Iron in PDB 1dy7: Cytochrome CD1 Nitrite Reductase, Co Complex

All present enzymatic activity of Cytochrome CD1 Nitrite Reductase, Co Complex:
1.7.2.1; 1.7.99.1;

The structure of Cytochrome CD1 Nitrite Reductase, Co Complex, PDB code: 1dy7 was solved by T.Sjogren, M.Svensson-Ek, J.Hajdu, P.Brzezinski, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	106.940, 61.040, 100.390, 90.00, 111.77, 90.00
R / Rfree (%)	17.8 / 19.9

The binding sites of Iron atom in the Cytochrome CD1 Nitrite Reductase, Co Complex (pdb code 1dy7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Cytochrome CD1 Nitrite Reductase, Co Complex, PDB code: 1dy7:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Cytochrome CD1 Nitrite Reductase, Co Complex


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, Co Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe602 b:11.7 occ:1.00 FE A:DHE602 0.0 11.7 1.0 NE2 A:HIS200 2.0 12.5 1.0 NB A:DHE602 2.0 12.2 1.0 ND A:DHE602 2.0 11.5 1.0 NC A:DHE602 2.0 11.6 1.0 C A:CMO603 2.0 17.3 1.0 NA A:DHE602 2.0 10.7 1.0 CE1 A:HIS200 3.0 12.0 1.0 C1C A:DHE602 3.0 13.9 1.0 C1B A:DHE602 3.0 12.9 1.0 CD2 A:HIS200 3.0 11.3 1.0 O A:CMO603 3.0 20.4 1.0 C1D A:DHE602 3.0 11.1 1.0 C4B A:DHE602 3.0 14.0 1.0 C4D A:DHE602 3.0 11.5 1.0 C1A A:DHE602 3.0 11.0 1.0 C4C A:DHE602 3.0 12.1 1.0 C4A A:DHE602 3.0 11.1 1.0 CHB A:DHE602 3.4 13.0 1.0 CHC A:DHE602 3.4 14.1 1.0 CHA A:DHE602 3.4 11.1 1.0 CHD A:DHE602 3.4 12.0 1.0 ND1 A:HIS200 4.1 11.2 1.0 CG A:HIS200 4.1 12.0 1.0 C3B A:DHE602 4.2 14.8 1.0 C2B A:DHE602 4.2 15.7 1.0 C2C A:DHE602 4.2 14.6 1.0 C3D A:DHE602 4.2 11.1 1.0 C2D A:DHE602 4.2 10.6 1.0 C2A A:DHE602 4.2 11.6 1.0 C3A A:DHE602 4.3 11.3 1.0 C3C A:DHE602 4.3 12.8 1.0 O A:HOH2252 4.4 22.1 1.0 O2C A:DHE602 4.9 16.6 1.0 O2B A:DHE602 4.9 19.1 1.0

Iron binding site 2 out of 3 in the Cytochrome CD1 Nitrite Reductase, Co Complex


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, Co Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe601 b:19.7 occ:1.00 FE B:HEC601 0.0 19.7 1.0 NB B:HEC601 2.0 18.3 1.0 NC B:HEC601 2.0 20.8 1.0 NA B:HEC601 2.0 20.5 1.0 ND B:HEC601 2.0 21.5 1.0 NE2 B:HIS69 2.1 18.5 1.0 SD B:MET106 2.3 19.2 1.0 CE1 B:HIS69 2.9 19.3 1.0 C1D B:HEC601 3.0 23.1 1.0 C1B B:HEC601 3.0 17.6 1.0 C4B B:HEC601 3.0 17.6 1.0 C4A B:HEC601 3.0 19.1 1.0 C4D B:HEC601 3.0 23.2 1.0 C1C B:HEC601 3.0 19.9 1.0 C4C B:HEC601 3.1 22.0 1.0 C1A B:HEC601 3.1 20.2 1.0 CD2 B:HIS69 3.2 18.4 1.0 CHD B:HEC601 3.4 22.4 1.0 CHB B:HEC601 3.4 16.7 1.0 CE B:MET106 3.4 20.0 1.0 CHA B:HEC601 3.4 22.1 1.0 CHC B:HEC601 3.4 19.6 1.0 CG B:MET106 3.5 22.6 1.0 CB B:MET106 4.1 24.7 1.0 ND1 B:HIS69 4.1 18.3 1.0 CG B:HIS69 4.2 18.6 1.0 C3B B:HEC601 4.2 17.9 1.0 C2B B:HEC601 4.2 17.8 1.0 C2D B:HEC601 4.3 24.4 1.0 C3C B:HEC601 4.3 21.6 1.0 C3A B:HEC601 4.3 19.5 1.0 C3D B:HEC601 4.3 25.2 1.0 C2A B:HEC601 4.3 20.5 1.0 C2C B:HEC601 4.3 21.4 1.0 CA B:MET106 4.6 26.4 1.0 CD B:PRO107 5.0 22.9 1.0

Iron binding site 3 out of 3 in the Cytochrome CD1 Nitrite Reductase, Co Complex


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, Co Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe602 b:12.2 occ:1.00 FE B:DHE602 0.0 12.2 1.0 C B:CMO603 1.9 14.1 1.0 NC B:DHE602 2.0 12.2 1.0 ND B:DHE602 2.0 11.7 1.0 NB B:DHE602 2.0 12.6 1.0 NA B:DHE602 2.0 11.4 1.0 NE2 B:HIS200 2.1 11.9 1.0 O B:CMO603 3.0 19.3 1.0 C1C B:DHE602 3.0 14.3 1.0 C4B B:DHE602 3.0 14.0 1.0 C4D B:DHE602 3.0 11.6 1.0 C1D B:DHE602 3.0 11.6 1.0 C1B B:DHE602 3.0 13.6 1.0 C1A B:DHE602 3.0 12.6 1.0 C4C B:DHE602 3.0 13.6 1.0 C4A B:DHE602 3.0 12.1 1.0 CE1 B:HIS200 3.1 12.2 1.0 CD2 B:HIS200 3.1 11.4 1.0 CHC B:DHE602 3.4 14.5 1.0 CHB B:DHE602 3.4 12.5 1.0 CHA B:DHE602 3.4 12.2 1.0 CHD B:DHE602 3.4 12.9 1.0 ND1 B:HIS200 4.2 12.2 1.0 C2C B:DHE602 4.2 15.0 1.0 C3D B:DHE602 4.2 11.7 1.0 CG B:HIS200 4.2 11.2 1.0 C3B B:DHE602 4.2 14.2 1.0 C2D B:DHE602 4.2 11.6 1.0 C2B B:DHE602 4.2 15.0 1.0 C2A B:DHE602 4.3 12.1 1.0 C3C B:DHE602 4.3 13.8 1.0 C3A B:DHE602 4.3 12.3 1.0 O B:HOH2287 4.4 21.9 1.0 O2B B:DHE602 4.9 18.4 1.0 O2C B:DHE602 4.9 17.1 1.0

T.Sjogren, M.Svensson-Ek, J.Hajdu, P.Brzezinski. Proton-Coupled Structural Changes Upon Binding of Carbon Monoxide to Cytochrome Cd(1): A Combined Flash Photolysis and X-Ray Crystallography Study Biochemistry V. 39 10967 2000.
ISSN: ISSN 0006-2960
PubMed: 10998233
DOI: 10.1021/BI000179Q