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Iron in PDB 6nkn: Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature

Enzymatic activity of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature

All present enzymatic activity of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 10.50 / 2.50
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.700, 189.800, 211.300, 90.00, 90.00, 90.00
R / Rfree (%) 17.6 / 21.7

Other elements in 6nkn:

The structure of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature 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 Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature (pdb code 6nkn). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature, PDB code: 6nkn:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 6nkn

Go back to Iron Binding Sites List in 6nkn
Iron binding site 1 out of 4 in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe604

b:36.1
occ:1.00
 FE A:HEA604 0.0 36.1 1.0
NE2 A:HIS378 2.0 36.4 1.0
NE2 A:HIS61 2.1 35.4 1.0
ND A:HEA604 2.1 37.4 1.0
NB A:HEA604 2.1 39.6 1.0
NC A:HEA604 2.1 41.8 1.0
NA A:HEA604 2.1 41.9 1.0
CE1 A:HIS378 3.0 42.0 1.0
CD2 A:HIS61 3.1 39.3 1.0
C1D A:HEA604 3.1 38.6 1.0
C4D A:HEA604 3.1 36.5 1.0
C1B A:HEA604 3.1 42.2 1.0
C4A A:HEA604 3.1 40.9 1.0
CD2 A:HIS378 3.1 40.7 1.0
CE1 A:HIS61 3.1 37.0 1.0
C4C A:HEA604 3.1 37.7 1.0
C1C A:HEA604 3.1 37.0 1.0
C1A A:HEA604 3.1 38.1 1.0
C4B A:HEA604 3.1 39.9 1.0
CHB A:HEA604 3.4 40.4 1.0
CHC A:HEA604 3.5 37.9 1.0
CHD A:HEA604 3.5 36.5 1.0
CHA A:HEA604 3.5 37.3 1.0
ND1 A:HIS378 4.1 41.9 1.0
CG A:HIS378 4.2 40.5 1.0
CG A:HIS61 4.2 38.5 1.0
ND1 A:HIS61 4.2 36.2 1.0
C3D A:HEA604 4.4 37.3 1.0
C2D A:HEA604 4.4 39.1 1.0
C3A A:HEA604 4.4 41.1 1.0
C3C A:HEA604 4.4 40.4 1.0
C2C A:HEA604 4.4 39.7 1.0
C2B A:HEA604 4.4 41.4 1.0
C2A A:HEA604 4.4 38.4 1.0
C3B A:HEA604 4.5 41.5 1.0
CE1 A:PHE377 4.9 42.5 1.0

Iron binding site 2 out of 4 in 6nkn

Go back to Iron Binding Sites List in 6nkn
Iron binding site 2 out of 4 in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe605

b:39.9
occ:1.00
 FE A:HEA605 0.0 39.9 1.0
O A:O610 1.7 35.2 1.0
ND A:HEA605 2.1 37.4 1.0
NB A:HEA605 2.1 38.9 1.0
NC A:HEA605 2.1 40.1 1.0
NA A:HEA605 2.1 39.7 1.0
NE2 A:HIS376 2.1 44.2 1.0
CE1 A:HIS376 3.1 40.8 1.0
C1D A:HEA605 3.1 37.4 1.0
C4D A:HEA605 3.1 39.8 1.0
C4C A:HEA605 3.1 36.8 1.0
C1B A:HEA605 3.1 40.8 1.0
C4B A:HEA605 3.1 38.4 1.0
C4A A:HEA605 3.1 40.3 1.0
C1A A:HEA605 3.1 36.9 1.0
C1C A:HEA605 3.1 40.4 1.0
CD2 A:HIS376 3.2 43.2 1.0
CHD A:HEA605 3.4 38.9 1.0
CHA A:HEA605 3.5 38.4 1.0
CHC A:HEA605 3.5 39.0 1.0
CHB A:HEA605 3.5 41.4 1.0
O A:OH611 3.7 44.9 1.0
ND1 A:HIS376 4.2 41.1 1.0
CG A:HIS376 4.3 41.3 1.0
C2D A:HEA605 4.4 37.4 1.0
C3D A:HEA605 4.4 38.4 1.0
C3A A:HEA605 4.4 39.8 1.0
C2B A:HEA605 4.4 37.6 1.0
C3C A:HEA605 4.4 38.4 1.0
C3B A:HEA605 4.4 37.9 1.0
C2A A:HEA605 4.4 36.1 1.0
C2C A:HEA605 4.5 43.3 1.0
CU A:CU601 4.8 46.9 1.0

Iron binding site 3 out of 4 in 6nkn

Go back to Iron Binding Sites List in 6nkn
Iron binding site 3 out of 4 in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe605

b:54.6
occ:1.00
 FE N:HEA605 0.0 54.6 1.0
NE2 N:HIS61 2.0 57.8 1.0
NC N:HEA605 2.1 50.4 1.0
NA N:HEA605 2.1 51.9 1.0
NB N:HEA605 2.1 57.3 1.0
ND N:HEA605 2.1 54.4 1.0
NE2 N:HIS378 2.1 53.3 1.0
CD2 N:HIS61 2.9 57.5 1.0
CE1 N:HIS378 3.0 53.1 1.0
C4C N:HEA605 3.1 52.6 1.0
C1C N:HEA605 3.1 54.2 1.0
C1B N:HEA605 3.1 56.2 1.0
C4A N:HEA605 3.1 53.4 1.0
C1A N:HEA605 3.1 58.7 1.0
C4D N:HEA605 3.1 51.6 1.0
C1D N:HEA605 3.1 52.2 1.0
C4B N:HEA605 3.1 54.1 1.0
CE1 N:HIS61 3.2 62.9 1.0
CD2 N:HIS378 3.3 53.5 1.0
CHD N:HEA605 3.4 50.5 1.0
CHC N:HEA605 3.4 55.5 1.0
CHA N:HEA605 3.5 56.1 1.0
CHB N:HEA605 3.5 52.5 1.0
CG N:HIS61 4.1 62.5 1.0
ND1 N:HIS378 4.2 56.0 1.0
ND1 N:HIS61 4.2 60.8 1.0
CG N:HIS378 4.3 54.5 1.0
C3C N:HEA605 4.3 53.8 1.0
C2C N:HEA605 4.4 54.3 1.0
C2B N:HEA605 4.4 60.7 1.0
C3A N:HEA605 4.4 59.6 1.0
C3B N:HEA605 4.4 56.9 1.0
C3D N:HEA605 4.4 53.8 1.0
C2D N:HEA605 4.4 53.2 1.0
C2A N:HEA605 4.4 57.4 1.0
CE1 N:PHE377 5.0 55.0 1.0

Iron binding site 4 out of 4 in 6nkn

Go back to Iron Binding Sites List in 6nkn
Iron binding site 4 out of 4 in the Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Time-Resolved Sfx Structure of the Pr Intermediate of Cytochrome C Oxidase at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Fe606

b:51.8
occ:1.00
 FE N:HEA606 0.0 51.8 1.0
O N:O611 1.7 50.5 1.0
NA N:HEA606 2.1 43.5 1.0
NC N:HEA606 2.1 44.5 1.0
NB N:HEA606 2.1 46.0 1.0
ND N:HEA606 2.1 45.6 1.0
NE2 N:HIS376 2.2 58.8 1.0
C4A N:HEA606 3.1 49.5 1.0
C1A N:HEA606 3.1 44.1 1.0
C1B N:HEA606 3.1 46.8 1.0
C1C N:HEA606 3.1 46.5 1.0
C4C N:HEA606 3.1 45.4 1.0
C4D N:HEA606 3.1 42.2 1.0
C4B N:HEA606 3.1 42.2 1.0
CE1 N:HIS376 3.1 55.1 1.0
C1D N:HEA606 3.1 44.3 1.0
CD2 N:HIS376 3.2 60.4 1.0
CHA N:HEA606 3.4 43.0 1.0
CHB N:HEA606 3.4 47.6 1.0
CHC N:HEA606 3.5 43.0 1.0
CHD N:HEA606 3.5 44.2 1.0
O N:OH612 4.1 64.6 1.0
ND1 N:HIS376 4.3 55.7 1.0
CG N:HIS376 4.3 60.9 1.0
C3A N:HEA606 4.4 50.8 1.0
C3C N:HEA606 4.4 47.0 1.0
C2B N:HEA606 4.4 43.1 1.0
C2A N:HEA606 4.4 46.1 1.0
C2C N:HEA606 4.4 46.8 1.0
C3B N:HEA606 4.4 43.3 1.0
C3D N:HEA606 4.4 42.5 1.0
C2D N:HEA606 4.5 42.5 1.0
CU N:CU602 4.6 58.8 1.0

Reference:

I.Ishigami, A.Lewis-Ballester, A.Echelmeier, G.Brehm, N.A.Zatsepin, T.D.Grant, J.D.Coe, S.Lisova, G.Nelson, S.Zhang, Z.F.Dobson, S.Boutet, R.G.Sierra, A.Batyuk, P.Fromme, R.Fromme, J.C.H.Spence, A.Ros, S.R.Yeh, D.L.Rousseau. Snapshot of An Oxygen Intermediate in the Catalytic Reaction of Cytochromecoxidase. Proc. Natl. Acad. Sci. V. 116 3572 2019U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30808749
DOI: 10.1073/PNAS.1814526116
Page generated: Wed Aug 7 03:29:05 2024

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