Nickel in PDB 8zvg: Crystal Structure of Aetd in Complex with L-Tyrosine

The structure of Crystal Structure of Aetd in Complex with L-Tyrosine, PDB code: 8zvg was solved by H.Li, L.Dai, H.B.Zheng, C.-C.Chen, R.-T.Guo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	36.02 / 1.89
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	64.932, 64.932, 115.958, 90, 90, 90
R / Rfree (%)	20.2 / 25.7

The structure of Crystal Structure of Aetd in Complex with L-Tyrosine also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Nickel atom in the Crystal Structure of Aetd in Complex with L-Tyrosine (pdb code 8zvg). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total 5 binding sites of Nickel where determined in the Crystal Structure of Aetd in Complex with L-Tyrosine, PDB code: 8zvg:
Jump to Nickel binding site number: 1; 2; 3; 4; 5;

Nickel binding site 1 out of 5 in the Crystal Structure of Aetd in Complex with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Crystal Structure of Aetd in Complex with L-Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:36.8 occ:1.00 O A:HOH428 2.0 29.9 1.0 ND1 A:HIS72 2.1 35.2 1.0 O A:HOH401 2.1 30.1 1.0 O A:HOH471 2.1 28.8 1.0 O A:HOH517 2.3 41.6 1.0 O A:HOH520 2.3 39.1 1.0 CE1 A:HIS72 2.8 35.5 1.0 CG A:HIS72 3.2 37.9 1.0 OE2 A:GLU75 3.4 74.5 1.0 CB A:HIS72 3.7 33.6 1.0 O A:GLU176 3.8 37.6 1.0 O A:HOH530 3.8 46.3 1.0 OD1 A:ASP76 3.9 37.0 1.0 NE2 A:HIS72 4.1 33.4 1.0 OD2 A:ASP76 4.1 31.8 1.0 CA A:HIS72 4.2 37.1 1.0 CD2 A:HIS72 4.2 40.8 1.0 CG A:ASP76 4.4 37.5 1.0 O A:HIS72 4.4 34.4 1.0 CD A:GLU75 4.5 52.7 1.0 O A:HOH548 4.7 43.5 1.0 C A:HIS72 4.8 36.1 1.0 O A:HOH557 4.9 43.4 1.0 OE1 A:GLU75 4.9 43.1 1.0 C A:GLU176 4.9 38.2 1.0 O A:VAL175 4.9 40.4 1.0 CA A:GLY178 4.9 48.1 1.0

Nickel binding site 2 out of 5 in the Crystal Structure of Aetd in Complex with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 2 of Crystal Structure of Aetd in Complex with L-Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:49.9 occ:1.00 NE2 B:HIS125 2.1 39.2 1.0 O B:HOH508 2.1 38.0 1.0 NE2 A:HIS125 2.2 46.0 1.0 O B:HOH500 2.3 49.4 1.0 O B:HOH415 2.5 51.7 1.0 O A:HOH538 2.5 52.8 1.0 CD2 B:HIS125 3.0 38.2 1.0 CD2 A:HIS125 3.1 44.0 1.0 CE1 B:HIS125 3.1 40.0 1.0 CE1 A:HIS125 3.3 45.3 1.0 OD2 A:ASP126 3.8 61.1 1.0 OD2 B:ASP126 3.9 47.8 1.0 CG B:HIS125 4.2 34.2 1.0 ND1 B:HIS125 4.2 37.0 1.0 CG A:HIS125 4.3 43.4 1.0 ND1 A:HIS125 4.3 44.3 1.0 CB B:ASP126 4.4 43.8 1.0 CG B:ASP126 4.5 43.8 1.0 CG A:ASP126 4.5 54.5 1.0 O A:VAL122 4.7 39.4 1.0 O A:HOH413 4.9 54.2 1.0 OD1 A:ASP126 5.0 54.5 1.0

Nickel binding site 3 out of 5 in the Crystal Structure of Aetd in Complex with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 3 of Crystal Structure of Aetd in Complex with L-Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:62.2 occ:1.00 O A:HOH402 1.8 27.4 1.0 O A:HOH544 1.9 40.5 1.0 NE2 A:HIS228 2.6 40.0 1.0 O A:HOH553 2.9 52.7 1.0 O A:HOH543 3.0 49.0 1.0 CE1 A:HIS228 3.5 39.3 1.0 CD2 A:HIS228 3.6 42.0 1.0 O A:HOH409 4.4 54.1 1.0 ND1 A:HIS228 4.6 44.9 1.0 CG A:HIS228 4.7 45.0 1.0 CE2 A:TYR224 4.8 33.6 1.0 OH A:TYR224 4.9 35.8 1.0 O A:HOH563 4.9 64.8 1.0

Nickel binding site 4 out of 5 in the Crystal Structure of Aetd in Complex with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 4 of Crystal Structure of Aetd in Complex with L-Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni303 b:73.1 occ:1.00 O B:HOH520 2.0 42.8 1.0 O B:HOH456 2.3 49.0 1.0 ND1 B:HIS72 2.4 66.8 1.0 O B:HOH473 2.5 50.6 1.0 O B:HOH482 2.9 47.0 1.0 CE1 B:HIS72 3.2 60.5 1.0 CG B:HIS72 3.5 59.7 1.0 CB B:HIS72 3.9 50.0 1.0 OD2 B:ASP76 4.2 50.5 1.0 OD1 B:ASP76 4.2 51.6 1.0 O B:GLU176 4.3 72.4 1.0 NE2 B:HIS72 4.4 56.2 1.0 CA B:HIS72 4.4 48.2 1.0 O B:HOH526 4.5 48.2 1.0 CD2 B:HIS72 4.5 57.8 1.0 CG B:ASP76 4.6 54.2 1.0 CD1 B:ILE186 4.6 74.3 1.0 O B:HIS72 4.8 44.6 1.0

Nickel binding site 5 out of 5 in the Crystal Structure of Aetd in Complex with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 5 of Crystal Structure of Aetd in Complex with L-Tyrosine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni304 b:52.8 occ:1.00 O B:HOH472 2.0 47.9 1.0 NE2 B:HIS228 2.2 32.3 1.0 O B:HOH487 2.3 40.2 1.0 O B:HOH544 2.5 49.4 1.0 O B:HOH532 3.0 50.9 1.0 CD2 B:HIS228 3.1 33.5 1.0 CE1 B:HIS228 3.2 37.0 1.0 O B:HOH527 3.9 48.5 1.0 O B:HOH502 4.0 47.2 1.0 ND1 B:HIS228 4.3 33.1 1.0 CG B:HIS228 4.3 33.5 1.0 CE2 B:TYR224 4.3 28.9 1.0 OH B:TYR224 4.6 30.0 1.0 O B:HOH521 4.8 42.5 1.0 CZ B:TYR224 4.8 31.9 1.0

C.C.Chen, H.Li, J.W.Huang, R.T.Guo. Structural and Molecular Insights of Two Unique Enzymes Involved in the Biosynthesis of A Natural Halogenated Nitrile. Febs J. 2024.
ISSN: ISSN 1742-464X
PubMed: 39308083
DOI: 10.1111/FEBS.17279