Iron in PDB 4xyd: Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor)

All present enzymatic activity of Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor):
1.7.2.5;

The structure of Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor), PDB code: 4xyd was solved by A.Crow, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	53.36 / 2.85
Space group	P 2 21 21
Cell size a, b, c (Å), α, β, γ (°)	86.220, 98.830, 126.780, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 24.3

The structure of Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor) also contains other interesting chemical elements:

Copper	(Cu)	1 atom
Calcium	(Ca)	1 atom

The binding sites of Iron atom in the Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor) (pdb code 4xyd). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor), PDB code: 4xyd:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe501 b:35.9 occ:1.00 FE A:HEM501 0.0 35.9 1.0 NE2 A:HIS336 1.8 44.4 1.0 ND A:HEM501 1.9 36.7 1.0 NE2 A:HIS53 1.9 39.6 1.0 NA A:HEM501 2.0 36.2 1.0 NC A:HEM501 2.1 35.0 1.0 NB A:HEM501 2.1 36.3 1.0 CE1 A:HIS336 2.7 48.4 1.0 CD2 A:HIS53 2.9 41.2 1.0 C1D A:HEM501 2.9 37.3 1.0 CE1 A:HIS53 2.9 39.2 1.0 C4D A:HEM501 2.9 36.9 1.0 CD2 A:HIS336 2.9 47.6 1.0 C1A A:HEM501 3.0 36.8 1.0 C4A A:HEM501 3.0 38.9 1.0 C4C A:HEM501 3.0 37.1 1.0 C4B A:HEM501 3.0 36.8 1.0 C1B A:HEM501 3.1 36.1 1.0 C1C A:HEM501 3.1 35.3 1.0 CHA A:HEM501 3.4 36.7 1.0 CHD A:HEM501 3.4 36.3 1.0 CHB A:HEM501 3.4 36.2 1.0 CHC A:HEM501 3.5 36.5 1.0 ND1 A:HIS336 3.8 48.9 1.0 CG A:HIS336 4.0 47.2 1.0 ND1 A:HIS53 4.0 36.0 1.0 CG A:HIS53 4.0 37.6 1.0 C3A A:HEM501 4.2 38.3 1.0 C2A A:HEM501 4.2 38.5 1.0 C2D A:HEM501 4.2 38.2 1.0 C3D A:HEM501 4.2 39.7 1.0 C3C A:HEM501 4.2 38.4 1.0 C3B A:HEM501 4.3 39.1 1.0 C2B A:HEM501 4.3 38.8 1.0 C2C A:HEM501 4.3 36.3 1.0 CE A:MET383 4.8 89.0 1.0 NE2 A:GLN23 4.9 50.2 1.0 CA A:GLY27 4.9 38.3 1.0

Iron binding site 2 out of 4 in the Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe504 b:50.8 occ:1.00 FE A:HEM504 0.0 50.8 1.0 ND A:HEM504 1.9 57.4 1.0 NE2 A:HIS334 1.9 48.9 1.0 NA A:HEM504 2.0 55.5 1.0 O2 A:UNL502 2.0 44.0 1.0 NC A:HEM504 2.1 59.2 1.0 NB A:HEM504 2.1 53.3 1.0 C4D A:HEM504 2.9 55.9 1.0 O1 A:UNL502 2.9 51.1 1.0 C1D A:HEM504 2.9 60.1 1.0 CD2 A:HIS334 3.0 45.7 1.0 CE1 A:HIS334 3.0 47.1 1.0 C1A A:HEM504 3.0 56.6 1.0 C4B A:HEM504 3.0 53.2 1.0 C4A A:HEM504 3.0 54.3 1.0 C1B A:HEM504 3.1 53.4 1.0 C1C A:HEM504 3.1 60.4 1.0 C4C A:HEM504 3.1 62.0 1.0 CHA A:HEM504 3.4 57.8 1.0 CHC A:HEM504 3.4 60.0 1.0 CHD A:HEM504 3.4 61.5 1.0 CHB A:HEM504 3.4 55.1 1.0 ND1 A:HIS334 4.1 43.0 1.0 CG A:HIS334 4.1 42.8 1.0 C3D A:HEM504 4.2 55.0 1.0 C2D A:HEM504 4.2 57.6 1.0 OE2 A:GLU198 4.2 72.5 1.0 C2A A:HEM504 4.2 54.5 1.0 C3A A:HEM504 4.2 52.6 1.0 C2C A:HEM504 4.3 60.1 1.0 C2B A:HEM504 4.3 51.9 1.0 C3C A:HEM504 4.3 61.0 1.0 C3B A:HEM504 4.3 51.9 1.0 FE A:FE505 4.3 56.6 1.0 CD A:GLU198 4.5 71.1 1.0 OE1 A:GLU198 4.5 71.0 1.0 CE1 A:HIS245 4.5 58.7 1.0 CE1 A:HIS246 4.7 50.3 1.0 NE2 A:HIS246 5.0 55.0 1.0

Iron binding site 3 out of 4 in the Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor) within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe505 b:56.6 occ:1.00 ND1 A:HIS194 1.9 49.6 1.0 NE2 A:HIS245 1.9 58.4 1.0 NE2 A:HIS246 1.9 55.0 1.0 OE1 A:GLU198 2.0 71.0 1.0 O1 A:UNL502 2.1 51.1 1.0 O2 A:UNL502 2.3 44.0 1.0 CE1 A:HIS194 2.5 47.5 1.0 OE2 A:GLU198 2.6 72.5 1.0 CE1 A:HIS245 2.7 58.7 1.0 CD A:GLU198 2.7 71.1 1.0 CE1 A:HIS246 2.8 50.3 1.0 CD2 A:HIS246 2.9 50.5 1.0 CD2 A:HIS245 3.1 55.5 1.0 CG A:HIS194 3.1 48.9 1.0 NE2 A:HIS194 3.8 46.1 1.0 CB A:HIS194 3.8 49.0 1.0 ND1 A:HIS245 3.8 56.1 1.0 ND1 A:HIS246 3.9 47.6 1.0 CG A:HIS246 3.9 48.4 1.0 CD2 A:HIS194 4.1 46.3 1.0 CG A:HIS245 4.1 55.4 1.0 CG A:GLU198 4.2 61.0 1.0 FE A:HEM504 4.3 50.8 1.0 ND A:HEM504 4.3 57.4 1.0 NC A:HEM504 4.4 59.2 1.0 CA A:HIS194 4.6 50.5 1.0 C1D A:HEM504 4.7 60.1 1.0 C4D A:HEM504 4.7 55.9 1.0 CB A:GLU198 4.8 53.9 1.0 C4C A:HEM504 4.9 62.0 1.0 O A:GLY242 4.9 51.8 1.0 C1C A:HEM504 4.9 60.4 1.0 OE2 A:GLU267 5.0 82.5 1.0

Iron binding site 4 out of 4 in the Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Nitric Oxide Reductase From Roseobacter Denitrificans (Rdnor) within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:42.1 occ:1.00 FE B:HEC201 0.0 42.1 1.0 NE2 B:HIS66 1.9 47.9 1.0 NA B:HEC201 2.1 39.6 1.0 NB B:HEC201 2.1 38.9 1.0 NC B:HEC201 2.1 38.2 1.0 ND B:HEC201 2.1 40.9 1.0 SD B:MET116 2.3 44.9 1.0 CE1 B:HIS66 2.8 47.5 1.0 CD2 B:HIS66 3.0 47.0 1.0 C4B B:HEC201 3.1 39.5 1.0 C4A B:HEC201 3.1 39.9 1.0 C4C B:HEC201 3.1 39.9 1.0 C1A B:HEC201 3.1 42.4 1.0 C1C B:HEC201 3.1 38.2 1.0 C1D B:HEC201 3.1 40.6 1.0 C4D B:HEC201 3.1 42.7 1.0 C1B B:HEC201 3.1 39.4 1.0 CE B:MET116 3.3 43.2 1.0 CHB B:HEC201 3.5 39.6 1.0 CHC B:HEC201 3.5 38.0 1.0 CHD B:HEC201 3.5 40.3 1.0 CHA B:HEC201 3.5 41.9 1.0 CG B:MET116 3.5 41.9 1.0 ND1 B:HIS66 3.9 47.5 1.0 CG B:HIS66 4.1 47.6 1.0 CB B:MET116 4.2 40.2 1.0 C3B B:HEC201 4.4 41.3 1.0 C3C B:HEC201 4.4 39.9 1.0 C3A B:HEC201 4.4 40.4 1.0 C3D B:HEC201 4.4 44.1 1.0 C2D B:HEC201 4.4 42.4 1.0 C2A B:HEC201 4.4 42.3 1.0 C2C B:HEC201 4.4 40.2 1.0 C2B B:HEC201 4.5 41.8 1.0 CD1 B:LEU79 4.8 42.7 1.0

A.Crow, Y.Matsuda, H.Arata, A.Oubrie. Structure of the Membrane-Intrinsic Nitric Oxide Reductase From Roseobacter Denitrificans. Biochemistry V. 55 3198 2016.
ISSN: ISSN 0006-2960
PubMed: 27185533
DOI: 10.1021/ACS.BIOCHEM.6B00332