Iron in PDB 5b3i: Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus

The structure of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus, PDB code: 5b3i was solved by S.Fujii, H.Oki, K.Kawahara, D.Yamane, M.Yamanaka, T.Maruno, Y.Kobayashi, M.Masanari, S.Wakai, H.Nishihara, T.Ohkubo, Y.Sambongi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.95 / 1.89
Space group	P 21 2 21
Cell size a, b, c (Å), α, β, γ (°)	54.243, 72.923, 132.365, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 24.3

The binding sites of Iron atom in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus (pdb code 5b3i). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus, PDB code: 5b3i:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe201 b:15.0 occ:1.00 FE A:HEC201 0.0 15.0 1.0 ND A:HEC201 1.9 14.8 1.0 NA A:HEC201 2.0 15.1 1.0 NC A:HEC201 2.1 15.3 1.0 NB A:HEC201 2.1 14.9 1.0 NE2 A:HIS128 2.2 15.5 1.0 C1D A:HEC201 2.9 14.8 1.0 CD1 A:TYR16 2.9 15.3 1.0 C4D A:HEC201 3.0 15.2 1.0 C1A A:HEC201 3.0 14.9 1.0 C4C A:HEC201 3.0 15.2 1.0 C4B A:HEC201 3.1 15.5 1.0 C4A A:HEC201 3.1 14.8 1.0 C1C A:HEC201 3.1 14.9 1.0 CD2 A:HIS128 3.1 15.2 1.0 C1B A:HEC201 3.1 15.1 1.0 CE1 A:HIS128 3.2 15.5 1.0 CE1 A:TYR16 3.3 15.5 1.0 CHD A:HEC201 3.3 14.9 1.0 CG A:TYR16 3.4 14.6 1.0 CHA A:HEC201 3.4 15.1 1.0 CHC A:HEC201 3.5 14.9 1.0 CHB A:HEC201 3.6 14.8 1.0 CB A:TYR16 3.9 14.2 1.0 CZ A:TYR16 4.1 15.3 1.0 C2D A:HEC201 4.2 15.1 1.0 CD2 A:TYR16 4.2 14.7 1.0 C3D A:HEC201 4.2 15.2 1.0 C2A A:HEC201 4.2 14.8 1.0 C3A A:HEC201 4.2 14.8 1.0 C3C A:HEC201 4.3 15.2 1.0 C2C A:HEC201 4.3 15.7 1.0 CG A:HIS128 4.3 16.5 1.0 ND1 A:HIS128 4.3 16.7 1.0 C3B A:HEC201 4.3 15.2 1.0 C2B A:HEC201 4.4 14.8 1.0 CE2 A:TYR16 4.5 15.3 1.0 NH1 A:ARG132 4.6 17.2 1.0 CD A:ARG132 4.9 16.4 1.0

Iron binding site 2 out of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:16.1 occ:1.00 FE B:HEC201 0.0 16.1 1.0 ND B:HEC201 1.9 15.9 1.0 NA B:HEC201 2.0 16.0 1.0 NC B:HEC201 2.1 15.8 1.0 NB B:HEC201 2.1 15.8 1.0 NE2 B:HIS128 2.2 16.7 1.0 CD1 B:TYR16 2.8 16.3 1.0 C1D B:HEC201 2.9 15.9 1.0 C4D B:HEC201 3.0 16.3 1.0 C1A B:HEC201 3.0 16.1 1.0 C4B B:HEC201 3.0 15.6 1.0 C4C B:HEC201 3.0 15.6 1.0 C4A B:HEC201 3.1 15.7 1.0 CE1 B:HIS128 3.1 16.5 1.0 C1B B:HEC201 3.1 15.8 1.0 C1C B:HEC201 3.1 15.8 1.0 CE1 B:TYR16 3.2 16.0 1.0 CD2 B:HIS128 3.2 16.6 1.0 CHD B:HEC201 3.4 15.3 1.0 CHA B:HEC201 3.4 15.8 1.0 CHC B:HEC201 3.4 15.5 1.0 CG B:TYR16 3.5 15.9 1.0 CHB B:HEC201 3.5 15.9 1.0 CZ B:TYR16 4.0 15.4 1.0 CB B:TYR16 4.1 14.9 1.0 C2D B:HEC201 4.2 15.7 1.0 C3D B:HEC201 4.2 16.2 1.0 CD2 B:TYR16 4.2 15.5 1.0 ND1 B:HIS128 4.2 17.6 1.0 C2A B:HEC201 4.2 16.0 1.0 C3A B:HEC201 4.3 16.1 1.0 C3C B:HEC201 4.3 15.2 1.0 C2C B:HEC201 4.3 15.6 1.0 C2B B:HEC201 4.3 15.9 1.0 CG B:HIS128 4.3 17.7 1.0 C3B B:HEC201 4.3 15.7 1.0 CE2 B:TYR16 4.5 15.2 1.0 NH1 B:ARG132 4.5 16.6 1.0 OH B:TYR16 4.8 15.3 1.0

Iron binding site 3 out of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:16.2 occ:1.00 FE C:HEC201 0.0 16.2 1.0 ND C:HEC201 1.9 15.7 1.0 NA C:HEC201 2.0 16.5 1.0 NC C:HEC201 2.1 16.1 1.0 NB C:HEC201 2.1 16.0 1.0 NE2 C:HIS128 2.2 17.0 1.0 C1D C:HEC201 2.9 16.0 1.0 CD1 C:TYR16 3.0 16.0 1.0 C4D C:HEC201 3.0 16.2 1.0 C4B C:HEC201 3.0 15.8 1.0 C1A C:HEC201 3.0 16.0 1.0 C4C C:HEC201 3.0 16.7 1.0 C1C C:HEC201 3.1 15.9 1.0 C4A C:HEC201 3.1 16.3 1.0 C1B C:HEC201 3.1 15.7 1.0 CD2 C:HIS128 3.1 17.0 1.0 CE1 C:HIS128 3.2 17.7 1.0 CE1 C:TYR16 3.3 15.8 1.0 CG C:TYR16 3.3 15.3 1.0 CHD C:HEC201 3.4 16.0 1.0 CHC C:HEC201 3.4 15.2 1.0 CHA C:HEC201 3.5 15.9 1.0 CHB C:HEC201 3.5 15.7 1.0 CB C:TYR16 3.9 15.0 1.0 CD2 C:TYR16 4.0 15.0 1.0 CZ C:TYR16 4.0 15.7 1.0 C2D C:HEC201 4.2 15.9 1.0 C3D C:HEC201 4.2 15.8 1.0 C2A C:HEC201 4.3 16.0 1.0 C2C C:HEC201 4.3 16.1 1.0 C3C C:HEC201 4.3 16.6 1.0 ND1 C:HIS128 4.3 17.7 1.0 C3B C:HEC201 4.3 15.7 1.0 C3A C:HEC201 4.3 15.9 1.0 C2B C:HEC201 4.3 15.2 1.0 CG C:HIS128 4.3 18.4 1.0 CE2 C:TYR16 4.3 15.2 1.0 NH1 C:ARG132 4.5 18.3 1.0 OH C:TYR16 4.9 16.5 1.0

Iron binding site 4 out of 4 in the Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Homo-Dimeric Structure of Cytochrome C' From Thermophilic Hydrogenophilus Thermoluteolus within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe201 b:15.4 occ:1.00 FE D:HEC201 0.0 15.4 1.0 ND D:HEC201 1.9 15.5 1.0 NA D:HEC201 2.0 15.3 1.0 NC D:HEC201 2.1 15.6 1.0 NB D:HEC201 2.1 15.2 1.0 NE2 D:HIS128 2.2 16.5 1.0 CD1 D:TYR16 2.8 15.5 1.0 C1D D:HEC201 2.9 14.9 1.0 C4D D:HEC201 3.0 15.1 1.0 C1A D:HEC201 3.0 15.4 1.0 C4B D:HEC201 3.0 15.4 1.0 C4C D:HEC201 3.0 16.2 1.0 C4A D:HEC201 3.1 15.6 1.0 C1C D:HEC201 3.1 15.7 1.0 C1B D:HEC201 3.1 15.1 1.0 CD2 D:HIS128 3.1 16.6 1.0 CE1 D:HIS128 3.2 16.9 1.0 CE1 D:TYR16 3.2 16.1 1.0 CG D:TYR16 3.3 14.9 1.0 CHD D:HEC201 3.3 15.4 1.0 CHA D:HEC201 3.4 15.8 1.0 CHC D:HEC201 3.4 15.6 1.0 CHB D:HEC201 3.5 15.2 1.0 CB D:TYR16 3.8 14.7 1.0 CZ D:TYR16 4.0 15.4 1.0 CD2 D:TYR16 4.0 15.4 1.0 C2D D:HEC201 4.2 15.8 1.0 C3D D:HEC201 4.2 15.7 1.0 C2A D:HEC201 4.2 15.9 1.0 C3A D:HEC201 4.3 15.5 1.0 ND1 D:HIS128 4.3 17.2 1.0 C2C D:HEC201 4.3 15.8 1.0 C3C D:HEC201 4.3 15.4 1.0 CG D:HIS128 4.3 17.5 1.0 C2B D:HEC201 4.3 15.2 1.0 C3B D:HEC201 4.3 15.6 1.0 CE2 D:TYR16 4.3 15.1 1.0 NH1 D:ARG132 4.5 18.7 1.0 OH D:TYR16 4.9 15.1 1.0

S.Fujii, H.Oki, K.Kawahara, D.Yamane, M.Yamanaka, T.Maruno, Y.Kobayashi, M.Masanari, S.Wakai, H.Nishihara, T.Ohkubo, Y.Sambongi. Structural and Functional Insights Into Thermally Stable Cytochrome C' From A Thermophile Protein Sci. V. 26 737 2017.
ISSN: ESSN 1469-896X
PubMed: 28097774
DOI: 10.1002/PRO.3120