Iron in PDB 3ayf: Crystal Structure of Nitric Oxide Reductase

The structure of Crystal Structure of Nitric Oxide Reductase, PDB code: 3ayf was solved by Y.Matsumoto, T.Tosha, A.V.Pisliakov, T.Hino, H.Sugimoti, S.Nagano, Y.Sugita, Y.Shiro, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.78 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	110.409, 149.648, 151.108, 90.00, 90.00, 90.00
R / Rfree (%)	24.4 / 28.2

The structure of Crystal Structure of Nitric Oxide Reductase also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Zinc	(Zn)	1 atom

The binding sites of Iron atom in the Crystal Structure of Nitric Oxide Reductase (pdb code 3ayf). 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 Nitric Oxide Reductase, PDB code: 3ayf:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Nitric Oxide Reductase


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 Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe801 b:42.4 occ:1.00 FE A:HEM801 0.0 42.4 1.0 ND A:HEM801 1.9 47.9 1.0 NE2 A:HIS355 2.0 56.6 1.0 NA A:HEM801 2.1 44.6 1.0 NB A:HEM801 2.1 49.0 1.0 NC A:HEM801 2.1 43.1 1.0 NE2 A:HIS653 2.2 38.8 1.0 CD2 A:HIS355 3.0 56.2 1.0 C4D A:HEM801 3.0 45.2 1.0 C1D A:HEM801 3.0 44.0 1.0 CD2 A:HIS653 3.0 36.3 1.0 CE1 A:HIS355 3.0 56.3 1.0 C1A A:HEM801 3.1 48.0 1.0 C4A A:HEM801 3.1 46.0 1.0 C1B A:HEM801 3.1 45.0 1.0 C4C A:HEM801 3.1 45.9 1.0 C1C A:HEM801 3.1 46.7 1.0 C4B A:HEM801 3.1 48.1 1.0 CE1 A:HIS653 3.3 35.1 1.0 CHA A:HEM801 3.4 46.7 1.0 CHD A:HEM801 3.4 44.3 1.0 CHB A:HEM801 3.5 45.8 1.0 CHC A:HEM801 3.5 48.3 1.0 CG A:HIS355 4.1 56.0 1.0 ND1 A:HIS355 4.1 57.5 1.0 CG A:HIS653 4.2 38.3 1.0 C2D A:HEM801 4.2 45.6 1.0 C3D A:HEM801 4.2 46.2 1.0 ND1 A:HIS653 4.3 36.4 1.0 C3A A:HEM801 4.3 47.1 1.0 C2B A:HEM801 4.3 48.6 1.0 C2A A:HEM801 4.4 46.8 1.0 C3B A:HEM801 4.4 49.3 1.0 C2C A:HEM801 4.4 45.7 1.0 C3C A:HEM801 4.4 46.0 1.0 NE2 A:GLN319 4.8 42.2 1.0 CA A:GLY323 5.0 47.6 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Nitric Oxide Reductase


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 Nitric Oxide Reductase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe802 b:40.8 occ:1.00 FE A:HEM802 0.0 40.8 1.0 ND A:HEM802 2.0 40.4 1.0 NB A:HEM802 2.0 29.9 1.0 NA A:HEM802 2.0 33.0 1.0 NE2 A:HIS651 2.1 34.9 1.0 NC A:HEM802 2.2 36.1 1.0 O A:HOH978 2.7 36.5 1.0 C1B A:HEM802 3.0 34.6 1.0 C4D A:HEM802 3.0 39.4 1.0 C1A A:HEM802 3.0 34.2 1.0 C1D A:HEM802 3.1 40.9 1.0 CE1 A:HIS651 3.1 35.6 1.0 C4A A:HEM802 3.1 31.5 1.0 C4B A:HEM802 3.1 32.9 1.0 CD2 A:HIS651 3.1 36.5 1.0 C1C A:HEM802 3.2 36.6 1.0 C4C A:HEM802 3.2 40.2 1.0 CHA A:HEM802 3.4 35.3 1.0 CHB A:HEM802 3.4 33.2 1.0 CHC A:HEM802 3.5 36.6 1.0 CHD A:HEM802 3.5 40.7 1.0 O A:HOH929 4.0 48.8 1.0 ND1 A:HIS651 4.2 38.5 1.0 C2B A:HEM802 4.3 31.9 1.0 C2D A:HEM802 4.3 42.4 1.0 CG A:HIS651 4.3 39.6 1.0 C3D A:HEM802 4.3 41.7 1.0 C2A A:HEM802 4.3 34.8 1.0 C3A A:HEM802 4.3 34.1 1.0 C3B A:HEM802 4.3 34.1 1.0 C2C A:HEM802 4.4 37.5 1.0 C3C A:HEM802 4.5 40.7 1.0 ZN A:ZN803 4.6 55.7 1.0

Y.Matsumoto, T.Tosha, A.V.Pisliakov, T.Hino, H.Sugimoto, S.Nagano, Y.Sugita, Y.Shiro. Crystal Structure of Quinol-Dependent Nitric Oxide Reductase From Geobacillus Stearothermophilus Nat.Struct.Mol.Biol. V. 19 238 2012.
ISSN: ISSN 1545-9993
PubMed: 22266822
DOI: 10.1038/NSMB.2213