Atomistry » Iron » PDB 7xgy-7y9j » 7y44
Atomistry »
  Iron »
    PDB 7xgy-7y9j »
      7y44 »

Iron in PDB 7y44: Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution

Enzymatic activity of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution

All present enzymatic activity of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution:
7.1.1.9;

Protein crystallography data

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44 was solved by T.Tsukihara, K.Hirata, H.Ago, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 27.31 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 182.6, 204.51, 178.29, 90, 90, 90
R / Rfree (%) 18.5 / 22.7

Other elements in 7y44:

The structure of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution also contains other interesting chemical elements:

Copper (Cu) 6 atoms
Zinc (Zn) 2 atoms
Magnesium (Mg) 2 atoms
Sodium (Na) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution (pdb code 7y44). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution, PDB code: 7y44:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 7y44

Go back to Iron Binding Sites List in 7y44
Iron binding site 1 out of 4 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:16.5
occ:1.00
 FE A:HEA601 0.0 16.5 1.0
NE2 A:HIS61 2.0 19.9 1.0
ND A:HEA601 2.0 17.3 1.0
NB A:HEA601 2.0 17.2 1.0
NC A:HEA601 2.0 13.7 1.0
NE2 A:HIS378 2.0 19.3 1.0
NA A:HEA601 2.1 16.7 1.0
CE1 A:HIS61 2.9 21.8 1.0
C1C A:HEA601 3.0 14.3 1.0
CD2 A:HIS378 3.0 15.5 1.0
CD2 A:HIS61 3.0 22.3 1.0
C4B A:HEA601 3.0 16.3 1.0
C1D A:HEA601 3.0 16.5 1.0
C4A A:HEA601 3.0 13.4 1.0
C4D A:HEA601 3.1 16.9 1.0
C4C A:HEA601 3.1 16.8 1.0
C1B A:HEA601 3.1 18.8 1.0
C1A A:HEA601 3.1 15.4 1.0
CE1 A:HIS378 3.1 15.7 1.0
CHC A:HEA601 3.3 16.0 1.0
CHD A:HEA601 3.4 12.0 1.0
CHB A:HEA601 3.4 14.5 1.0
CHA A:HEA601 3.5 15.2 1.0
ND1 A:HIS61 4.1 18.7 1.0
CG A:HIS61 4.1 16.0 1.0
CG A:HIS378 4.2 15.3 1.0
ND1 A:HIS378 4.2 18.9 1.0
C2C A:HEA601 4.2 15.5 1.0
C3D A:HEA601 4.3 18.6 1.0
C2D A:HEA601 4.3 19.4 1.0
C3B A:HEA601 4.3 16.1 1.0
C2B A:HEA601 4.3 15.8 1.0
C3C A:HEA601 4.3 15.6 1.0
C3A A:HEA601 4.3 15.3 1.0
C2A A:HEA601 4.3 13.5 1.0
CE2 A:PHE377 4.9 15.3 1.0

Iron binding site 2 out of 4 in 7y44

Go back to Iron Binding Sites List in 7y44
Iron binding site 2 out of 4 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:17.1
occ:1.00
 FE A:HEA602 0.0 17.1 1.0
ND A:HEA602 2.0 17.8 1.0
NB A:HEA602 2.0 15.2 1.0
NA A:HEA602 2.0 15.6 1.0
NC A:HEA602 2.0 18.4 1.0
NE2 A:HIS376 2.1 17.6 1.0
O1 A:PER606 2.4 12.6 1.0
C4D A:HEA602 3.0 13.2 1.0
CE1 A:HIS376 3.0 15.3 1.0
C1A A:HEA602 3.0 17.5 1.0
C4A A:HEA602 3.1 18.7 1.0
C1C A:HEA602 3.1 13.9 1.0
C4B A:HEA602 3.1 13.9 1.0
C4C A:HEA602 3.1 12.5 1.0
C1B A:HEA602 3.1 16.7 1.0
C1D A:HEA602 3.1 15.5 1.0
CD2 A:HIS376 3.1 16.0 1.0
CHC A:HEA602 3.4 17.8 1.0
CHA A:HEA602 3.4 13.8 1.0
CHB A:HEA602 3.5 15.4 1.0
CHD A:HEA602 3.5 14.8 1.0
O2 A:PER606 3.8 15.8 1.0
ND1 A:HIS376 4.2 15.9 1.0
CG A:HIS376 4.2 18.2 1.0
C3A A:HEA602 4.3 21.2 1.0
C3D A:HEA602 4.3 17.4 1.0
C2A A:HEA602 4.3 23.6 1.0
C3C A:HEA602 4.3 14.4 1.0
C3B A:HEA602 4.3 16.4 1.0
C2B A:HEA602 4.3 18.5 1.0
C2C A:HEA602 4.3 20.7 1.0
C2D A:HEA602 4.3 13.4 1.0
CU A:CU603 4.9 17.1 1.0

Iron binding site 3 out of 4 in 7y44

Go back to Iron Binding Sites List in 7y44
Iron binding site 3 out of 4 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe601

b:20.2
occ:1.00
 FE N:HEA601 0.0 20.2 1.0
NE2 N:HIS378 2.0 20.2 1.0
NE2 N:HIS61 2.0 16.7 1.0
NB N:HEA601 2.0 20.7 1.0
NA N:HEA601 2.0 23.5 1.0
ND N:HEA601 2.0 19.5 1.0
NC N:HEA601 2.0 20.4 1.0
CE1 N:HIS378 2.9 22.6 1.0
CD2 N:HIS61 3.0 18.5 1.0
CE1 N:HIS61 3.0 19.4 1.0
C1B N:HEA601 3.0 22.6 1.0
C1A N:HEA601 3.0 22.5 1.0
C4A N:HEA601 3.0 20.0 1.0
CD2 N:HIS378 3.1 23.6 1.0
C4D N:HEA601 3.1 15.3 1.0
C4C N:HEA601 3.1 27.1 1.0
C4B N:HEA601 3.1 20.8 1.0
C1D N:HEA601 3.1 24.4 1.0
C1C N:HEA601 3.1 21.9 1.0
CHA N:HEA601 3.4 23.7 1.0
CHB N:HEA601 3.4 18.1 1.0
CHD N:HEA601 3.5 25.1 1.0
CHC N:HEA601 3.5 16.0 1.0
ND1 N:HIS378 4.1 21.1 1.0
ND1 N:HIS61 4.1 22.0 1.0
CG N:HIS61 4.1 19.0 1.0
CG N:HIS378 4.2 15.4 1.0
C2B N:HEA601 4.2 17.4 1.0
C3A N:HEA601 4.2 28.0 1.0
C2A N:HEA601 4.3 14.9 1.0
C3B N:HEA601 4.3 19.9 1.0
C2D N:HEA601 4.3 23.4 1.0
C3D N:HEA601 4.3 14.7 1.0
C3C N:HEA601 4.3 18.8 1.0
C2C N:HEA601 4.3 19.1 1.0
CE2 N:PHE377 4.9 19.2 1.0

Iron binding site 4 out of 4 in 7y44

Go back to Iron Binding Sites List in 7y44
Iron binding site 4 out of 4 in the Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Re-Refinement of Damage Free X-Ray Structure of Bovine Cytochrome C Oxidase at 1.9 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe602

b:17.6
occ:1.00
 FE N:HEA602 0.0 17.6 1.0
ND N:HEA602 2.0 16.2 1.0
NB N:HEA602 2.0 21.0 1.0
NA N:HEA602 2.0 18.2 1.0
NC N:HEA602 2.0 15.6 1.0
NE2 N:HIS376 2.1 16.1 1.0
O1 N:PER606 2.4 18.1 1.0
C1D N:HEA602 3.0 18.5 1.0
C4D N:HEA602 3.0 18.2 1.0
C1B N:HEA602 3.0 18.1 1.0
C1A N:HEA602 3.0 20.8 1.0
C4A N:HEA602 3.0 24.6 1.0
CE1 N:HIS376 3.1 19.3 1.0
C1C N:HEA602 3.1 16.4 1.0
C4C N:HEA602 3.1 16.3 1.0
C4B N:HEA602 3.1 18.2 1.0
CD2 N:HIS376 3.1 20.2 1.0
CHB N:HEA602 3.5 18.3 1.0
CHA N:HEA602 3.5 17.0 1.0
CHC N:HEA602 3.5 19.8 1.0
CHD N:HEA602 3.5 14.9 1.0
O2 N:PER606 3.8 17.8 1.0
C2D N:HEA602 4.2 13.1 1.0
ND1 N:HIS376 4.2 20.5 1.0
C3A N:HEA602 4.2 17.9 1.0
C3D N:HEA602 4.2 16.7 1.0
C2A N:HEA602 4.2 17.8 1.0
C2B N:HEA602 4.2 13.8 1.0
CG N:HIS376 4.3 13.9 1.0
C3B N:HEA602 4.3 14.7 1.0
C2C N:HEA602 4.3 15.7 1.0
C3C N:HEA602 4.3 19.6 1.0
CU N:CU603 4.9 18.6 1.0
CG2 N:VAL243 5.0 13.2 1.0

Reference:

K.Hirata, T.Tsukihara, H.Ago. Determination of Damage-Free Crystal Structure of An X-Ray-Sensitive Protein Using An Xfel Nature Methods V. 11 734 2014.
DOI: 10.1038/NMETH.2962
Page generated: Fri Aug 9 11:17:32 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy