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Iron in PDB 8ijn: 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:
7.1.1.9;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase in the Nitric Oxide-Bound Fully Reduced State at 100 K, PDB code: 8ijn was solved by T.Tsukihara, A.Shimada, K.Muramoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.37 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.289, 208.358, 177.916, 90, 90, 90
R / Rfree (%) 16.9 / 19.2

Other elements in 8ijn:

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:

Sodium (Na) 2 atoms
Zinc (Zn) 2 atoms
Magnesium (Mg) 2 atoms
Copper (Cu) 6 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 8ijn). 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: 8ijn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 8ijn

Go back to Iron Binding Sites List in 8ijn
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:Fe601

b:22.0
occ:1.00
 FE A:HEA601 0.0 22.0 1.0
NE2 A:HIS378 2.0 22.0 1.0
ND A:HEA601 2.0 22.2 1.0
NE2 A:HIS61 2.0 22.0 1.0
NB A:HEA601 2.0 23.9 1.0
NA A:HEA601 2.0 20.7 1.0
NC A:HEA601 2.0 19.8 1.0
CE1 A:HIS378 2.9 24.5 1.0
CD2 A:HIS61 3.0 25.0 1.0
C1D A:HEA601 3.0 22.9 1.0
C4C A:HEA601 3.0 20.9 1.0
CE1 A:HIS61 3.0 22.9 1.0
C4A A:HEA601 3.0 21.2 1.0
C1B A:HEA601 3.0 21.7 1.0
CD2 A:HIS378 3.1 25.1 1.0
C1A A:HEA601 3.1 24.6 1.0
C4D A:HEA601 3.1 21.7 1.0
C1C A:HEA601 3.1 23.7 1.0
C4B A:HEA601 3.1 19.9 1.0
CHD A:HEA601 3.4 19.9 1.0
CHB A:HEA601 3.4 19.0 1.0
CHA A:HEA601 3.5 20.0 1.0
CHC A:HEA601 3.5 19.2 1.0
ND1 A:HIS378 4.1 22.9 1.0
ND1 A:HIS61 4.1 21.3 1.0
CG A:HIS61 4.1 22.4 1.0
CG A:HIS378 4.2 24.5 1.0
C2D A:HEA601 4.2 22.9 1.0
C2A A:HEA601 4.3 19.6 1.0
C3A A:HEA601 4.3 18.6 1.0
C3D A:HEA601 4.3 21.3 1.0
C3B A:HEA601 4.3 19.9 1.0
C3C A:HEA601 4.3 20.0 1.0
C2C A:HEA601 4.3 19.1 1.0
C2B A:HEA601 4.3 23.9 1.0
OG A:SER382 4.7 27.7 0.6
CE2 A:PHE377 4.9 24.6 1.0

Iron binding site 2 out of 4 in 8ijn

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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:Fe602

b:21.6
occ:1.00
 FE A:HEA602 0.0 21.6 1.0
N A:NO603 1.7 20.9 1.0
ND A:HEA602 2.0 21.0 1.0
NB A:HEA602 2.0 22.3 1.0
NC A:HEA602 2.0 19.9 1.0
NA A:HEA602 2.0 19.7 1.0
NE2 A:HIS376 2.1 22.1 1.0
O A:NO603 2.7 25.9 1.0
C4D A:HEA602 3.0 19.3 1.0
C1A A:HEA602 3.0 21.1 1.0
C4C A:HEA602 3.0 17.6 1.0
C4A A:HEA602 3.0 19.6 1.0
C4B A:HEA602 3.0 22.2 1.0
C1D A:HEA602 3.0 19.5 1.0
C1B A:HEA602 3.0 19.3 1.0
C1C A:HEA602 3.0 21.8 1.0
CE1 A:HIS376 3.1 24.0 1.0
CD2 A:HIS376 3.2 20.9 1.0
CHC A:HEA602 3.4 20.3 1.0
CHA A:HEA602 3.4 18.1 1.0
CHD A:HEA602 3.5 19.0 1.0
CHB A:HEA602 3.5 19.5 1.0
C2A A:HEA602 4.2 21.3 1.0
C3A A:HEA602 4.2 18.0 1.0
C3D A:HEA602 4.2 21.9 1.0
C2D A:HEA602 4.2 21.6 1.0
C2C A:HEA602 4.2 19.5 1.0
ND1 A:HIS376 4.3 23.8 1.0
C3B A:HEA602 4.3 20.9 1.0
C2B A:HEA602 4.3 21.8 1.0
C3C A:HEA602 4.3 17.1 1.0
CG A:HIS376 4.3 22.9 1.0
CG2 A:VAL380 4.9 20.1 0.6
CG2 A:VAL243 4.9 19.9 1.0
CU A:CU604 5.0 22.3 1.0

Iron binding site 3 out of 4 in 8ijn

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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:Fe601

b:26.6
occ:1.00
 FE N:HEA601 0.0 26.6 1.0
NE2 N:HIS378 2.0 29.8 1.0
NC N:HEA601 2.0 25.6 1.0
NB N:HEA601 2.0 27.0 1.0
NE2 N:HIS61 2.0 26.1 1.0
NA N:HEA601 2.0 28.9 1.0
ND N:HEA601 2.0 25.2 1.0
CE1 N:HIS378 2.9 29.6 1.0
CE1 N:HIS61 3.0 29.4 1.0
C4A N:HEA601 3.0 25.3 1.0
C1B N:HEA601 3.0 27.0 1.0
CD2 N:HIS61 3.0 25.3 1.0
C4C N:HEA601 3.0 25.9 1.0
C4B N:HEA601 3.0 21.6 1.0
C4D N:HEA601 3.0 24.3 1.0
C1A N:HEA601 3.0 27.4 1.0
C1D N:HEA601 3.1 23.3 1.0
C1C N:HEA601 3.1 28.8 1.0
CD2 N:HIS378 3.1 27.1 1.0
CHB N:HEA601 3.4 25.8 1.0
CHD N:HEA601 3.5 25.3 1.0
CHC N:HEA601 3.5 24.1 1.0
CHA N:HEA601 3.5 24.1 1.0
ND1 N:HIS378 4.1 26.2 1.0
ND1 N:HIS61 4.1 29.0 1.0
CG N:HIS378 4.2 30.6 1.0
CG N:HIS61 4.2 30.3 1.0
C2A N:HEA601 4.2 25.7 1.0
C3A N:HEA601 4.2 24.8 1.0
C3B N:HEA601 4.2 27.5 1.0
C2B N:HEA601 4.2 23.2 1.0
C3C N:HEA601 4.3 24.0 1.0
C2C N:HEA601 4.3 29.4 1.0
C2D N:HEA601 4.3 28.2 1.0
C3D N:HEA601 4.3 25.8 1.0
OG N:SER382 4.6 38.2 0.6
CE2 N:PHE377 4.9 27.6 1.0

Iron binding site 4 out of 4 in 8ijn

Go back to Iron Binding Sites List in 8ijn
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:Fe602

b:25.0
occ:1.00
 FE N:HEA602 0.0 25.0 1.0
N N:NO603 1.7 27.7 1.0
NC N:HEA602 2.0 22.7 1.0
NA N:HEA602 2.0 24.6 1.0
ND N:HEA602 2.0 24.2 1.0
NB N:HEA602 2.0 23.9 1.0
NE2 N:HIS376 2.1 23.9 1.0
O N:NO603 2.7 26.9 1.0
C4A N:HEA602 3.0 23.5 1.0
C1A N:HEA602 3.0 29.1 1.0
C4D N:HEA602 3.0 25.1 1.0
C1C N:HEA602 3.0 26.0 1.0
C4C N:HEA602 3.0 24.2 1.0
C1D N:HEA602 3.0 23.4 1.0
C1B N:HEA602 3.1 22.4 1.0
C4B N:HEA602 3.1 21.0 1.0
CD2 N:HIS376 3.1 25.2 1.0
CE1 N:HIS376 3.1 30.7 1.0
CHB N:HEA602 3.4 23.5 1.0
CHA N:HEA602 3.4 24.6 1.0
CHC N:HEA602 3.5 23.3 1.0
CHD N:HEA602 3.5 23.0 1.0
C3A N:HEA602 4.2 26.9 1.0
C3D N:HEA602 4.2 24.4 1.0
C2A N:HEA602 4.2 23.2 1.0
C3C N:HEA602 4.2 24.1 1.0
C2D N:HEA602 4.2 23.2 1.0
C2C N:HEA602 4.2 26.6 1.0
C3B N:HEA602 4.3 22.9 1.0
ND1 N:HIS376 4.3 28.5 1.0
C2B N:HEA602 4.3 22.5 1.0
CG N:HIS376 4.3 27.0 1.0
CG2 N:VAL380 4.8 27.9 0.6
CG2 N:VAL243 4.9 22.9 1.0
CU N:CU604 5.0 24.8 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: ESSN 1091-6490
PubMed: 20385840
DOI: 10.1073/PNAS.0910410107
Page generated: Sat Aug 10 05:54:54 2024

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