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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 Dec 13 15:00:49 2020

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