Atomistry » Iron » PDB 2d3y-2e1q » 2dys
Atomistry »
  Iron »
    PDB 2d3y-2e1q »
      2dys »

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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 2dys:

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

Iron Binding Sites:

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 2dys

Go back to Iron Binding Sites List in 2dys
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 2dys

Go back to Iron Binding Sites List in 2dys
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 2dys

Go back to Iron Binding Sites List in 2dys
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 2dys

Go back to Iron Binding Sites List in 2dys
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

Reference:

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
Page generated: Sat Aug 3 20:52:59 2024

Last articles

Cl in 3VBI
Cl in 3VBH
Cl in 3VBF
Cl in 3VAQ
Cl in 3VAS
Cl in 3VAV
Cl in 3VA9
Cl in 3V91
Cl in 3V90
Cl in 3V7J
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy