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Iron in PDB 3abk: Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)

Enzymatic activity of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)

All present enzymatic activity of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K):
1.9.3.1;

Protein crystallography data

The structure of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K), PDB code: 3abk was solved by K.Ohta, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.247, 207.944, 177.997, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 21.9

Other elements in 3abk:

The structure of Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K) 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 at the No-Bound Fully Reduced State (50K) (pdb code 3abk). 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 at the No-Bound Fully Reduced State (50K), PDB code: 3abk:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 3abk

Go back to Iron Binding Sites List in 3abk
Iron binding site 1 out of 4 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 at the No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe515

b:25.5
occ:1.00
 FE A:HEA515 0.0 25.5 1.0
NE2 A:HIS61 1.9 15.5 1.0
NE2 A:HIS378 1.9 15.5 1.0
NB A:HEA515 2.0 26.6 1.0
NC A:HEA515 2.1 27.8 1.0
ND A:HEA515 2.1 30.8 1.0
NA A:HEA515 2.1 25.5 1.0
CE1 A:HIS378 2.9 23.4 1.0
CE1 A:HIS61 2.9 24.8 1.0
CD2 A:HIS61 3.0 27.3 1.0
CD2 A:HIS378 3.0 26.0 1.0
C4C A:HEA515 3.1 30.5 1.0
C1B A:HEA515 3.1 28.9 1.0
C4A A:HEA515 3.1 27.7 1.0
C4D A:HEA515 3.1 31.4 1.0
C1A A:HEA515 3.1 25.8 1.0
C1D A:HEA515 3.1 33.9 1.0
C4B A:HEA515 3.1 25.9 1.0
C1C A:HEA515 3.1 29.5 1.0
CHA A:HEA515 3.4 23.1 1.0
CHB A:HEA515 3.4 24.0 1.0
CHD A:HEA515 3.4 26.7 1.0
CHC A:HEA515 3.5 24.6 1.0
ND1 A:HIS378 4.1 23.7 1.0
ND1 A:HIS61 4.1 20.7 1.0
CG A:HIS61 4.2 17.7 1.0
CG A:HIS378 4.2 21.1 1.0
C2A A:HEA515 4.3 22.5 1.0
C2B A:HEA515 4.3 30.6 1.0
C3A A:HEA515 4.3 24.6 1.0
C3B A:HEA515 4.3 30.4 1.0
C3C A:HEA515 4.3 28.4 1.0
C2D A:HEA515 4.3 28.1 1.0
C3D A:HEA515 4.3 25.6 1.0
C2C A:HEA515 4.3 25.9 1.0
OG A:SER382 4.7 30.2 0.5
CE2 A:PHE377 5.0 28.8 1.0

Iron binding site 2 out of 4 in 3abk

Go back to Iron Binding Sites List in 3abk
Iron binding site 2 out of 4 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 at the No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe516

b:27.4
occ:1.00
 FE A:HEA516 0.0 27.4 1.0
ND A:HEA516 1.9 18.5 1.0
NB A:HEA516 2.0 26.5 1.0
NC A:HEA516 2.0 23.9 1.0
NA A:HEA516 2.1 23.1 1.0
NE2 A:HIS376 2.2 29.6 1.0
N A:NO520 2.8 32.2 1.0
C4D A:HEA516 3.0 25.2 1.0
C4B A:HEA516 3.0 26.3 1.0
C1B A:HEA516 3.0 27.9 1.0
C1D A:HEA516 3.0 28.2 1.0
C4C A:HEA516 3.0 27.3 1.0
CE1 A:HIS376 3.0 28.8 1.0
C1A A:HEA516 3.1 25.7 1.0
C4A A:HEA516 3.1 24.4 1.0
C1C A:HEA516 3.1 29.1 1.0
CD2 A:HIS376 3.2 26.6 1.0
CHA A:HEA516 3.4 22.9 1.0
CHD A:HEA516 3.4 23.9 1.0
CHB A:HEA516 3.5 27.4 1.0
CHC A:HEA516 3.5 25.0 1.0
O A:NO520 3.7 36.3 1.0
C3D A:HEA516 4.2 22.5 1.0
ND1 A:HIS376 4.2 29.9 1.0
C2B A:HEA516 4.2 26.1 1.0
C3B A:HEA516 4.2 23.4 1.0
C2A A:HEA516 4.3 26.5 1.0
C2D A:HEA516 4.3 22.3 1.0
C3C A:HEA516 4.3 24.8 1.0
C3A A:HEA516 4.3 22.1 1.0
C2C A:HEA516 4.3 26.0 1.0
CG A:HIS376 4.3 30.6 1.0
CG2 A:VAL380 4.8 25.9 0.5
CU A:CU517 4.9 29.1 1.0
CG2 A:VAL243 4.9 27.6 1.0
CA A:GLY355 5.0 24.2 1.0

Iron binding site 3 out of 4 in 3abk

Go back to Iron Binding Sites List in 3abk
Iron binding site 3 out of 4 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 at the No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe515

b:33.6
occ:1.00
 FE N:HEA515 0.0 33.6 1.0
NE2 N:HIS61 2.0 33.2 1.0
NE2 N:HIS378 2.0 28.3 1.0
NB N:HEA515 2.1 35.3 1.0
NA N:HEA515 2.1 35.9 1.0
ND N:HEA515 2.1 35.3 1.0
NC N:HEA515 2.2 28.1 1.0
CD2 N:HIS378 2.9 31.9 1.0
CD2 N:HIS61 3.0 30.8 1.0
CE1 N:HIS61 3.0 33.9 1.0
C4B N:HEA515 3.0 39.4 1.0
C4A N:HEA515 3.1 31.4 1.0
CE1 N:HIS378 3.1 34.1 1.0
C1A N:HEA515 3.1 36.5 1.0
C1B N:HEA515 3.1 37.0 1.0
C4D N:HEA515 3.1 38.9 1.0
C4C N:HEA515 3.2 35.9 1.0
C1D N:HEA515 3.2 39.5 1.0
C1C N:HEA515 3.2 35.8 1.0
CHB N:HEA515 3.4 32.4 1.0
CHC N:HEA515 3.5 35.5 1.0
CHA N:HEA515 3.5 34.7 1.0
CHD N:HEA515 3.5 33.3 1.0
ND1 N:HIS61 4.1 32.6 1.0
CG N:HIS378 4.1 28.6 1.0
CG N:HIS61 4.1 33.9 1.0
ND1 N:HIS378 4.1 29.6 1.0
C3B N:HEA515 4.3 39.9 1.0
C2A N:HEA515 4.3 35.8 1.0
C3A N:HEA515 4.3 31.8 1.0
C2B N:HEA515 4.3 36.9 1.0
C3D N:HEA515 4.4 36.0 1.0
C2D N:HEA515 4.4 34.5 1.0
C3C N:HEA515 4.4 31.1 1.0
C2C N:HEA515 4.4 33.3 1.0
CE2 N:PHE377 4.9 29.6 1.0

Iron binding site 4 out of 4 in 3abk

Go back to Iron Binding Sites List in 3abk
Iron binding site 4 out of 4 in the Bovine Heart Cytochrome C Oxidase at the No-Bound Fully Reduced State (50K)


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 at the No-Bound Fully Reduced State (50K) within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe516

b:34.6
occ:1.00
 FE N:HEA516 0.0 34.6 1.0
ND N:HEA516 2.0 30.2 1.0
NA N:HEA516 2.0 33.0 1.0
NB N:HEA516 2.1 31.7 1.0
NC N:HEA516 2.1 31.1 1.0
NE2 N:HIS376 2.3 37.7 1.0
N N:NO520 2.7 39.5 1.0
C1A N:HEA516 3.0 31.7 1.0
C4D N:HEA516 3.0 33.4 1.0
C1B N:HEA516 3.0 33.3 1.0
C4A N:HEA516 3.1 27.6 1.0
C1D N:HEA516 3.1 34.1 1.0
C1C N:HEA516 3.1 31.4 1.0
C4B N:HEA516 3.1 29.4 1.0
C4C N:HEA516 3.1 31.0 1.0
CD2 N:HIS376 3.3 32.1 1.0
CE1 N:HIS376 3.3 40.8 1.0
CHA N:HEA516 3.4 32.9 1.0
CHB N:HEA516 3.4 33.2 1.0
CHC N:HEA516 3.5 32.6 1.0
CHD N:HEA516 3.6 33.2 1.0
O N:NO520 3.6 42.9 1.0
C3D N:HEA516 4.2 29.1 1.0
C2A N:HEA516 4.2 30.5 1.0
C3A N:HEA516 4.3 29.7 1.0
C2D N:HEA516 4.3 29.5 1.0
C2B N:HEA516 4.3 33.8 1.0
C3B N:HEA516 4.3 30.0 1.0
C2C N:HEA516 4.3 34.5 1.0
C3C N:HEA516 4.3 29.2 1.0
ND1 N:HIS376 4.4 34.6 1.0
CG N:HIS376 4.4 37.4 1.0
CG2 N:VAL380 4.6 29.7 0.5
CU N:CU517 4.9 35.7 1.0

Reference:

K.Ohta, K.Muramoto, K.Shinzawa-Itoh, E.Yamashita, S.Yoshikawa, T.Tsukihara. X-Ray Structure of the No-Bound Cu(B) in Bovine Cytochrome C Oxidase Acta Crystallogr.,Sect.F V. 66 251 2010.
ISSN: ESSN 1744-3091
PubMed: 20208153
DOI: 10.1107/S1744309109055109
Page generated: Sun Aug 4 06:45:58 2024

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