Iron in PDB 3vrc: Crystal Structure of Cytochrome C' From Thermochromatium Tepidum

The structure of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum, PDB code: 3vrc was solved by Y.Hirano, Y.Kimura, H.Suzuki, K.Miki, Z.-Y.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.00 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	41.310, 57.189, 54.225, 90.00, 94.81, 90.00
R / Rfree (%)	12.9 / 15.3

The structure of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum also contains other interesting chemical elements:

Cadmium	(Cd)	9 atoms
Chlorine	(Cl)	1 atom

The binding sites of Iron atom in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum (pdb code 3vrc). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum, PDB code: 3vrc:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe200 b:8.2 occ:1.00 FE A:HEC200 0.0 8.2 1.0 NC A:HEC200 2.1 8.2 1.0 ND A:HEC200 2.1 9.1 1.0 NB A:HEC200 2.1 9.1 1.0 NA A:HEC200 2.1 8.3 1.0 NE2 A:HIS125 2.1 9.1 1.0 C1C A:HEC200 3.0 7.8 1.0 C4A A:HEC200 3.1 8.5 1.0 C4C A:HEC200 3.1 8.2 1.0 C4B A:HEC200 3.1 7.7 1.0 C1D A:HEC200 3.1 8.3 1.0 C1A A:HEC200 3.1 8.7 1.0 C1B A:HEC200 3.1 8.3 1.0 CD2 A:HIS125 3.1 8.8 1.0 C4D A:HEC200 3.1 9.1 1.0 CE1 A:HIS125 3.1 11.6 1.0 CD1 A:TYR16 3.4 8.6 1.0 CHC A:HEC200 3.4 8.2 1.0 CHB A:HEC200 3.4 8.9 1.0 CHA A:HEC200 3.4 8.8 1.0 CHD A:HEC200 3.4 8.7 1.0 CG A:TYR16 3.6 7.9 1.0 CE1 A:TYR16 3.8 8.5 1.0 CD2 A:TYR16 4.0 8.3 1.0 CB A:TYR16 4.1 9.4 1.0 CZ A:TYR16 4.2 8.4 1.0 ND1 A:HIS125 4.3 10.6 1.0 CG A:HIS125 4.3 9.2 1.0 C3B A:HEC200 4.3 8.0 1.0 C2B A:HEC200 4.3 8.5 1.0 C3C A:HEC200 4.3 8.2 1.0 C3A A:HEC200 4.3 9.1 1.0 C2C A:HEC200 4.3 8.6 1.0 C2A A:HEC200 4.3 9.3 1.0 C2D A:HEC200 4.3 9.1 1.0 C3D A:HEC200 4.3 9.2 1.0 CE2 A:TYR16 4.4 9.0 1.0 NH1 A:ARG129 4.5 12.9 1.0 CD A:ARG129 4.8 10.9 1.0

Iron binding site 2 out of 2 in the Crystal Structure of Cytochrome C' From Thermochromatium Tepidum


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Cytochrome C' From Thermochromatium Tepidum within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe201 b:9.0 occ:1.00 FE B:HEC201 0.0 9.0 1.0 ND B:HEC201 2.0 9.9 1.0 NC B:HEC201 2.0 9.8 1.0 NB B:HEC201 2.0 9.0 1.0 NA B:HEC201 2.1 9.7 1.0 NE2 B:HIS125 2.1 9.8 1.0 C4B B:HEC201 3.0 8.7 1.0 C1D B:HEC201 3.0 9.7 1.0 C4C B:HEC201 3.0 9.3 1.0 C1B B:HEC201 3.0 9.1 1.0 C4D B:HEC201 3.0 9.5 1.0 C4A B:HEC201 3.1 9.3 1.0 C1C B:HEC201 3.1 9.5 1.0 C1A B:HEC201 3.1 9.2 1.0 CD2 B:HIS125 3.1 9.7 1.0 CE1 B:HIS125 3.1 11.4 1.0 CD1 B:TYR16 3.3 10.0 1.0 CHC B:HEC201 3.4 9.3 1.0 CHD B:HEC201 3.4 10.6 1.0 CHB B:HEC201 3.4 9.8 1.0 CHA B:HEC201 3.5 9.6 1.0 CE1 B:TYR16 3.6 10.4 1.0 CG B:TYR16 3.6 9.3 1.0 CB B:TYR16 4.2 10.2 1.0 CD2 B:TYR16 4.2 10.0 1.0 CZ B:TYR16 4.2 10.2 1.0 ND1 B:HIS125 4.3 11.5 1.0 C3B B:HEC201 4.3 9.1 1.0 C2D B:HEC201 4.3 10.2 1.0 CG B:HIS125 4.3 10.7 1.0 C2A B:HEC201 4.3 10.4 1.0 C3C B:HEC201 4.3 9.7 1.0 C2B B:HEC201 4.3 9.1 1.0 C3D B:HEC201 4.3 9.5 1.0 C3A B:HEC201 4.3 10.2 1.0 C2C B:HEC201 4.3 9.6 1.0 CE2 B:TYR16 4.4 10.3 1.0 NH1 B:ARG129 4.5 15.1 1.0 CD B:ARG129 4.8 12.5 1.0

Y.Hirano, Y.Kimura, H.Suzuki, K.Miki, Z.-Y.Wang. Structure Analysis and Comparative Characterization of the Cytochrome C' and Flavocytochrome C From Thermophilic Purple Photosynthetic Bacterium Thermochromatium Tepidum Biochemistry V. 51 6556 2012.
ISSN: ISSN 0006-2960
PubMed: 22827326
DOI: 10.1021/BI3005522