Atomistry » Iron » PDB 3a0g-3ae5 » 3abk
Atomistry »
  Iron »
    PDB 3a0g-3ae5 »
      3abk »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy