Atomistry » Iron » PDB 3ae6-3arj » 3ag1
Atomistry »
  Iron »
    PDB 3ae6-3arj »
      3ag1 »

Iron in PDB 3ag1: Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K, PDB code: 3ag1 was solved by K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, 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 (°) 189.493, 210.887, 178.301, 90.00, 90.00, 90.00
R / Rfree (%) 16.2 / 19.2

Other elements in 3ag1:

The structure of Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K 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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K (pdb code 3ag1). 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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K, PDB code: 3ag1:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3ag1

Go back to Iron Binding Sites List in 3ag1
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K


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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:38.0
occ:1.00
 FE A:HEA515 0.0 38.0 1.0
NE2 A:HIS61 2.0 36.4 1.0
NB A:HEA515 2.0 41.1 1.0
NE2 A:HIS378 2.0 38.1 1.0
ND A:HEA515 2.0 39.0 1.0
NC A:HEA515 2.1 42.1 1.0
NA A:HEA515 2.1 37.9 1.0
CE1 A:HIS378 2.9 41.1 1.0
CE1 A:HIS61 3.0 39.9 1.0
CD2 A:HIS61 3.0 37.9 1.0
C4B A:HEA515 3.0 40.2 1.0
C4A A:HEA515 3.0 38.6 1.0
C1D A:HEA515 3.0 42.0 1.0
C1B A:HEA515 3.0 43.6 1.0
C4D A:HEA515 3.1 37.8 1.0
C4C A:HEA515 3.1 43.0 1.0
CD2 A:HIS378 3.1 39.4 1.0
C1C A:HEA515 3.1 39.2 1.0
C1A A:HEA515 3.1 35.9 1.0
CHB A:HEA515 3.4 35.1 1.0
CHC A:HEA515 3.4 35.0 1.0
CHD A:HEA515 3.5 35.8 1.0
CHA A:HEA515 3.6 36.6 1.0
ND1 A:HIS378 4.1 38.8 1.0
ND1 A:HIS61 4.1 39.1 1.0
CG A:HIS61 4.1 36.0 1.0
CG A:HIS378 4.2 43.4 1.0
C3A A:HEA515 4.3 39.1 1.0
C3B A:HEA515 4.3 38.8 1.0
C2D A:HEA515 4.3 37.9 1.0
C3D A:HEA515 4.3 41.3 1.0
C2A A:HEA515 4.3 38.0 1.0
C2B A:HEA515 4.3 39.2 1.0
C3C A:HEA515 4.3 37.4 1.0
C2C A:HEA515 4.3 45.1 1.0
CE2 A:PHE377 5.0 39.2 1.0

Iron binding site 2 out of 4 in 3ag1

Go back to Iron Binding Sites List in 3ag1
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K


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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:40.6
occ:1.00
 FE A:HEA516 0.0 40.6 1.0
C A:CMO520 1.8 39.6 1.0
NB A:HEA516 2.0 39.2 1.0
ND A:HEA516 2.0 41.2 1.0
NE2 A:HIS376 2.1 41.4 1.0
NC A:HEA516 2.1 40.4 1.0
NA A:HEA516 2.2 40.6 1.0
O A:CMO520 3.0 41.8 1.0
C1B A:HEA516 3.0 43.1 1.0
C4D A:HEA516 3.0 37.7 1.0
C4B A:HEA516 3.0 38.6 1.0
C1D A:HEA516 3.0 39.5 1.0
CE1 A:HIS376 3.1 37.3 1.0
CD2 A:HIS376 3.1 40.3 1.0
C4C A:HEA516 3.1 40.3 1.0
C1C A:HEA516 3.1 38.0 1.0
C4A A:HEA516 3.1 41.6 1.0
C1A A:HEA516 3.2 39.8 1.0
CHD A:HEA516 3.5 36.8 1.0
CHB A:HEA516 3.5 37.2 1.0
CHC A:HEA516 3.5 35.3 1.0
CHA A:HEA516 3.5 33.0 1.0
ND1 A:HIS376 4.2 41.8 1.0
C2B A:HEA516 4.2 42.8 1.0
C3B A:HEA516 4.2 41.5 1.0
C3D A:HEA516 4.2 41.7 1.0
C2D A:HEA516 4.2 34.9 1.0
CG A:HIS376 4.2 40.0 1.0
C3C A:HEA516 4.3 41.6 1.0
C2C A:HEA516 4.3 41.3 1.0
C3A A:HEA516 4.3 39.3 1.0
C2A A:HEA516 4.4 39.0 1.0

Iron binding site 3 out of 4 in 3ag1

Go back to Iron Binding Sites List in 3ag1
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K


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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:49.5
occ:1.00
 FE N:HEA515 0.0 49.5 1.0
NE2 N:HIS61 1.9 52.2 1.0
NC N:HEA515 2.0 54.8 1.0
NB N:HEA515 2.0 54.4 1.0
NA N:HEA515 2.1 52.6 1.0
NE2 N:HIS378 2.1 49.1 1.0
ND N:HEA515 2.1 52.2 1.0
CD2 N:HIS61 2.8 50.3 1.0
C4C N:HEA515 2.9 50.5 1.0
C4A N:HEA515 3.0 48.5 1.0
C1B N:HEA515 3.0 52.5 1.0
CE1 N:HIS378 3.0 48.7 1.0
CE1 N:HIS61 3.0 54.9 1.0
C1C N:HEA515 3.1 53.8 1.0
C4B N:HEA515 3.1 53.5 1.0
C1D N:HEA515 3.1 53.5 1.0
C1A N:HEA515 3.1 51.3 1.0
C4D N:HEA515 3.2 50.0 1.0
CD2 N:HIS378 3.2 48.0 1.0
CHD N:HEA515 3.4 51.6 1.0
CHB N:HEA515 3.4 50.4 1.0
CHC N:HEA515 3.6 48.8 1.0
CHA N:HEA515 3.6 52.4 1.0
CG N:HIS61 4.0 50.7 1.0
ND1 N:HIS61 4.1 53.2 1.0
C3C N:HEA515 4.1 52.3 1.0
ND1 N:HIS378 4.2 48.5 1.0
C3A N:HEA515 4.2 48.7 1.0
C2C N:HEA515 4.2 50.3 1.0
C2B N:HEA515 4.3 53.3 1.0
C3B N:HEA515 4.3 52.3 1.0
CG N:HIS378 4.3 46.2 1.0
C2A N:HEA515 4.3 51.3 1.0
C2D N:HEA515 4.3 54.2 1.0
C3D N:HEA515 4.4 47.5 1.0
CE2 N:PHE377 4.9 48.8 1.0

Iron binding site 4 out of 4 in 3ag1

Go back to Iron Binding Sites List in 3ag1
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Carbon Monoxide-Bound Fully Reduced State at 280 K


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 in the Carbon Monoxide-Bound Fully Reduced State at 280 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:48.6
occ:1.00
 FE N:HEA516 0.0 48.6 1.0
C N:CMO520 1.7 47.9 1.0
NB N:HEA516 2.0 43.8 1.0
ND N:HEA516 2.0 47.0 1.0
NC N:HEA516 2.0 48.8 1.0
NA N:HEA516 2.1 46.7 1.0
NE2 N:HIS376 2.1 48.1 1.0
O N:CMO520 2.8 48.4 1.0
C1B N:HEA516 3.0 49.8 1.0
C4D N:HEA516 3.0 45.4 1.0
C4C N:HEA516 3.0 48.4 1.0
C1D N:HEA516 3.0 48.3 1.0
CD2 N:HIS376 3.0 48.4 1.0
C4B N:HEA516 3.0 44.7 1.0
C1A N:HEA516 3.1 50.5 1.0
C1C N:HEA516 3.1 46.9 1.0
C4A N:HEA516 3.1 49.0 1.0
CE1 N:HIS376 3.2 44.8 1.0
CHD N:HEA516 3.4 45.5 1.0
CHA N:HEA516 3.4 45.3 1.0
CHB N:HEA516 3.5 47.8 1.0
CHC N:HEA516 3.6 42.4 1.0
C3D N:HEA516 4.2 48.3 1.0
C2B N:HEA516 4.2 46.9 1.0
C3C N:HEA516 4.2 47.3 1.0
C3B N:HEA516 4.2 46.2 1.0
CG N:HIS376 4.2 46.0 1.0
C2D N:HEA516 4.2 47.8 1.0
ND1 N:HIS376 4.3 47.5 1.0
C2C N:HEA516 4.3 45.4 1.0
C3A N:HEA516 4.3 48.0 1.0
C2A N:HEA516 4.3 48.6 1.0

Reference:

K.Muramoto, K.Ohta, K.Shinzawa-Itoh, K.Kanda, M.Taniguchi, H.Nabekura, E.Yamashita, T.Tsukihara, S.Yoshikawa. Bovine Cytochrome C Oxidase Structures Enable O2 Reduction with Minimization of Reactive Oxygens and Provide A Proton-Pumping Gate Proc.Natl.Acad.Sci.Usa V. 107 7740 2010.
ISSN: ISSN 0027-8424
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Sun Aug 4 07:08:30 2024

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy