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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

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