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Iron in PDB 5w97: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature

Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature

All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97 was solved by D.L.Rousseau, S.-R.Yeh, I.Ishigami, N.A.Zatsepin, T.D.Grant, P.Fromme, R.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.86 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.300, 189.000, 209.000, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 25.2

Other elements in 5w97:

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature (pdb code 5w97). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature, PDB code: 5w97:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5w97

Go back to Iron Binding Sites List in 5w97
Iron binding site 1 out of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:24.9
occ:1.00
FE A:HEA601 0.0 24.9 1.0
NE2 A:HIS378 1.9 23.5 1.0
NE2 A:HIS61 1.9 21.0 1.0
NA A:HEA601 2.0 25.4 1.0
ND A:HEA601 2.1 23.9 1.0
NB A:HEA601 2.1 24.6 1.0
NC A:HEA601 2.1 25.3 1.0
CE1 A:HIS378 2.8 25.5 1.0
CD2 A:HIS61 2.9 21.6 1.0
CE1 A:HIS61 3.0 22.1 1.0
CD2 A:HIS378 3.0 23.4 1.0
C1A A:HEA601 3.1 22.9 1.0
C4A A:HEA601 3.1 24.9 1.0
C1D A:HEA601 3.1 24.7 1.0
C4B A:HEA601 3.1 24.1 1.0
C4D A:HEA601 3.1 22.7 1.0
C1C A:HEA601 3.1 25.0 1.0
C4C A:HEA601 3.1 24.3 1.0
C1B A:HEA601 3.1 27.5 1.0
CHC A:HEA601 3.4 24.1 1.0
CHD A:HEA601 3.4 24.5 1.0
CHA A:HEA601 3.5 24.2 1.0
CHB A:HEA601 3.5 26.2 1.0
ND1 A:HIS378 4.0 24.2 1.0
CG A:HIS61 4.1 21.8 1.0
ND1 A:HIS61 4.1 21.3 1.0
CG A:HIS378 4.1 22.7 1.0
C3A A:HEA601 4.3 25.1 1.0
C2A A:HEA601 4.3 25.8 1.0
C3D A:HEA601 4.4 22.9 1.0
C3C A:HEA601 4.4 25.4 1.0
C2D A:HEA601 4.4 24.9 1.0
C3B A:HEA601 4.4 26.0 1.0
C2C A:HEA601 4.4 26.0 1.0
C2B A:HEA601 4.5 25.5 1.0
CE1 A:PHE377 4.9 23.7 1.0

Iron binding site 2 out of 4 in 5w97

Go back to Iron Binding Sites List in 5w97
Iron binding site 2 out of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:23.8
occ:1.00
FE A:HEA602 0.0 23.8 1.0
C A:CMO609 1.9 23.5 1.0
NE2 A:HIS376 2.0 26.6 1.0
NA A:HEA602 2.0 21.3 1.0
ND A:HEA602 2.0 20.4 1.0
NB A:HEA602 2.1 21.7 1.0
NC A:HEA602 2.1 23.6 1.0
CE1 A:HIS376 2.9 26.2 1.0
O A:CMO609 2.9 24.4 1.0
C4D A:HEA602 3.0 22.3 1.0
C1A A:HEA602 3.0 21.4 1.0
C1D A:HEA602 3.1 22.0 1.0
C4A A:HEA602 3.1 21.0 1.0
CD2 A:HIS376 3.1 24.7 1.0
C4B A:HEA602 3.1 22.2 1.0
C1C A:HEA602 3.1 23.2 1.0
C1B A:HEA602 3.1 23.1 1.0
C4C A:HEA602 3.1 22.7 1.0
CHC A:HEA602 3.4 22.2 1.0
CHA A:HEA602 3.4 22.5 1.0
CHD A:HEA602 3.5 21.5 1.0
CHB A:HEA602 3.5 22.6 1.0
ND1 A:HIS376 4.1 24.0 1.0
CG A:HIS376 4.2 24.1 1.0
C3A A:HEA602 4.3 21.9 1.0
C2A A:HEA602 4.3 23.0 1.0
C3D A:HEA602 4.4 22.9 1.0
C2D A:HEA602 4.4 22.2 1.0
C3B A:HEA602 4.4 22.1 1.0
C2B A:HEA602 4.4 21.7 1.0
C3C A:HEA602 4.4 22.9 1.0
C2C A:HEA602 4.4 23.9 1.0

Iron binding site 3 out of 4 in 5w97

Go back to Iron Binding Sites List in 5w97
Iron binding site 3 out of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe601

b:40.9
occ:1.00
FE a:HEA601 0.0 40.9 1.0
NE2 a:HIS61 1.9 42.0 1.0
NE2 a:HIS378 1.9 33.6 1.0
NA a:HEA601 2.0 38.3 1.0
NC a:HEA601 2.1 39.1 1.0
ND a:HEA601 2.1 40.4 1.0
NB a:HEA601 2.1 43.5 1.0
CD2 a:HIS61 2.8 41.0 1.0
CE1 a:HIS378 2.9 33.2 1.0
CE1 a:HIS61 3.0 41.3 1.0
C4A a:HEA601 3.0 40.2 1.0
CD2 a:HIS378 3.0 32.0 1.0
C4C a:HEA601 3.1 38.7 1.0
C1A a:HEA601 3.1 41.8 1.0
C1C a:HEA601 3.1 43.1 1.0
C1D a:HEA601 3.1 39.7 1.0
C4B a:HEA601 3.1 39.5 1.0
C4D a:HEA601 3.1 39.3 1.0
C1B a:HEA601 3.1 41.6 1.0
CHD a:HEA601 3.4 39.5 1.0
CHC a:HEA601 3.5 40.6 1.0
CHB a:HEA601 3.5 40.0 1.0
CHA a:HEA601 3.5 42.2 1.0
CG a:HIS61 4.0 40.9 1.0
ND1 a:HIS378 4.0 31.0 1.0
ND1 a:HIS61 4.1 40.0 1.0
CG a:HIS378 4.1 34.9 1.0
C3A a:HEA601 4.3 40.8 1.0
C2A a:HEA601 4.3 38.1 1.0
C3C a:HEA601 4.3 40.4 1.0
C2C a:HEA601 4.4 39.8 1.0
C2D a:HEA601 4.4 41.8 1.0
C3D a:HEA601 4.4 38.7 1.0
C3B a:HEA601 4.5 43.3 1.0
C2B a:HEA601 4.5 44.0 1.0
CE1 a:PHE377 4.8 36.4 1.0

Iron binding site 4 out of 4 in 5w97

Go back to Iron Binding Sites List in 5w97
Iron binding site 4 out of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography 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 Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe602

b:33.1
occ:1.00
FE a:HEA602 0.0 33.1 1.0
C a:CMO608 1.9 36.6 1.0
NA a:HEA602 1.9 28.1 1.0
NE2 a:HIS376 1.9 44.7 1.0
NC a:HEA602 2.0 27.3 1.0
ND a:HEA602 2.1 28.9 1.0
NB a:HEA602 2.1 28.7 1.0
O a:CMO608 2.8 33.9 1.0
CE1 a:HIS376 2.9 43.2 1.0
CD2 a:HIS376 3.0 41.1 1.0
C1A a:HEA602 3.0 28.0 1.0
C1C a:HEA602 3.0 29.6 1.0
C4A a:HEA602 3.0 31.2 1.0
C4C a:HEA602 3.0 28.6 1.0
C4D a:HEA602 3.1 29.0 1.0
C4B a:HEA602 3.1 27.5 1.0
C1D a:HEA602 3.1 28.5 1.0
C1B a:HEA602 3.1 28.2 1.0
CHA a:HEA602 3.4 28.2 1.0
CHC a:HEA602 3.4 27.7 1.0
CHD a:HEA602 3.5 29.6 1.0
CHB a:HEA602 3.5 29.4 1.0
ND1 a:HIS376 4.1 36.8 1.0
CG a:HIS376 4.1 37.9 1.0
C3A a:HEA602 4.2 30.8 1.0
C2A a:HEA602 4.3 29.7 1.0
C3C a:HEA602 4.3 28.4 1.0
C2C a:HEA602 4.3 30.5 1.0
C3D a:HEA602 4.4 29.9 1.0
C3B a:HEA602 4.4 27.0 1.0
C2B a:HEA602 4.4 27.3 1.0
C2D a:HEA602 4.4 29.6 1.0

Reference:

I.Ishigami, N.A.Zatsepin, M.Hikita, C.E.Conrad, G.Nelson, J.D.Coe, S.Basu, T.D.Grant, M.H.Seaberg, R.G.Sierra, M.S.Hunter, P.Fromme, R.Fromme, S.R.Yeh, D.L.Rousseau. Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Serial Femtosecond X-Ray Crystallography at Room Temperature. Proc. Natl. Acad. Sci. V. 114 8011 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28698372
DOI: 10.1073/PNAS.1705628114
Page generated: Tue Aug 6 11:05:55 2024

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