Iron in PDB 1fs8: Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex

The structure of Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex, PDB code: 1fs8 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 / 1.60
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	119.010, 119.010, 186.525, 90.00, 90.00, 90.00
R / Rfree (%)	18.4 / 20.6

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

Yttrium	(Y)	4 atoms
Calcium	(Ca)	1 atom

The binding sites of Iron atom in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate Complex (pdb code 1fs8). 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-Sulfate Complex, PDB code: 1fs8:
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-Sulfate 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-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe508 b:14.6 occ:1.00 FE A:HEM508 0.0 14.6 1.0 ND A:HEM508 2.0 12.7 1.0 NB A:HEM508 2.0 13.3 1.0 NA A:HEM508 2.0 14.0 1.0 NC A:HEM508 2.0 13.7 1.0 O1 A:SO4656 2.0 18.6 1.0 NZ A:LYS134 2.1 13.5 1.0 C4D A:HEM508 3.0 13.5 1.0 C1B A:HEM508 3.0 13.8 1.0 C1D A:HEM508 3.0 15.3 1.0 C1A A:HEM508 3.0 9.8 1.0 C1C A:HEM508 3.0 13.3 1.0 C4A A:HEM508 3.0 17.0 1.0 C4B A:HEM508 3.0 13.8 1.0 C4C A:HEM508 3.0 11.8 1.0 CE A:LYS134 3.1 16.7 1.0 CHB A:HEM508 3.4 14.1 1.0 CHA A:HEM508 3.4 12.4 1.0 CHD A:HEM508 3.4 12.6 1.0 S A:SO4656 3.4 27.9 1.0 CHC A:HEM508 3.4 13.9 1.0 O3 A:SO4656 3.8 34.2 1.0 O2 A:SO4656 4.0 36.5 1.0 NE2 A:HIS277 4.2 18.1 1.0 O A:HOH723 4.2 14.6 1.0 C3D A:HEM508 4.2 12.8 1.0 C2D A:HEM508 4.2 16.2 1.0 C2B A:HEM508 4.2 14.7 1.0 C2C A:HEM508 4.3 14.3 1.0 C3A A:HEM508 4.3 16.0 1.0 C2A A:HEM508 4.3 12.1 1.0 C3B A:HEM508 4.3 16.9 1.0 C3C A:HEM508 4.3 13.0 1.0 CD A:LYS134 4.4 15.4 1.0 O4 A:SO4656 4.4 29.2 1.0 O A:HOH711 4.6 18.8 1.0 CD2 A:HIS277 4.8 14.7 1.0 CMD A:HEM510 4.9 12.5 1.0

Iron binding site 2 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate 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-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe509 b:19.6 occ:1.00 FE A:HEM509 0.0 19.6 1.0 ND A:HEM509 2.0 19.6 1.0 NC A:HEM509 2.0 20.8 1.0 NB A:HEM509 2.0 16.8 1.0 NE2 A:HIS172 2.0 21.1 1.0 NA A:HEM509 2.0 21.9 1.0 NE2 A:HIS313 2.1 20.6 1.0 CE1 A:HIS172 2.9 18.3 1.0 C1D A:HEM509 3.0 19.9 1.0 C4D A:HEM509 3.0 20.7 1.0 C4C A:HEM509 3.0 19.5 1.0 C1B A:HEM509 3.0 19.5 1.0 C4A A:HEM509 3.0 21.7 1.0 C4B A:HEM509 3.0 17.8 1.0 C1A A:HEM509 3.0 17.9 1.0 C1C A:HEM509 3.0 16.1 1.0 CD2 A:HIS172 3.0 19.4 1.0 CD2 A:HIS313 3.0 18.1 1.0 CE1 A:HIS313 3.1 17.7 1.0 CHD A:HEM509 3.4 18.5 1.0 CHA A:HEM509 3.4 21.0 1.0 CHB A:HEM509 3.4 19.2 1.0 CHC A:HEM509 3.4 16.0 1.0 ND1 A:HIS172 4.1 20.7 1.0 CG A:HIS172 4.2 18.5 1.0 ND1 A:HIS313 4.2 17.6 1.0 CG A:HIS313 4.2 16.8 1.0 C3D A:HEM509 4.3 19.9 1.0 C2B A:HEM509 4.3 20.3 1.0 C2D A:HEM509 4.3 20.5 1.0 C3A A:HEM509 4.3 21.2 1.0 C3C A:HEM509 4.3 18.9 1.0 C2C A:HEM509 4.3 16.0 1.0 C3B A:HEM509 4.3 18.2 1.0 C2A A:HEM509 4.3 20.8 1.0 CE A:MET300 4.5 18.3 1.0

Iron binding site 3 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate 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-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe510 b:15.0 occ:1.00 FE A:HEM510 0.0 15.0 1.0 NA A:HEM510 2.0 14.6 1.0 ND A:HEM510 2.0 12.3 1.0 NB A:HEM510 2.0 13.3 1.0 NC A:HEM510 2.0 16.1 1.0 NE2 A:HIS215 2.0 12.9 1.0 NE2 A:HIS102 2.1 12.3 1.0 CE1 A:HIS215 3.0 14.6 1.0 C4A A:HEM510 3.0 13.8 1.0 C1B A:HEM510 3.0 14.2 1.0 CE1 A:HIS102 3.0 17.5 1.0 C1D A:HEM510 3.0 13.1 1.0 C1C A:HEM510 3.0 14.5 1.0 C4C A:HEM510 3.0 16.4 1.0 C1A A:HEM510 3.0 14.8 1.0 C4D A:HEM510 3.0 14.2 1.0 C4B A:HEM510 3.0 14.0 1.0 CD2 A:HIS215 3.1 16.6 1.0 CD2 A:HIS102 3.2 14.8 1.0 CHB A:HEM510 3.3 13.4 1.0 CHD A:HEM510 3.4 15.6 1.0 CHC A:HEM510 3.4 16.2 1.0 CHA A:HEM510 3.4 13.8 1.0 ND1 A:HIS215 4.1 13.4 1.0 ND1 A:HIS102 4.2 14.5 1.0 CG A:HIS215 4.2 17.9 1.0 C3A A:HEM510 4.2 13.7 1.0 C2B A:HEM510 4.2 14.5 1.0 C2C A:HEM510 4.2 14.4 1.0 C2D A:HEM510 4.2 12.0 1.0 C2A A:HEM510 4.3 11.7 1.0 C3D A:HEM510 4.3 12.5 1.0 CG A:HIS102 4.3 14.4 1.0 C3C A:HEM510 4.3 14.7 1.0 C3B A:HEM510 4.3 14.9 1.0 CD1 A:ILE166 5.0 29.5 1.0

Iron binding site 4 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate 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-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe511 b:15.7 occ:1.00 FE A:HEM511 0.0 15.7 1.0 ND A:HEM511 1.9 17.3 1.0 NA A:HEM511 2.0 12.8 1.0 NB A:HEM511 2.0 15.2 1.0 NC A:HEM511 2.0 11.2 1.0 NE2 A:HIS405 2.0 10.8 1.0 NE2 A:HIS299 2.1 13.1 1.0 CE1 A:HIS405 2.9 14.1 1.0 C1D A:HEM511 3.0 16.8 1.0 C4D A:HEM511 3.0 18.4 1.0 C1A A:HEM511 3.0 13.3 1.0 C1B A:HEM511 3.0 16.0 1.0 C4C A:HEM511 3.0 14.0 1.0 C4B A:HEM511 3.0 13.2 1.0 C4A A:HEM511 3.0 15.5 1.0 C1C A:HEM511 3.0 13.3 1.0 CE1 A:HIS299 3.1 16.7 1.0 CD2 A:HIS299 3.1 16.0 1.0 CD2 A:HIS405 3.2 16.9 1.0 CHD A:HEM511 3.4 14.5 1.0 CHA A:HEM511 3.4 15.6 1.0 CHB A:HEM511 3.4 14.0 1.0 CHC A:HEM511 3.4 14.3 1.0 ND1 A:HIS405 4.1 15.8 1.0 ND1 A:HIS299 4.2 15.1 1.0 C2D A:HEM511 4.2 14.2 1.0 C3D A:HEM511 4.2 15.7 1.0 CG A:HIS299 4.2 14.9 1.0 C2B A:HEM511 4.2 14.5 1.0 CG A:HIS405 4.2 15.0 1.0 C2A A:HEM511 4.2 12.6 1.0 C3A A:HEM511 4.3 13.0 1.0 C3B A:HEM511 4.3 14.7 1.0 C2C A:HEM511 4.3 12.8 1.0 C3C A:HEM511 4.3 13.8 1.0

Iron binding site 5 out of 5 in the Cytochrome C Nitrite Reductase From Wolinella Succinogenes-Sulfate 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-Sulfate Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe512 b:18.7 occ:1.00 FE A:HEM512 0.0 18.7 1.0 ND A:HEM512 2.0 18.6 1.0 NA A:HEM512 2.0 16.0 1.0 NC A:HEM512 2.0 16.1 1.0 NB A:HEM512 2.0 18.3 1.0 NE2 A:HIS330 2.0 20.7 1.0 NE2 A:HIS288 2.0 16.3 1.0 CE1 A:HIS330 2.9 23.5 1.0 C1A A:HEM512 3.0 19.8 1.0 CE1 A:HIS288 3.0 17.8 1.0 C4D A:HEM512 3.0 19.1 1.0 C1C A:HEM512 3.0 20.3 1.0 C4B A:HEM512 3.0 16.7 1.0 C4C A:HEM512 3.0 21.6 1.0 C1D A:HEM512 3.0 21.5 1.0 C4A A:HEM512 3.0 15.8 1.0 C1B A:HEM512 3.0 17.2 1.0 CD2 A:HIS288 3.1 17.6 1.0 CD2 A:HIS330 3.2 21.0 1.0 CHA A:HEM512 3.3 21.0 1.0 CHC A:HEM512 3.4 18.0 1.0 CHD A:HEM512 3.4 19.6 1.0 CHB A:HEM512 3.4 14.6 1.0 ND1 A:HIS330 4.1 24.7 1.0 ND1 A:HIS288 4.1 17.0 1.0 C2A A:HEM512 4.2 18.9 1.0 C3D A:HEM512 4.2 22.8 1.0 CG A:HIS288 4.2 16.6 1.0 C2C A:HEM512 4.2 19.5 1.0 CG A:HIS330 4.3 23.5 1.0 C2D A:HEM512 4.3 22.8 1.0 C3A A:HEM512 4.3 19.7 1.0 C3C A:HEM512 4.3 20.8 1.0 C3B A:HEM512 4.3 17.9 1.0 C2B A:HEM512 4.3 16.9 1.0 CBC A:HEM511 4.8 17.8 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