Iron in PDB 3vth: Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form

The structure of Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form, PDB code: 3vth 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 / 2.00
Space group	P 64
Cell size a, b, c (Å), α, β, γ (°)	232.983, 232.983, 65.665, 90.00, 90.00, 120.00
R / Rfree (%)	20.9 / 23.8

The structure of Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	3 atoms

The binding sites of Iron atom in the Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form (pdb code 3vth). 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 Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form, PDB code: 3vth:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form


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 Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe807 b:27.8 occ:1.00 O2B A:AP2806 2.0 34.0 1.0 OD2 A:ASP507 2.1 26.0 1.0 NE2 A:HIS487 2.2 20.7 1.0 NE2 A:HIS483 2.2 23.9 1.0 OD1 A:ASP734 2.2 27.0 1.0 O2A A:AP2806 2.2 29.3 1.0 CD2 A:HIS483 3.1 24.0 1.0 CD2 A:HIS487 3.1 20.7 1.0 CG A:ASP507 3.1 27.7 1.0 CE1 A:HIS487 3.2 20.2 1.0 CG A:ASP734 3.2 25.6 1.0 PB A:AP2806 3.3 38.8 1.0 CE1 A:HIS483 3.3 23.3 1.0 PA A:AP2806 3.3 34.5 1.0 OD2 A:ASP734 3.6 30.5 1.0 C3A A:AP2806 3.6 34.1 1.0 CB A:ASP507 3.6 25.2 1.0 O1B A:AP2806 4.1 38.1 1.0 OD1 A:ASP507 4.2 28.6 1.0 CG A:HIS483 4.3 23.1 1.0 ND1 A:HIS487 4.3 20.3 1.0 CG A:HIS487 4.3 21.8 1.0 ND1 A:HIS483 4.3 24.3 1.0 O5' A:AP2806 4.4 34.2 1.0 O3B A:AP2806 4.4 40.7 1.0 O1A A:AP2806 4.4 30.1 1.0 CB A:ASP734 4.6 22.0 1.0 O A:THR509 4.6 33.7 1.0 CD1 A:ILE737 4.7 27.2 1.0 N A:GLY702 4.8 21.5 1.0 N A:ASP734 4.8 20.3 1.0 CA A:ASP734 4.8 21.6 1.0 CG1 A:ILE737 4.9 25.3 1.0 CA A:GLY701 5.0 21.7 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form


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 Full-Length Hypf in the Phosphate- and Nucleotide-Bound Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe807 b:37.6 occ:1.00 O2B B:AP2806 2.0 45.9 1.0 NE2 B:HIS483 2.1 29.9 1.0 OD2 B:ASP507 2.1 33.9 1.0 OD1 B:ASP734 2.2 32.0 1.0 O2A B:AP2806 2.2 47.0 1.0 NE2 B:HIS487 2.2 29.4 1.0 CD2 B:HIS483 3.1 27.4 1.0 CE1 B:HIS483 3.1 29.3 1.0 CD2 B:HIS487 3.1 29.4 1.0 CG B:ASP507 3.2 35.2 1.0 CG B:ASP734 3.2 34.4 1.0 CE1 B:HIS487 3.3 30.1 1.0 PB B:AP2806 3.3 51.5 1.0 PA B:AP2806 3.4 50.8 1.0 OD2 B:ASP734 3.6 37.4 1.0 C3A B:AP2806 3.7 50.4 1.0 CB B:ASP507 3.7 33.2 1.0 O B:HOH993 4.1 34.4 1.0 O1B B:AP2806 4.2 51.2 1.0 OD1 B:ASP507 4.2 35.4 1.0 ND1 B:HIS483 4.2 28.1 1.0 CG B:HIS483 4.2 28.0 1.0 CG B:HIS487 4.3 29.5 1.0 O1A B:AP2806 4.3 50.3 1.0 ND1 B:HIS487 4.3 30.3 1.0 O3B B:AP2806 4.4 51.3 1.0 O5' B:AP2806 4.5 51.2 1.0 CB B:ASP734 4.6 33.9 1.0 O B:THR509 4.6 41.2 1.0 N B:ASP734 4.7 33.4 1.0 CA B:ASP734 4.8 33.9 1.0 N B:GLY702 4.8 32.2 1.0 CD1 B:ILE737 4.8 35.1 1.0 CG1 B:ILE737 4.9 34.8 1.0 CA B:GLY701 5.0 31.0 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