Iron in PDB 1e2r: Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound

All present enzymatic activity of Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound:
1.7.2.1; 1.7.99.1;

The structure of Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound, PDB code: 1e2r was solved by V.Fulop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 1.59
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.500, 60.900, 100.100, 90.00, 111.90, 90.00
R / Rfree (%)	19.2 / 20.8

The binding sites of Iron atom in the Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound (pdb code 1e2r). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound, PDB code: 1e2r:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe601 b:23.3 occ:0.50 FE A:HEC601 0.0 23.3 0.5 NB A:HEC601 1.9 21.5 0.5 NA A:HEC601 2.0 22.1 0.5 NE2 A:HIS69 2.0 21.7 0.5 NC A:HEC601 2.0 21.7 0.5 ND A:HEC601 2.0 22.6 0.5 SD A:MET106 2.3 23.5 0.5 CE1 A:HIS69 2.8 21.4 0.5 C1B A:HEC601 3.0 20.8 0.5 C4B A:HEC601 3.0 20.7 0.5 C4A A:HEC601 3.0 21.3 0.5 C1A A:HEC601 3.0 21.8 0.5 C1C A:HEC601 3.0 20.6 0.5 C4D A:HEC601 3.0 23.2 0.5 C4C A:HEC601 3.0 21.1 0.5 C1D A:HEC601 3.0 22.8 0.5 CD2 A:HIS69 3.2 21.4 0.5 CHB A:HEC601 3.4 21.6 0.5 CHC A:HEC601 3.4 21.1 0.5 CHA A:HEC601 3.4 22.2 0.5 CHD A:HEC601 3.4 21.9 0.5 CE A:MET106 3.5 24.9 0.5 CG A:MET106 3.8 26.6 0.5 ND1 A:HIS69 4.0 21.5 0.5 CG A:HIS69 4.2 21.2 0.5 CB A:MET106 4.2 28.2 0.5 C2B A:HEC601 4.2 20.1 0.5 C3B A:HEC601 4.2 19.9 0.5 C2A A:HEC601 4.2 21.1 0.5 C3A A:HEC601 4.3 21.0 0.5 C2C A:HEC601 4.3 20.5 0.5 C3D A:HEC601 4.3 23.8 0.5 C3C A:HEC601 4.3 20.2 0.5 C2D A:HEC601 4.3 23.2 0.5 CA A:MET106 4.6 29.3 0.5 CD A:PRO107 4.9 29.5 0.5

Iron binding site 2 out of 4 in the Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:9.5 occ:1.00 FE A:DHE602 0.0 9.5 1.0 NE2 A:HIS200 2.0 8.5 1.0 C A:CYN603 2.0 9.1 1.0 ND A:DHE602 2.1 7.9 1.0 NC A:DHE602 2.1 8.8 1.0 NB A:DHE602 2.1 9.8 1.0 NA A:DHE602 2.1 9.4 1.0 CE1 A:HIS200 2.9 8.4 1.0 N A:CYN603 3.0 10.6 1.0 CD2 A:HIS200 3.0 7.2 1.0 C1B A:DHE602 3.0 10.7 1.0 C1C A:DHE602 3.0 10.5 1.0 C4B A:DHE602 3.1 10.5 1.0 C4C A:DHE602 3.1 10.2 1.0 C4D A:DHE602 3.1 7.1 1.0 C1D A:DHE602 3.1 8.1 1.0 C1A A:DHE602 3.1 9.0 1.0 C4A A:DHE602 3.1 9.6 1.0 CHC A:DHE602 3.4 10.8 1.0 CHA A:DHE602 3.4 9.2 1.0 CHD A:DHE602 3.4 9.2 1.0 CHB A:DHE602 3.4 9.7 1.0 ND1 A:HIS200 4.1 8.5 1.0 CG A:HIS200 4.1 7.5 1.0 C3D A:DHE602 4.3 7.5 1.0 C2A A:DHE602 4.3 9.4 1.0 C2D A:DHE602 4.3 7.8 1.0 C3A A:DHE602 4.3 9.4 1.0 C2C A:DHE602 4.3 12.0 1.0 C2B A:DHE602 4.3 11.7 1.0 C3C A:DHE602 4.4 11.8 1.0 C3B A:DHE602 4.4 11.7 1.0 O2C A:DHE602 4.9 18.4 1.0 NE2 A:HIS345 4.9 8.1 1.0 O A:HOH2408 5.0 8.0 1.0

Iron binding site 3 out of 4 in the Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:17.0 occ:1.00 FE B:HEC601 0.0 17.0 1.0 ND B:HEC601 2.0 15.8 1.0 NA B:HEC601 2.0 14.6 1.0 NC B:HEC601 2.0 14.4 1.0 NB B:HEC601 2.0 14.1 1.0 NE2 B:HIS69 2.0 13.3 1.0 SD B:MET106 2.3 14.6 1.0 CE1 B:HIS69 2.9 13.3 1.0 C1A B:HEC601 3.0 15.3 1.0 C4D B:HEC601 3.0 16.8 1.0 C1C B:HEC601 3.0 14.3 1.0 C1D B:HEC601 3.0 15.9 1.0 C4B B:HEC601 3.0 12.5 1.0 C4A B:HEC601 3.0 14.4 1.0 C4C B:HEC601 3.0 15.0 1.0 C1B B:HEC601 3.0 12.0 1.0 CD2 B:HIS69 3.2 12.8 1.0 CHA B:HEC601 3.4 15.9 1.0 CHC B:HEC601 3.4 13.7 1.0 CHD B:HEC601 3.4 14.7 1.0 CHB B:HEC601 3.4 14.1 1.0 CE B:MET106 3.4 16.1 1.0 CG B:MET106 3.6 18.2 1.0 ND1 B:HIS69 4.1 12.3 1.0 CB B:MET106 4.2 21.0 1.0 CG B:HIS69 4.2 13.3 1.0 C2A B:HEC601 4.2 16.2 1.0 C3A B:HEC601 4.3 15.3 1.0 C2D B:HEC601 4.3 17.2 1.0 C2C B:HEC601 4.3 14.7 1.0 C3D B:HEC601 4.3 18.4 1.0 C3B B:HEC601 4.3 12.9 1.0 C3C B:HEC601 4.3 14.4 1.0 C2B B:HEC601 4.3 13.1 1.0 CA B:MET106 4.6 22.7 1.0 CD B:PRO107 4.9 22.3 1.0

Iron binding site 4 out of 4 in the Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome CD1 Nitrite Reductase, Reduced and Cyanide Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:8.3 occ:1.00 FE B:DHE602 0.0 8.3 1.0 C B:CYN603 2.0 7.7 1.0 NE2 B:HIS200 2.0 6.5 1.0 NA B:DHE602 2.1 6.2 1.0 NB B:DHE602 2.1 7.5 1.0 ND B:DHE602 2.1 7.5 1.0 NC B:DHE602 2.1 7.4 1.0 CE1 B:HIS200 2.9 7.3 1.0 C1B B:DHE602 3.0 8.6 1.0 C1C B:DHE602 3.0 8.7 1.0 C4B B:DHE602 3.1 9.2 1.0 C4A B:DHE602 3.1 7.7 1.0 N B:CYN603 3.1 8.2 1.0 C1A B:DHE602 3.1 6.5 1.0 C4D B:DHE602 3.1 6.5 1.0 C1D B:DHE602 3.1 7.3 1.0 C4C B:DHE602 3.1 8.2 1.0 CD2 B:HIS200 3.1 7.5 1.0 CHC B:DHE602 3.4 9.1 1.0 CHB B:DHE602 3.4 7.4 1.0 CHA B:DHE602 3.4 6.6 1.0 CHD B:DHE602 3.4 9.1 1.0 ND1 B:HIS200 4.1 7.5 1.0 CG B:HIS200 4.2 8.5 1.0 C2A B:DHE602 4.3 7.3 1.0 C3A B:DHE602 4.3 8.0 1.0 C3D B:DHE602 4.3 6.9 1.0 C2D B:DHE602 4.3 6.6 1.0 C2B B:DHE602 4.3 10.0 1.0 OH B:TYR25 4.3 15.7 1.0 C2C B:DHE602 4.3 9.2 1.0 C3B B:DHE602 4.4 10.1 1.0 C3C B:DHE602 4.4 8.6 1.0 NE2 B:HIS345 4.9 8.7 1.0 O2B B:DHE602 5.0 14.5 1.0

A.Jafferji, J.W.Allen, S.J.Ferguson, V.Fulop. X-Ray Crystallographic Study of Cyanide Binding Provides Insights Into the Structure-Function Relationship For Cytochrome CD1 Nitrite Reductase From Paracoccus Pantotrophus. J.Biol.Chem. V. 275 25089 2000.
ISSN: ISSN 0021-9258
PubMed: 10827177
DOI: 10.1074/JBC.M001377200