 3.6 91.3 1.0 OE1 D:GLU86 3.7 83.2 1.0 CD2 B:HIS100 3.7 70.4 1.0 CD B:LYS104 3.8 70.7 1.0 ND1 B:HIS100 4.3 71.1 1.0 CA D:GLU86 4.5 83.4 1.0 OD2 B:ASP60 4.6 67.9 1.0 CB D:GLU86 4.6 82.8 1.0 CG B:HIS100 4.6 69.9 1.0 OD1 B:ASP60 4.8 67.0 1.0

W.J.Song, F.A.Tezcan. A Designed Supramolecular Protein Assembly with in Vivo Enzymatic Activity. Science V. 346 1525 2014.
ISSN: ESSN 1095-9203
PubMed: 25525249
DOI: 10.1126/SCIENCE.1259680