Iron in PDB 1fs9: Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex, PDB code: 1fs9 was solved by O.Einsle, P.Stach, A.Messerschmidt, J.Simon, A.Kroeger, R.Huber, P.M.H.Kroneck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.00
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.532, 119.532, 186.056, 90.00, 90.00, 90.00
R / Rfree (%)	18 / 20.8

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex also contains other interesting chemical elements:

Yttrium	(Y)	3 atoms
Calcium	(Ca)	1 atom

The binding sites of Iron atom in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex (pdb code 1fs9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex, PDB code: 1fs9:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe508 b:22.8 occ:1.00 FE A:HEM508 0.0 22.8 1.0 NB A:HEM508 1.9 21.2 1.0 NC A:HEM508 2.0 20.9 1.0 ND A:HEM508 2.0 19.6 1.0 NA A:HEM508 2.0 19.5 1.0 O A:HOH518 2.1 29.1 1.0 NZ A:LYS134 2.2 20.6 1.0 C1B A:HEM508 3.0 22.9 1.0 C4C A:HEM508 3.0 21.9 1.0 C4A A:HEM508 3.0 21.4 1.0 C4B A:HEM508 3.0 26.2 1.0 C1D A:HEM508 3.0 21.2 1.0 C4D A:HEM508 3.0 20.1 1.0 C1C A:HEM508 3.0 20.5 1.0 C1A A:HEM508 3.0 21.7 1.0 CE A:LYS134 3.2 22.2 1.0 CHB A:HEM508 3.3 20.0 1.0 CHD A:HEM508 3.4 21.9 1.0 CHC A:HEM508 3.4 22.0 1.0 CHA A:HEM508 3.4 19.2 1.0 NE2 A:HIS277 4.1 22.3 1.0 O A:HOH582 4.2 23.1 1.0 C2B A:HEM508 4.2 23.1 1.0 C3B A:HEM508 4.3 28.8 1.0 C3C A:HEM508 4.3 23.1 1.0 C3A A:HEM508 4.3 22.0 1.0 C2C A:HEM508 4.3 21.6 1.0 C2A A:HEM508 4.3 20.7 1.0 C2D A:HEM508 4.3 18.7 1.0 C3D A:HEM508 4.3 19.9 1.0 CD A:LYS134 4.6 17.1 1.0 CD2 A:HIS277 4.8 21.9 1.0 N2 A:AZI517 4.9 54.2 1.0 N1 A:AZI517 4.9 41.4 1.0 NH2 A:ARG114 5.0 23.6 1.0 O A:HOH519 5.0 29.1 1.0

Iron binding site 2 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe509 b:27.9 occ:1.00 FE A:HEM509 0.0 27.9 1.0 NE2 A:HIS172 2.0 24.5 1.0 ND A:HEM509 2.0 27.7 1.0 NA A:HEM509 2.0 30.5 1.0 NB A:HEM509 2.0 26.8 1.0 NC A:HEM509 2.0 29.3 1.0 NE2 A:HIS313 2.0 26.9 1.0 CE1 A:HIS172 2.9 32.0 1.0 C4A A:HEM509 3.0 34.9 1.0 CD2 A:HIS313 3.0 24.6 1.0 C4D A:HEM509 3.0 31.7 1.0 C1D A:HEM509 3.0 25.4 1.0 C1B A:HEM509 3.0 29.9 1.0 C1A A:HEM509 3.0 33.9 1.0 C4C A:HEM509 3.0 31.3 1.0 C4B A:HEM509 3.0 28.6 1.0 C1C A:HEM509 3.0 29.3 1.0 CE1 A:HIS313 3.1 29.9 1.0 CD2 A:HIS172 3.1 23.1 1.0 CHB A:HEM509 3.4 23.7 1.0 CHA A:HEM509 3.4 25.6 1.0 CHD A:HEM509 3.4 24.6 1.0 CHC A:HEM509 3.4 26.4 1.0 ND1 A:HIS172 4.1 24.7 1.0 CG A:HIS172 4.2 27.2 1.0 CG A:HIS313 4.2 26.8 1.0 ND1 A:HIS313 4.2 24.0 1.0 C3A A:HEM509 4.3 36.7 1.0 C3D A:HEM509 4.3 31.2 1.0 C2A A:HEM509 4.3 35.1 1.0 C2D A:HEM509 4.3 32.5 1.0 C2B A:HEM509 4.3 30.9 1.0 C3C A:HEM509 4.3 30.7 1.0 C3B A:HEM509 4.3 29.8 1.0 C2C A:HEM509 4.3 30.9 1.0 CE A:MET300 4.6 25.2 1.0

Iron binding site 3 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe510 b:24.4 occ:1.00 FE A:HEM510 0.0 24.4 1.0 NA A:HEM510 1.9 19.2 1.0 NC A:HEM510 2.0 24.9 1.0 ND A:HEM510 2.0 26.1 1.0 NB A:HEM510 2.0 25.6 1.0 NE2 A:HIS102 2.1 23.4 1.0 NE2 A:HIS215 2.1 24.2 1.0 C4A A:HEM510 3.0 20.4 1.0 C1A A:HEM510 3.0 19.1 1.0 C1B A:HEM510 3.0 21.5 1.0 C1C A:HEM510 3.0 23.8 1.0 C1D A:HEM510 3.0 21.1 1.0 C4C A:HEM510 3.0 22.9 1.0 C4D A:HEM510 3.0 19.9 1.0 C4B A:HEM510 3.0 21.0 1.0 CE1 A:HIS102 3.0 22.7 1.0 CE1 A:HIS215 3.1 22.6 1.0 CD2 A:HIS215 3.1 23.5 1.0 CD2 A:HIS102 3.2 17.4 1.0 CHB A:HEM510 3.3 21.0 1.0 CHD A:HEM510 3.4 23.3 1.0 CHC A:HEM510 3.4 25.1 1.0 CHA A:HEM510 3.4 17.5 1.0 C3A A:HEM510 4.2 22.8 1.0 ND1 A:HIS102 4.2 25.0 1.0 C2A A:HEM510 4.2 18.9 1.0 ND1 A:HIS215 4.2 20.6 1.0 C2C A:HEM510 4.2 21.9 1.0 C2D A:HEM510 4.3 24.4 1.0 C2B A:HEM510 4.3 24.8 1.0 C3C A:HEM510 4.3 21.7 1.0 C3D A:HEM510 4.3 20.6 1.0 CG A:HIS215 4.3 20.2 1.0 CG A:HIS102 4.3 25.3 1.0 C3B A:HEM510 4.3 21.6 1.0

Iron binding site 4 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe511 b:26.7 occ:1.00 FE A:HEM511 0.0 26.7 1.0 ND A:HEM511 1.9 23.9 1.0 NB A:HEM511 1.9 20.5 1.0 NA A:HEM511 2.0 21.2 1.0 NC A:HEM511 2.0 22.2 1.0 NE2 A:HIS405 2.1 23.8 1.0 NE2 A:HIS299 2.1 21.6 1.0 CE1 A:HIS405 2.8 24.0 1.0 C1D A:HEM511 3.0 25.9 1.0 C1B A:HEM511 3.0 21.5 1.0 C4D A:HEM511 3.0 22.5 1.0 C4C A:HEM511 3.0 18.6 1.0 C4A A:HEM511 3.0 16.8 1.0 C4B A:HEM511 3.0 22.5 1.0 C1A A:HEM511 3.0 20.3 1.0 C1C A:HEM511 3.0 21.2 1.0 CE1 A:HIS299 3.1 18.4 1.0 CD2 A:HIS299 3.1 24.1 1.0 CD2 A:HIS405 3.3 21.3 1.0 CHD A:HEM511 3.3 19.8 1.0 CHB A:HEM511 3.4 20.8 1.0 CHA A:HEM511 3.4 19.2 1.0 CHC A:HEM511 3.4 19.3 1.0 ND1 A:HIS405 4.1 24.4 1.0 C2D A:HEM511 4.2 26.0 1.0 C3D A:HEM511 4.2 23.5 1.0 C2B A:HEM511 4.2 22.4 1.0 C3B A:HEM511 4.2 18.0 1.0 C3A A:HEM511 4.2 21.3 1.0 C2C A:HEM511 4.2 19.2 1.0 ND1 A:HIS299 4.3 21.2 1.0 C2A A:HEM511 4.3 20.1 1.0 C3C A:HEM511 4.3 19.8 1.0 CG A:HIS299 4.3 25.9 1.0 CG A:HIS405 4.3 27.4 1.0

Iron binding site 5 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Azide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe512 b:32.1 occ:1.00 FE A:HEM512 0.0 32.1 1.0 ND A:HEM512 2.0 34.8 1.0 NB A:HEM512 2.0 28.2 1.0 NC A:HEM512 2.0 33.0 1.0 NA A:HEM512 2.0 32.0 1.0 NE2 A:HIS330 2.0 41.9 1.0 NE2 A:HIS288 2.1 23.4 1.0 CE1 A:HIS330 2.9 38.7 1.0 CE1 A:HIS288 3.0 28.2 1.0 C1D A:HEM512 3.0 41.4 1.0 C4B A:HEM512 3.0 28.8 1.0 C4D A:HEM512 3.0 38.5 1.0 C1B A:HEM512 3.0 28.8 1.0 C4C A:HEM512 3.0 37.2 1.0 C1C A:HEM512 3.0 30.5 1.0 C1A A:HEM512 3.0 37.3 1.0 C4A A:HEM512 3.0 32.8 1.0 CD2 A:HIS330 3.1 38.7 1.0 CD2 A:HIS288 3.1 23.0 1.0 CHA A:HEM512 3.4 30.6 1.0 CHD A:HEM512 3.4 37.7 1.0 CHC A:HEM512 3.4 27.6 1.0 CHB A:HEM512 3.4 28.3 1.0 ND1 A:HIS330 4.1 40.5 1.0 ND1 A:HIS288 4.2 23.8 1.0 CG A:HIS330 4.2 37.3 1.0 C2B A:HEM512 4.2 29.0 1.0 C3B A:HEM512 4.3 31.4 1.0 C2D A:HEM512 4.3 45.6 1.0 C3D A:HEM512 4.3 37.3 1.0 C2C A:HEM512 4.3 34.9 1.0 CG A:HIS288 4.3 21.4 1.0 C3C A:HEM512 4.3 34.0 1.0 C2A A:HEM512 4.3 34.8 1.0 C3A A:HEM512 4.3 36.5 1.0 CBC A:HEM511 4.8 22.8 1.0

O.Einsle, P.Stach, A.Messerschmidt, J.Simon, A.Kroger, R.Huber, P.M.Kroneck. Cytochrome C Nitrite Reductase From Wolinella Succinogenes. Structure at 1.6 A Resolution, Inhibitor Binding, and Heme-Packing Motifs. J.Biol.Chem. V. 275 39608 2000.
ISSN: ISSN 0021-9258
PubMed: 10984487
DOI: 10.1074/JBC.M006188200