Iron in PDB 2yk3: Crithidia Fasciculata Cytochrome C

The structure of Crithidia Fasciculata Cytochrome C, PDB code: 2yk3 was solved by V.Fulop, K.A.Sam, S.J.Ferguson, M.L.Ginger, J.W.A.Allen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	55.81 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	85.930, 110.880, 60.930, 90.00, 131.20, 90.00
R / Rfree (%)	20.6 / 24.1

The binding sites of Iron atom in the Crithidia Fasciculata Cytochrome C (pdb code 2yk3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 3 binding sites of Iron where determined in the Crithidia Fasciculata Cytochrome C, PDB code: 2yk3:
Jump to Iron binding site number: 1; 2; 3;

Iron binding site 1 out of 3 in the Crithidia Fasciculata Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crithidia Fasciculata Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:14.8 occ:1.00 FE A:HEC200 0.0 14.8 1.0 ND A:HEC200 2.0 13.2 1.0 NE2 A:HIS29 2.0 13.1 1.0 NA A:HEC200 2.1 14.9 1.0 NB A:HEC200 2.1 12.6 1.0 NC A:HEC200 2.1 14.5 1.0 SD A:MET91 2.3 14.1 1.0 CE1 A:HIS29 3.0 13.0 1.0 C1D A:HEC200 3.0 15.2 1.0 C4B A:HEC200 3.0 11.6 1.0 C4D A:HEC200 3.0 14.4 1.0 C1C A:HEC200 3.1 12.5 1.0 C1A A:HEC200 3.1 13.5 1.0 CD2 A:HIS29 3.1 15.5 1.0 C4A A:HEC200 3.1 14.9 1.0 C4C A:HEC200 3.1 13.8 1.0 C1B A:HEC200 3.1 16.0 1.0 CE A:MET91 3.3 16.7 1.0 CG A:MET91 3.3 14.9 1.0 CHA A:HEC200 3.4 14.5 1.0 CHC A:HEC200 3.4 16.4 1.0 CHD A:HEC200 3.4 13.1 1.0 CHB A:HEC200 3.5 16.8 1.0 ND1 A:HIS29 4.1 15.8 1.0 CG A:HIS29 4.2 15.8 1.0 CB A:MET91 4.2 12.6 1.0 C2D A:HEC200 4.3 16.0 1.0 C3A A:HEC200 4.3 15.6 1.0 C2A A:HEC200 4.3 17.2 1.0 C2C A:HEC200 4.3 14.4 1.0 C2B A:HEC200 4.3 14.4 1.0 C3D A:HEC200 4.3 14.2 1.0 C3C A:HEC200 4.3 16.0 1.0 C3B A:HEC200 4.3 15.9 1.0 OH A:TYR78 4.7 26.0 1.0

Iron binding site 2 out of 3 in the Crithidia Fasciculata Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crithidia Fasciculata Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe200 b:14.4 occ:1.00 FE B:HEC200 0.0 14.4 1.0 NE2 B:HIS29 2.0 11.5 1.0 NA B:HEC200 2.0 15.1 1.0 ND B:HEC200 2.0 11.5 1.0 NC B:HEC200 2.0 13.1 1.0 NB B:HEC200 2.0 11.8 1.0 SD B:MET91 2.3 14.1 1.0 CE1 B:HIS29 2.9 12.3 1.0 C1D B:HEC200 3.0 14.8 1.0 C4D B:HEC200 3.0 12.9 1.0 C4B B:HEC200 3.0 12.3 1.0 C4A B:HEC200 3.0 13.5 1.0 C1C B:HEC200 3.1 11.3 1.0 C1A B:HEC200 3.1 14.1 1.0 C1B B:HEC200 3.1 15.3 1.0 C4C B:HEC200 3.1 12.2 1.0 CD2 B:HIS29 3.1 14.3 1.0 CG B:MET91 3.4 15.9 1.0 CE B:MET91 3.4 17.6 1.0 CHB B:HEC200 3.4 16.7 1.0 CHC B:HEC200 3.4 14.3 1.0 CHD B:HEC200 3.4 14.8 1.0 CHA B:HEC200 3.4 15.0 1.0 ND1 B:HIS29 4.1 16.4 1.0 CG B:HIS29 4.2 13.4 1.0 C3A B:HEC200 4.2 14.6 1.0 C2A B:HEC200 4.3 16.0 1.0 CB B:MET91 4.3 12.8 1.0 C2C B:HEC200 4.3 13.8 1.0 C2D B:HEC200 4.3 15.8 1.0 C3D B:HEC200 4.3 15.2 1.0 C2B B:HEC200 4.3 16.5 1.0 C3C B:HEC200 4.3 13.9 1.0 C3B B:HEC200 4.3 15.3 1.0 OH B:TYR78 4.7 22.9 1.0

Iron binding site 3 out of 3 in the Crithidia Fasciculata Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crithidia Fasciculata Cytochrome C within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe200 b:15.2 occ:1.00 FE C:HEC200 0.0 15.2 1.0 NE2 C:HIS29 2.0 14.9 1.0 ND C:HEC200 2.0 13.3 1.0 NC C:HEC200 2.0 16.1 1.0 NA C:HEC200 2.1 17.3 1.0 NB C:HEC200 2.1 15.2 1.0 SD C:MET91 2.3 14.4 1.0 CE1 C:HIS29 2.9 14.0 1.0 C1D C:HEC200 3.0 14.7 1.0 C1C C:HEC200 3.0 13.0 1.0 C4B C:HEC200 3.0 15.5 1.0 C4D C:HEC200 3.0 15.9 1.0 C4C C:HEC200 3.1 13.1 1.0 C4A C:HEC200 3.1 14.9 1.0 C1B C:HEC200 3.1 16.6 1.0 C1A C:HEC200 3.1 14.4 1.0 CD2 C:HIS29 3.1 16.4 1.0 CE C:MET91 3.3 16.6 1.0 CHC C:HEC200 3.4 16.1 1.0 CG C:MET91 3.4 15.9 1.0 CHD C:HEC200 3.4 14.4 1.0 CHB C:HEC200 3.4 18.1 1.0 CHA C:HEC200 3.5 15.0 1.0 ND1 C:HIS29 4.1 17.1 1.0 CG C:HIS29 4.2 15.4 1.0 C2C C:HEC200 4.2 12.5 1.0 C3C C:HEC200 4.3 14.6 1.0 C3A C:HEC200 4.3 15.4 1.0 C2A C:HEC200 4.3 15.7 1.0 C2D C:HEC200 4.3 15.2 1.0 CB C:MET91 4.3 14.4 1.0 C2B C:HEC200 4.3 16.7 1.0 C3D C:HEC200 4.3 15.3 1.0 C3B C:HEC200 4.4 15.9 1.0 OH C:TYR78 4.6 24.7 1.0

V.Fulop, K.A.Sam, S.J.Ferguson, M.L.Ginger, J.W.A.Allen. Structure of A Trypanosomatid Mitochondrial Cytochrome C with Heme Attached Via Only One Thioether Bond and Implications For the Substrate Recognition Requirements of Heme Lyase. Febs J. V. 276 2822 2009.
ISSN: ISSN 1742-464X
PubMed: 19459937
DOI: 10.1111/J.1742-4658.2009.07005.X