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Iron in PDB 3ag3: Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K

Enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 3ag3 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 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.289, 208.358, 177.916, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 20.3

Other elements in 3ag3:

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 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 Nitric Oxide-Bound Fully Reduced State at 100 K (pdb code 3ag3). 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 Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 3ag3:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3ag3

Go back to Iron Binding Sites List in 3ag3
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:22.9
occ:1.00
FE A:HEA515 0.0 22.9 1.0
NE2 A:HIS378 2.0 19.3 1.0
ND A:HEA515 2.0 23.6 1.0
NA A:HEA515 2.0 20.6 1.0
NE2 A:HIS61 2.0 19.0 1.0
NB A:HEA515 2.1 23.6 1.0
NC A:HEA515 2.1 21.5 1.0
CE1 A:HIS378 2.9 24.6 1.0
CE1 A:HIS61 3.0 20.8 1.0
C4A A:HEA515 3.0 21.5 1.0
C4D A:HEA515 3.0 23.2 1.0
C1A A:HEA515 3.0 21.7 1.0
C4C A:HEA515 3.0 22.8 1.0
C1D A:HEA515 3.1 23.2 1.0
C1B A:HEA515 3.1 21.4 1.0
CD2 A:HIS61 3.1 26.8 1.0
C1C A:HEA515 3.1 23.1 1.0
CD2 A:HIS378 3.1 25.9 1.0
C4B A:HEA515 3.1 21.4 1.0
CHD A:HEA515 3.4 22.0 1.0
CHB A:HEA515 3.4 21.4 1.0
CHA A:HEA515 3.4 20.5 1.0
CHC A:HEA515 3.5 19.9 1.0
ND1 A:HIS378 4.0 22.2 1.0
ND1 A:HIS61 4.1 21.2 1.0
CG A:HIS378 4.1 22.1 1.0
CG A:HIS61 4.2 20.6 1.0
C2A A:HEA515 4.2 21.3 1.0
C3A A:HEA515 4.3 19.9 1.0
C3B A:HEA515 4.3 21.0 1.0
C2D A:HEA515 4.3 22.1 1.0
C3D A:HEA515 4.3 23.1 1.0
C3C A:HEA515 4.3 21.1 1.0
C2B A:HEA515 4.3 21.1 1.0
C2C A:HEA515 4.3 20.1 1.0
OG A:SER382 4.7 28.2 0.6
CE2 A:PHE377 4.9 22.1 1.0

Iron binding site 2 out of 4 in 3ag3

Go back to Iron Binding Sites List in 3ag3
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:23.1
occ:1.00
FE A:HEA516 0.0 23.1 1.0
N A:NO520 1.8 25.8 1.0
ND A:HEA516 1.9 21.0 1.0
NB A:HEA516 1.9 21.8 1.0
NA A:HEA516 2.0 20.0 1.0
NC A:HEA516 2.0 19.4 1.0
NE2 A:HIS376 2.3 24.9 1.0
O A:NO520 2.7 24.9 1.0
C4D A:HEA516 2.9 21.3 1.0
C4B A:HEA516 3.0 24.9 1.0
C1A A:HEA516 3.0 20.3 1.0
C1B A:HEA516 3.0 21.4 1.0
C1D A:HEA516 3.0 23.2 1.0
C4A A:HEA516 3.0 20.8 1.0
C4C A:HEA516 3.0 23.3 1.0
C1C A:HEA516 3.1 23.3 1.0
CE1 A:HIS376 3.3 25.3 1.0
CD2 A:HIS376 3.3 23.2 1.0
CHC A:HEA516 3.4 21.4 1.0
CHD A:HEA516 3.4 20.8 1.0
CHA A:HEA516 3.4 20.8 1.0
CHB A:HEA516 3.5 21.1 1.0
C2D A:HEA516 4.2 21.8 1.0
C3D A:HEA516 4.2 22.8 1.0
C2A A:HEA516 4.2 22.0 1.0
C3A A:HEA516 4.2 20.7 1.0
C3B A:HEA516 4.3 20.5 1.0
C2B A:HEA516 4.3 22.1 1.0
C2C A:HEA516 4.3 20.0 1.0
C3C A:HEA516 4.3 20.2 1.0
ND1 A:HIS376 4.4 23.8 1.0
CG A:HIS376 4.4 23.9 1.0
CG2 A:VAL243 4.8 21.4 1.0
CG2 A:VAL380 4.9 22.2 0.6
CU A:CU517 4.9 24.6 1.0

Iron binding site 3 out of 4 in 3ag3

Go back to Iron Binding Sites List in 3ag3
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:26.6
occ:1.00
FE N:HEA515 0.0 26.6 1.0
NE2 N:HIS61 2.0 22.7 1.0
NE2 N:HIS378 2.0 26.3 1.0
NB N:HEA515 2.0 26.0 1.0
NA N:HEA515 2.0 28.0 1.0
NC N:HEA515 2.0 26.3 1.0
ND N:HEA515 2.1 26.1 1.0
CE1 N:HIS378 2.9 27.1 1.0
CE1 N:HIS61 3.0 26.6 1.0
CD2 N:HIS61 3.0 26.4 1.0
C4A N:HEA515 3.0 24.3 1.0
C4B N:HEA515 3.0 24.5 1.0
C1C N:HEA515 3.0 25.9 1.0
C1A N:HEA515 3.0 25.5 1.0
C4D N:HEA515 3.0 23.6 1.0
C4C N:HEA515 3.0 24.6 1.0
C1B N:HEA515 3.0 27.1 1.0
CD2 N:HIS378 3.1 28.2 1.0
C1D N:HEA515 3.1 24.4 1.0
CHB N:HEA515 3.4 25.7 1.0
CHA N:HEA515 3.5 23.9 1.0
CHC N:HEA515 3.5 25.8 1.0
CHD N:HEA515 3.5 25.8 1.0
ND1 N:HIS378 4.1 26.7 1.0
ND1 N:HIS61 4.1 25.6 1.0
CG N:HIS61 4.1 24.1 1.0
CG N:HIS378 4.2 24.0 1.0
C2B N:HEA515 4.2 21.9 1.0
C2A N:HEA515 4.2 25.1 1.0
C3A N:HEA515 4.2 22.6 1.0
C3B N:HEA515 4.2 26.4 1.0
C2C N:HEA515 4.3 26.6 1.0
C3C N:HEA515 4.3 24.0 1.0
C2D N:HEA515 4.3 26.8 1.0
C3D N:HEA515 4.3 26.4 1.0
OG N:SER382 4.7 36.5 0.6
CE2 N:PHE377 4.9 25.6 1.0

Iron binding site 4 out of 4 in 3ag3

Go back to Iron Binding Sites List in 3ag3
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 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 Nitric Oxide-Bound Fully Reduced State at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:26.2
occ:1.00
FE N:HEA516 0.0 26.2 1.0
N N:NO520 1.7 32.0 1.0
ND N:HEA516 1.9 24.2 1.0
NC N:HEA516 2.0 23.4 1.0
NA N:HEA516 2.0 25.8 1.0
NB N:HEA516 2.0 23.0 1.0
NE2 N:HIS376 2.3 27.9 1.0
O N:NO520 2.7 26.3 1.0
C4D N:HEA516 3.0 26.8 1.0
C1A N:HEA516 3.0 27.4 1.0
C1D N:HEA516 3.0 28.4 1.0
C1C N:HEA516 3.0 26.1 1.0
C4C N:HEA516 3.0 26.6 1.0
C4A N:HEA516 3.0 24.2 1.0
C4B N:HEA516 3.1 24.6 1.0
C1B N:HEA516 3.1 25.4 1.0
CD2 N:HIS376 3.2 26.6 1.0
CE1 N:HIS376 3.3 32.8 1.0
CHA N:HEA516 3.4 24.6 1.0
CHB N:HEA516 3.5 25.2 1.0
CHC N:HEA516 3.5 26.4 1.0
CHD N:HEA516 3.6 25.6 1.0
C3D N:HEA516 4.2 27.6 1.0
C2D N:HEA516 4.2 26.1 1.0
C2C N:HEA516 4.2 25.7 1.0
C3C N:HEA516 4.2 25.4 1.0
C3A N:HEA516 4.2 28.4 1.0
C2A N:HEA516 4.3 24.9 1.0
C3B N:HEA516 4.3 23.0 1.0
C2B N:HEA516 4.3 22.9 1.0
CG N:HIS376 4.4 27.3 1.0
ND1 N:HIS376 4.4 28.7 1.0
CG2 N:VAL380 4.8 30.7 0.6
CG2 N:VAL243 4.9 24.3 1.0
CU N:CU517 4.9 26.7 1.0
CE1 N:HIS240 5.0 25.0 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 15:00:50 2020

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