Iron 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:

Nickel

(Ni)

5 atoms

The binding sites of Iron 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 Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Aetd in Complex with L-Tyrosine, PDB code: 8zvg:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Aetd in Complex with L-Tyrosine


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe301 b:25.2 occ:1.00 O A:HOH430 1.9 31.1 1.0 NE2 A:HIS172 2.0 30.3 1.0 N A:TYR302 2.1 23.7 1.0 OXT A:TYR302 2.1 29.4 1.0 OE1 A:GLU176 2.1 32.1 1.0 ND1 A:HIS79 2.3 29.8 1.0 C A:TYR302 2.8 27.5 1.0 CA A:TYR302 2.9 25.7 1.0 CE1 A:HIS172 3.0 30.7 1.0 CD A:GLU176 3.1 39.7 1.0 CD2 A:HIS172 3.1 30.3 1.0 CE1 A:HIS79 3.2 33.9 1.0 CG A:HIS79 3.3 27.6 1.0 OE2 A:GLU176 3.4 36.9 1.0 CB A:HIS79 3.6 26.2 1.0 CB A:TYR302 3.8 27.6 1.0 O A:TYR302 4.0 27.6 1.0 ND1 A:HIS172 4.1 31.4 1.0 CG A:HIS172 4.2 32.4 1.0 NE2 A:HIS79 4.3 26.5 1.0 CD2 A:HIS79 4.4 27.3 1.0 CG A:GLU176 4.4 40.1 1.0 O A:ASP76 4.6 33.3 1.0 CG A:TYR302 4.9 26.9 1.0 CB A:GLU176 4.9 36.2 1.0 CE2 A:PHE48 5.0 27.8 1.0

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


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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 B:Fe301 b:33.1 occ:1.00 O B:HOH405 2.0 39.2 1.0 ND1 B:HIS79 2.0 29.6 1.0 NE2 B:HIS172 2.1 29.6 1.0 OE1 B:GLU176 2.1 41.6 1.0 O B:TYR302 2.2 33.8 1.0 N B:TYR302 2.3 37.5 1.0 C B:TYR302 2.9 36.0 1.0 CD B:GLU176 3.0 62.1 1.0 CE1 B:HIS79 3.0 32.4 1.0 CD2 B:HIS172 3.0 27.7 1.0 CE1 B:HIS172 3.1 28.1 1.0 CA B:TYR302 3.1 37.5 1.0 CG B:HIS79 3.1 30.2 1.0 OE2 B:GLU176 3.2 58.8 1.0 CB B:HIS79 3.5 29.7 1.0 CB B:TYR302 4.0 36.0 1.0 OXT B:TYR302 4.1 34.2 1.0 NE2 B:HIS79 4.1 30.3 1.0 ND1 B:HIS172 4.2 31.4 1.0 CG B:HIS172 4.2 27.9 1.0 CD2 B:HIS79 4.2 29.8 1.0 CG B:GLU176 4.4 68.5 1.0 O B:ASP76 4.6 39.4 1.0 CE2 B:PHE48 4.9 28.9 1.0 CA B:HIS79 5.0 32.4 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