Iron in PDB 3vti: Crystal Structure of Hype-Hypf Complex

The structure of Crystal Structure of Hype-Hypf Complex, PDB code: 3vti was solved by Y.Shomura, Y.Higuchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.56
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	118.739, 119.101, 174.631, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 25.1

The structure of Crystal Structure of Hype-Hypf Complex also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	4 atoms

The binding sites of Iron atom in the Crystal Structure of Hype-Hypf Complex (pdb code 3vti). 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 Hype-Hypf Complex, PDB code: 3vti:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Hype-Hypf Complex


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 Hype-Hypf Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe803 b:43.5 occ:1.00 OD2 A:ASP507 2.1 39.8 1.0 OD1 A:ASP734 2.1 31.6 1.0 O A:HOH1075 2.2 31.4 1.0 NE2 A:HIS483 2.3 36.0 1.0 NE2 A:HIS487 2.3 34.8 1.0 O A:HOH939 2.4 11.9 1.0 CG A:ASP734 3.1 31.9 1.0 CD2 A:HIS483 3.2 35.0 1.0 CG A:ASP507 3.2 36.8 1.0 CD2 A:HIS487 3.3 34.3 1.0 CE1 A:HIS487 3.3 34.5 1.0 CE1 A:HIS483 3.4 36.0 1.0 OD2 A:ASP734 3.4 34.1 1.0 CB A:ASP507 3.9 35.5 1.0 O A:THR509 4.1 38.6 1.0 O A:HOH1070 4.1 49.7 1.0 OD1 A:ASP507 4.2 37.3 1.0 CG A:HIS483 4.4 35.0 1.0 ND1 A:HIS483 4.4 35.0 1.0 CG A:HIS487 4.4 34.2 1.0 ND1 A:HIS487 4.4 33.3 1.0 CB A:ASP734 4.4 31.5 1.0 O A:HOH901 4.6 13.3 1.0 N A:ASP734 4.6 30.0 1.0 CA A:ASP734 4.7 30.7 1.0 CD1 A:ILE737 4.8 35.7 1.0 N A:GLY702 4.9 33.1 1.0 CG1 A:ILE737 4.9 34.9 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Hype-Hypf Complex


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 Hype-Hypf Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe803 b:61.1 occ:1.00 OD1 B:ASP734 2.1 51.1 1.0 OD2 B:ASP507 2.1 49.1 1.0 NE2 B:HIS483 2.2 52.1 1.0 O B:HOH1011 2.4 32.0 1.0 NE2 B:HIS487 2.5 51.9 1.0 O B:HOH917 2.8 15.8 1.0 CG B:ASP734 3.0 49.0 1.0 CG B:ASP507 3.1 48.8 1.0 CD2 B:HIS483 3.2 52.8 1.0 CE1 B:HIS483 3.2 52.7 1.0 OD2 B:ASP734 3.3 49.0 1.0 CE1 B:HIS487 3.4 52.0 1.0 CD2 B:HIS487 3.5 52.2 1.0 CB B:ASP507 3.7 47.4 1.0 O B:THR509 3.8 51.4 1.0 OD1 B:ASP507 4.1 49.0 1.0 ND1 B:HIS483 4.3 53.0 1.0 CG B:HIS483 4.4 53.6 1.0 CB B:ASP734 4.4 48.2 1.0 ND1 B:HIS487 4.5 52.7 1.0 N B:ASP734 4.6 47.5 1.0 CG B:HIS487 4.6 53.3 1.0 O B:HOH903 4.7 7.2 1.0 CA B:ASP734 4.7 48.4 1.0 N B:GLY702 4.8 47.0 1.0 CD1 B:ILE737 4.9 54.4 1.0 C B:THR509 5.0 51.5 1.0

Y.Shomura, Y.Higuchi. Structural Basis For the Reaction Mechanism of S-Carbamoylation of Hype By Hypf in the Maturation of [Nife]-Hydrogenases J.Biol.Chem. V. 287 28409 2012.
ISSN: ISSN 0021-9258
PubMed: 22740694
DOI: 10.1074/JBC.M112.387134