Iron in PDB 3hb3: High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase

All present enzymatic activity of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase:
1.9.3.1;

The structure of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase, PDB code: 3hb3 was solved by J.Koepke, H.Angerer, G.Peng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.98 / 2.25
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	83.403, 150.473, 157.185, 90.00, 90.00, 90.00
R / Rfree (%)	21.8 / 28

The structure of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Copper	(Cu)	3 atoms
Calcium	(Ca)	1 atom

The binding sites of Iron atom in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase (pdb code 3hb3). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase, PDB code: 3hb3:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe559 b:30.8 occ:1.00 FE A:HEA559 0.0 30.8 1.0 NE2 A:HIS94 1.9 38.7 1.0 NE2 A:HIS413 1.9 42.4 1.0 ND A:HEA559 2.0 21.0 1.0 NB A:HEA559 2.0 21.7 1.0 NA A:HEA559 2.1 26.1 1.0 NC A:HEA559 2.1 27.9 1.0 CE1 A:HIS413 2.8 43.2 1.0 CE1 A:HIS94 2.8 42.0 1.0 C4D A:HEA559 2.9 22.7 1.0 C1A A:HEA559 2.9 12.8 1.0 C4B A:HEA559 2.9 23.7 1.0 C1B A:HEA559 3.0 29.8 1.0 CD2 A:HIS94 3.0 42.3 1.0 C1D A:HEA559 3.0 23.6 1.0 C1C A:HEA559 3.0 20.4 1.0 C4A A:HEA559 3.1 24.7 1.0 C4C A:HEA559 3.1 28.3 1.0 CD2 A:HIS413 3.1 40.9 1.0 CHA A:HEA559 3.4 16.8 1.0 CHC A:HEA559 3.5 21.2 1.0 CHD A:HEA559 3.6 24.5 1.0 CHB A:HEA559 3.7 26.8 1.0 ND1 A:HIS413 3.9 41.3 1.0 ND1 A:HIS94 3.9 38.2 1.0 CG A:HIS94 4.1 37.0 1.0 CG A:HIS413 4.1 36.5 1.0 C2A A:HEA559 4.2 21.1 1.0 C3A A:HEA559 4.2 11.3 1.0 C3B A:HEA559 4.2 31.6 1.0 C3D A:HEA559 4.3 18.9 1.0 C2B A:HEA559 4.3 19.4 1.0 C2C A:HEA559 4.3 27.0 1.0 C3C A:HEA559 4.3 20.7 1.0 C2D A:HEA559 4.3 14.2 1.0 OG1 A:THR50 4.7 25.8 1.0 CE1 A:PHE412 4.9 39.9 1.0

Iron binding site 2 out of 2 in the High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe560 b:26.6 occ:1.00 FE A:HEA560 0.0 26.6 1.0 O1 A:PEO576 1.9 17.5 1.0 NE2 A:HIS411 1.9 8.8 1.0 NB A:HEA560 2.1 35.4 1.0 ND A:HEA560 2.1 38.8 1.0 NA A:HEA560 2.1 34.7 1.0 NC A:HEA560 2.2 41.2 1.0 O2 A:PEO576 2.8 32.9 1.0 CD2 A:HIS411 2.9 27.2 1.0 CE1 A:HIS411 3.0 28.8 1.0 C4B A:HEA560 3.0 39.0 1.0 C1A A:HEA560 3.0 34.6 1.0 C4D A:HEA560 3.0 37.5 1.0 C1C A:HEA560 3.1 36.9 1.0 C4A A:HEA560 3.1 34.9 1.0 C1B A:HEA560 3.1 39.4 1.0 C1D A:HEA560 3.1 42.8 1.0 C4C A:HEA560 3.2 44.5 1.0 CHA A:HEA560 3.4 36.2 1.0 CHC A:HEA560 3.4 33.6 1.0 CHD A:HEA560 3.6 44.9 1.0 CHB A:HEA560 3.7 35.5 1.0 ND1 A:HIS411 4.1 23.8 1.0 CG A:HIS411 4.1 23.5 1.0 C3B A:HEA560 4.3 43.8 1.0 C3D A:HEA560 4.3 40.9 1.0 C2A A:HEA560 4.4 39.6 1.0 C3A A:HEA560 4.4 36.6 1.0 C2B A:HEA560 4.4 39.9 1.0 C2C A:HEA560 4.4 45.7 1.0 C2D A:HEA560 4.4 40.5 1.0 C3C A:HEA560 4.5 44.3 1.0 CU A:CU1561 4.6 43.4 1.0 CE1 A:HIS326 5.0 38.1 1.0

J.Koepke, E.Olkhova, H.Angerer, H.Muller, G.Peng, H.Michel. High Resolution Crystal Structure of Paracoccus Denitrificans Cytochrome C Oxidase: New Insights Into the Active Site and the Proton Transfer Pathways Biochim.Biophys.Acta V.1787 635 2009.
ISSN: ISSN 0006-3002
PubMed: 19374884
DOI: 10.1016/J.BBABIO.2009.04.003