Nickel in PDB 8zvh: Crystal Structure of Aetd in Complex with L-Phenylalanine

The structure of Crystal Structure of Aetd in Complex with L-Phenylalanine, PDB code: 8zvh 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)	32.54 / 1.87
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	65.043, 65.043, 116.211, 90, 90, 90
R / Rfree (%)	19.2 / 25

The structure of Crystal Structure of Aetd in Complex with L-Phenylalanine 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-Phenylalanine (pdb code 8zvh). 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-Phenylalanine, PDB code: 8zvh:
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-Phenylalanine


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-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni303 b:31.1 occ:1.00 O A:HOH441 2.0 28.1 1.0 O A:HOH525 2.1 24.9 1.0 ND1 A:HIS72 2.1 28.1 1.0 O A:HOH509 2.2 23.3 1.0 O A:HOH547 2.3 33.8 1.0 O A:HOH560 2.6 34.3 1.0 CE1 A:HIS72 2.9 27.1 1.0 CG A:HIS72 3.2 28.4 1.0 CB A:HIS72 3.7 26.0 1.0 O A:GLU176 3.9 32.7 1.0 OD1 A:ASP76 3.9 30.6 1.0 OD2 A:ASP76 3.9 26.9 1.0 O A:HOH527 4.1 31.9 1.0 NE2 A:HIS72 4.1 25.5 1.0 CA A:HIS72 4.2 29.2 1.0 CD2 A:HIS72 4.3 30.5 1.0 CG A:ASP76 4.3 28.0 1.0 O A:HOH590 4.4 40.8 1.0 O A:HIS72 4.5 27.4 1.0 O A:HOH436 4.8 32.1 1.0 C A:HIS72 4.8 27.7 1.0 CD1 A:ILE186 4.8 33.9 1.0 CA A:GLY178 4.8 39.1 1.0 C A:GLU176 4.9 34.4 1.0 O A:HOH607 5.0 31.9 1.0

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


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-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni304 b:48.7 occ:1.00 NE2 A:HIS228 2.1 33.7 1.0 O A:HOH566 2.1 28.1 1.0 O A:HOH554 2.5 46.5 1.0 O A:HOH576 2.5 39.8 1.0 CD2 A:HIS228 2.8 34.0 1.0 CE1 A:HIS228 3.2 32.3 1.0 O A:HOH600 3.5 48.2 1.0 O A:HOH401 3.7 35.8 1.0 CG A:HIS228 4.1 36.7 1.0 ND1 A:HIS228 4.2 34.7 1.0 OH A:TYR224 4.5 32.3 1.0 OE2 A:GLU231 4.6 61.8 1.0 CZ A:TYR224 4.9 27.8 1.0 CE2 A:TYR224 4.9 27.5 1.0

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


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-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni305 b:44.4 occ:1.00 O B:HOH509 2.1 41.9 1.0 NE2 B:HIS125 2.1 34.2 1.0 NE2 A:HIS125 2.1 35.6 1.0 O B:HOH523 2.3 40.1 1.0 O A:HOH453 2.3 37.8 1.0 O B:HOH440 2.3 43.6 1.0 CE1 B:HIS125 3.0 35.5 1.0 CD2 A:HIS125 3.1 34.8 1.0 CD2 B:HIS125 3.2 34.1 1.0 CE1 A:HIS125 3.2 38.2 1.0 OD2 B:ASP126 4.1 42.6 1.0 ND1 B:HIS125 4.2 33.4 1.0 CG A:HIS125 4.2 36.4 1.0 ND1 A:HIS125 4.2 33.6 1.0 CG B:HIS125 4.3 33.5 1.0 O B:HOH516 4.3 53.0 1.0 OD2 A:ASP126 4.3 48.6 1.0 CB B:ASP126 4.4 35.9 1.0 O B:HOH568 4.4 45.2 1.0 O A:HOH494 4.5 45.4 1.0 CG B:ASP126 4.6 39.8 1.0 O A:VAL122 4.7 34.9 1.0 CG A:ASP126 4.7 43.5 1.0 O A:HOH508 4.7 49.0 1.0 OD1 A:ASP126 4.8 46.2 1.0

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


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-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni303 b:70.2 occ:1.00 O B:HOH517 2.3 46.6 1.0 O B:HOH513 2.4 52.8 1.0 ND1 B:HIS72 2.4 64.0 1.0 O B:HOH450 2.5 51.6 1.0 O B:HOH528 2.6 43.5 1.0 CE1 B:HIS72 3.2 61.1 1.0 CG B:HIS72 3.5 57.5 1.0 O B:HOH531 3.5 49.4 1.0 CB B:HIS72 3.8 50.0 1.0 O B:GLU176 4.2 75.1 1.0 OD1 B:ASP76 4.3 50.1 1.0 NE2 B:HIS72 4.4 56.6 1.0 CA B:HIS72 4.4 44.4 1.0 CD2 B:HIS72 4.5 58.6 1.0 O B:HIS72 4.7 37.8 1.0 OD2 B:ASP76 4.7 50.1 1.0 CG B:ASP76 4.9 48.2 1.0

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


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-Phenylalanine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ni304 b:46.5 occ:1.00 O B:HOH456 2.0 45.1 1.0 NE2 B:HIS228 2.1 28.0 1.0 O B:HOH503 2.3 38.9 1.0 O B:HOH560 2.5 43.5 1.0 CE1 B:HIS228 3.0 31.3 1.0 CD2 B:HIS228 3.2 28.9 1.0 O B:HOH519 4.1 44.4 1.0 ND1 B:HIS228 4.2 29.3 1.0 CG B:HIS228 4.3 30.6 1.0 CE2 B:TYR224 4.3 25.8 1.0 O B:HOH555 4.4 42.0 1.0 OH B:TYR224 4.5 26.8 1.0 CZ B:TYR224 4.8 26.1 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