Iron in PDB 2dys: Bovine Heart Cytochrome C Oxidase Modified By Dccd

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase Modified By Dccd:
1.9.3.1;

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd, PDB code: 2dys was solved by K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, T.Kurauchi, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.00 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	184.130, 207.232, 178.242, 90.00, 90.00, 90.00
R / Rfree (%)	19.7 / 24.2

The structure of Bovine Heart Cytochrome C Oxidase Modified By Dccd also contains other interesting chemical elements:

Magnesium	(Mg)	2 atoms
Zinc	(Zn)	2 atoms
Copper	(Cu)	6 atoms
Sodium	(Na)	2 atoms

The binding sites of Iron atom in the Bovine Heart Cytochrome C Oxidase Modified By Dccd (pdb code 2dys). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Bovine Heart Cytochrome C Oxidase Modified By Dccd, PDB code: 2dys:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Bovine Heart Cytochrome C Oxidase Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe604 b:20.3 occ:1.00 FE A:HEA604 0.0 20.3 1.0 NE2 A:HIS378 1.9 20.3 1.0 ND A:HEA604 1.9 25.1 1.0 NE2 A:HIS61 1.9 17.7 1.0 NB A:HEA604 2.0 20.9 1.0 NA A:HEA604 2.1 27.9 1.0 NC A:HEA604 2.1 29.6 1.0 CE1 A:HIS378 2.7 22.0 1.0 CE1 A:HIS61 2.9 23.0 1.0 C4D A:HEA604 3.0 28.7 1.0 C1D A:HEA604 3.0 26.9 1.0 CD2 A:HIS61 3.0 27.9 1.0 C1B A:HEA604 3.0 26.9 1.0 C4B A:HEA604 3.0 24.7 1.0 C1A A:HEA604 3.0 25.4 1.0 CD2 A:HIS378 3.1 26.7 1.0 C4A A:HEA604 3.1 25.4 1.0 C1C A:HEA604 3.1 23.5 1.0 C4C A:HEA604 3.1 27.1 1.0 CHA A:HEA604 3.4 25.7 1.0 CHC A:HEA604 3.4 22.6 1.0 CHD A:HEA604 3.4 22.7 1.0 CHB A:HEA604 3.4 24.7 1.0 ND1 A:HIS378 3.9 17.3 1.0 ND1 A:HIS61 4.1 18.6 1.0 CG A:HIS378 4.1 22.1 1.0 CG A:HIS61 4.1 23.0 1.0 C3D A:HEA604 4.2 26.9 1.0 C2D A:HEA604 4.2 21.1 1.0 C2A A:HEA604 4.2 29.2 1.0 C2B A:HEA604 4.3 21.5 1.0 C3B A:HEA604 4.3 22.8 1.0 C3A A:HEA604 4.3 27.2 1.0 C3C A:HEA604 4.4 24.3 1.0 C2C A:HEA604 4.4 30.6 1.0 CE2 A:PHE377 4.8 20.3 1.0

Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Bovine Heart Cytochrome C Oxidase Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ A:Fe605 b:23.2 occ:1.00 FE A:HEA605 0.0 23.2 1.0 NB A:HEA605 1.9 24.1 1.0 ND A:HEA605 1.9 29.5 1.0 NA A:HEA605 1.9 27.3 1.0 NE2 A:HIS376 2.1 17.7 1.0 NC A:HEA605 2.1 24.5 1.0 C4B A:HEA605 2.9 30.1 1.0 C4D A:HEA605 2.9 28.1 1.0 C1B A:HEA605 2.9 27.2 1.0 CE1 A:HIS376 3.0 26.4 1.0 C1D A:HEA605 3.0 29.2 1.0 C1A A:HEA605 3.0 18.4 1.0 C4A A:HEA605 3.0 27.4 1.0 C1C A:HEA605 3.1 23.8 1.0 C4C A:HEA605 3.2 22.6 1.0 CD2 A:HIS376 3.3 23.5 1.0 CHB A:HEA605 3.4 30.0 1.0 CHA A:HEA605 3.4 21.6 1.0 CHC A:HEA605 3.4 26.4 1.0 CHD A:HEA605 3.5 24.1 1.0 C3D A:HEA605 4.1 23.6 1.0 C2B A:HEA605 4.2 24.0 1.0 C2D A:HEA605 4.2 24.2 1.0 ND1 A:HIS376 4.2 22.7 1.0 C3B A:HEA605 4.2 27.4 1.0 C2A A:HEA605 4.2 26.1 1.0 C3A A:HEA605 4.2 26.0 1.0 CG A:HIS376 4.4 23.1 1.0 C2C A:HEA605 4.4 26.9 1.0 C3C A:HEA605 4.4 29.1 1.0 CU A:CU601 4.6 23.4 1.0 CG2 A:VAL243 5.0 14.8 1.0

Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Bovine Heart Cytochrome C Oxidase Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe604 b:31.8 occ:1.00 FE N:HEA604 0.0 31.8 1.0 ND N:HEA604 1.9 29.9 1.0 NE2 N:HIS61 1.9 29.2 1.0 NA N:HEA604 2.0 32.7 1.0 NE2 N:HIS378 2.0 21.5 1.0 NB N:HEA604 2.0 29.3 1.0 NC N:HEA604 2.1 33.0 1.0 CE1 N:HIS378 2.8 26.6 1.0 C4D N:HEA604 2.9 32.4 1.0 CD2 N:HIS61 2.9 30.8 1.0 C1D N:HEA604 3.0 31.6 1.0 C1A N:HEA604 3.0 32.3 1.0 CE1 N:HIS61 3.0 36.6 1.0 C1B N:HEA604 3.0 32.5 1.0 C4B N:HEA604 3.1 31.0 1.0 C4A N:HEA604 3.1 32.8 1.0 C4C N:HEA604 3.1 35.1 1.0 C1C N:HEA604 3.1 33.3 1.0 CD2 N:HIS378 3.2 24.2 1.0 CHA N:HEA604 3.3 32.5 1.0 CHD N:HEA604 3.5 29.7 1.0 CHC N:HEA604 3.5 30.1 1.0 CHB N:HEA604 3.5 28.7 1.0 ND1 N:HIS378 4.0 24.2 1.0 CG N:HIS61 4.1 32.8 1.0 ND1 N:HIS61 4.1 24.5 1.0 C3D N:HEA604 4.2 28.6 1.0 C2A N:HEA604 4.2 33.5 1.0 CG N:HIS378 4.2 24.6 1.0 C2D N:HEA604 4.2 29.8 1.0 C3A N:HEA604 4.3 31.2 1.0 C2B N:HEA604 4.3 35.7 1.0 C3B N:HEA604 4.3 34.4 1.0 C3C N:HEA604 4.4 33.9 1.0 C2C N:HEA604 4.4 35.7 1.0 CE2 N:PHE377 4.8 20.3 1.0

Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase Modified By Dccd


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Bovine Heart Cytochrome C Oxidase Modified By Dccd within 5.0Å range: probe atom residue distance (Å) B Occ N:Fe605 b:27.0 occ:1.00 FE N:HEA605 0.0 27.0 1.0 ND N:HEA605 1.8 27.5 1.0 NB N:HEA605 1.9 27.0 1.0 NA N:HEA605 2.0 30.9 1.0 NC N:HEA605 2.1 28.2 1.0 NE2 N:HIS376 2.2 31.2 1.0 C4D N:HEA605 2.9 26.6 1.0 C1D N:HEA605 2.9 31.9 1.0 C4B N:HEA605 3.0 29.2 1.0 C1B N:HEA605 3.0 27.8 1.0 C1A N:HEA605 3.0 29.3 1.0 C4A N:HEA605 3.0 28.0 1.0 C1C N:HEA605 3.1 28.4 1.0 C4C N:HEA605 3.1 30.2 1.0 CD2 N:HIS376 3.2 32.3 1.0 CE1 N:HIS376 3.2 31.0 1.0 CHA N:HEA605 3.3 28.6 1.0 CHC N:HEA605 3.4 27.8 1.0 CHB N:HEA605 3.4 28.9 1.0 CHD N:HEA605 3.4 27.0 1.0 C3D N:HEA605 4.1 27.8 1.0 C2D N:HEA605 4.1 26.4 1.0 C2A N:HEA605 4.2 28.1 1.0 C2B N:HEA605 4.2 25.6 1.0 C3B N:HEA605 4.2 27.1 1.0 C3A N:HEA605 4.3 25.4 1.0 ND1 N:HIS376 4.3 31.5 1.0 CG N:HIS376 4.3 28.8 1.0 C2C N:HEA605 4.4 30.6 1.0 C3C N:HEA605 4.4 28.5 1.0 CU N:CU601 4.6 28.9 1.0 CG2 N:VAL243 5.0 22.5 1.0

K.Shinzawa-Itoh, H.Aoyama, K.Muramoto, H.Terada, T.Kurauchi, Y.Tadehara, A.Yamasaki, T.Sugimura, S.Kurono, K.Tsujimoto, T.Mizushima, E.Yamashita, T.Tsukihara, S.Yoshikawa. Structures and Physiological Roles of 13 Integral Lipids of Bovine Heart Cytochrome C Oxidase Embo J. V. 26 1713 2007.
ISSN: ISSN 0261-4189
PubMed: 17332748
DOI: 10.1038/SJ.EMBOJ.7601618