Iron in PDB 5wau: Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K

Enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K

All present enzymatic activity of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K:
1.9.3.1;

Protein crystallography data

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K, PDB code: 5wau was solved by R.Fromme, I.Ishigami, S.Y.Yeh, N.Zatsepin, T.Grant, P.Fromme, D.Rousseau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.00 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 177.923, 182.555, 208.450, 90.00, 90.00, 90.00
R / Rfree (%) 21.7 / 24.4

Other elements in 5wau:

The structure of Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K 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 Synchrotron X-Ray Crystallography at 100 K (pdb code 5wau). 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 Synchrotron X-Ray Crystallography at 100 K, PDB code: 5wau:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5wau

Go back to Iron Binding Sites List in 5wau
Iron binding site 1 out of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


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 Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe601

b:22.3
occ:1.00
FE A:HEA601 0.0 22.3 1.0
NE2 A:HIS378 1.9 18.9 1.0
NE2 A:HIS61 1.9 19.2 1.0
NA A:HEA601 2.0 23.6 1.0
NB A:HEA601 2.1 23.6 1.0
ND A:HEA601 2.1 21.6 1.0
NC A:HEA601 2.1 22.9 1.0
CE1 A:HIS378 2.8 21.9 1.0
CD2 A:HIS61 2.9 19.2 1.0
CE1 A:HIS61 3.0 20.8 1.0
CD2 A:HIS378 3.0 19.2 1.0
C4A A:HEA601 3.1 22.9 1.0
C1A A:HEA601 3.1 21.8 1.0
C4B A:HEA601 3.1 23.2 1.0
C1B A:HEA601 3.1 23.5 1.0
C1D A:HEA601 3.1 23.0 1.0
C4C A:HEA601 3.1 21.1 1.0
C4D A:HEA601 3.1 22.4 1.0
C1C A:HEA601 3.1 21.3 1.0
CHC A:HEA601 3.4 21.4 1.0
CHD A:HEA601 3.5 22.9 1.0
CHB A:HEA601 3.5 22.5 1.0
CHA A:HEA601 3.5 22.0 1.0
ND1 A:HIS378 4.0 20.2 1.0
ND1 A:HIS61 4.1 19.4 1.0
CG A:HIS61 4.1 19.5 1.0
CG A:HIS378 4.1 19.7 1.0
C3A A:HEA601 4.3 21.8 1.0
C2A A:HEA601 4.3 23.1 1.0
C3B A:HEA601 4.4 24.2 1.0
C2B A:HEA601 4.4 21.9 1.0
C3D A:HEA601 4.4 22.4 1.0
C2D A:HEA601 4.4 22.1 1.0
C3C A:HEA601 4.4 21.4 1.0
C2C A:HEA601 4.5 21.4 1.0
CE1 A:PHE377 5.0 22.5 1.0

Iron binding site 2 out of 4 in 5wau

Go back to Iron Binding Sites List in 5wau
Iron binding site 2 out of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


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 Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe602

b:25.3
occ:1.00
FE A:HEA602 0.0 25.3 1.0
NE2 A:HIS376 2.0 27.7 1.0
NA A:HEA602 2.0 25.4 1.0
NB A:HEA602 2.1 24.5 1.0
NC A:HEA602 2.1 27.1 1.0
ND A:HEA602 2.1 24.7 1.0
CE1 A:HIS376 2.9 28.9 1.0
O A:CMO610 3.0 46.3 1.0
C4B A:HEA602 3.0 24.3 1.0
C1A A:HEA602 3.0 23.1 1.0
C1C A:HEA602 3.1 24.8 1.0
CD2 A:HIS376 3.1 28.3 1.0
C4A A:HEA602 3.1 23.0 1.0
C1B A:HEA602 3.1 25.9 1.0
C4D A:HEA602 3.1 24.5 1.0
C1D A:HEA602 3.1 25.9 1.0
C4C A:HEA602 3.1 24.0 1.0
CHC A:HEA602 3.4 23.6 1.0
CHA A:HEA602 3.5 23.9 1.0
CHD A:HEA602 3.5 24.5 1.0
CHB A:HEA602 3.5 23.9 1.0
C A:CMO610 3.7 46.1 1.0
ND1 A:HIS376 4.0 26.1 1.0
CG A:HIS376 4.2 25.7 1.0
C2A A:HEA602 4.3 24.2 1.0
C3A A:HEA602 4.3 23.5 1.0
C3B A:HEA602 4.4 25.1 1.0
C2B A:HEA602 4.4 24.0 1.0
C2C A:HEA602 4.4 25.4 1.0
C3C A:HEA602 4.4 24.8 1.0
C3D A:HEA602 4.4 24.4 1.0
C2D A:HEA602 4.5 24.4 1.0
CG2 A:VAL380 4.8 34.3 1.0
CU A:CU603 4.9 25.7 1.0

Iron binding site 3 out of 4 in 5wau

Go back to Iron Binding Sites List in 5wau
Iron binding site 3 out of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


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 Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe601

b:37.4
occ:1.00
FE a:HEA601 0.0 37.4 1.0
NE2 a:HIS378 1.9 35.9 1.0
NE2 a:HIS61 1.9 35.8 1.0
NA a:HEA601 2.0 34.2 1.0
NC a:HEA601 2.1 34.4 1.0
ND a:HEA601 2.1 36.5 1.0
NB a:HEA601 2.1 37.1 1.0
CD2 a:HIS61 2.9 34.6 1.0
CE1 a:HIS378 2.9 34.6 1.0
CD2 a:HIS378 3.0 32.0 1.0
CE1 a:HIS61 3.0 35.1 1.0
C1A a:HEA601 3.1 38.7 1.0
C4A a:HEA601 3.1 36.3 1.0
C4C a:HEA601 3.1 34.4 1.0
C1D a:HEA601 3.1 33.8 1.0
C1B a:HEA601 3.1 36.4 1.0
C1C a:HEA601 3.1 37.4 1.0
C4D a:HEA601 3.1 36.6 1.0
C4B a:HEA601 3.1 36.7 1.0
CHD a:HEA601 3.4 34.4 1.0
CHB a:HEA601 3.5 37.1 1.0
CHA a:HEA601 3.5 36.0 1.0
CHC a:HEA601 3.5 36.3 1.0
ND1 a:HIS378 4.0 32.6 1.0
CG a:HIS61 4.0 35.1 1.0
ND1 a:HIS61 4.1 33.5 1.0
CG a:HIS378 4.1 32.5 1.0
C3A a:HEA601 4.3 35.1 1.0
C2A a:HEA601 4.3 34.8 1.0
C3C a:HEA601 4.4 32.6 1.0
C2D a:HEA601 4.4 36.2 1.0
C2B a:HEA601 4.4 37.0 1.0
C3D a:HEA601 4.4 35.0 1.0
C3B a:HEA601 4.4 38.2 1.0
C2C a:HEA601 4.4 33.9 1.0
CE1 a:PHE377 5.0 31.2 1.0

Iron binding site 4 out of 4 in 5wau

Go back to Iron Binding Sites List in 5wau
Iron binding site 4 out of 4 in the Crystal Structure of Co-Bound Cytochrome C Oxidase Determined By Synchrotron X-Ray Crystallography at 100 K


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 Synchrotron X-Ray Crystallography at 100 K within 5.0Å range:
probe atom residue distance (Å) B Occ
a:Fe602

b:34.5
occ:1.00
FE a:HEA602 0.0 34.5 1.0
NE2 a:HIS376 2.0 38.2 1.0
NA a:HEA602 2.0 32.2 1.0
NC a:HEA602 2.1 31.2 1.0
NB a:HEA602 2.1 32.5 1.0
ND a:HEA602 2.1 32.3 1.0
O a:CMO608 2.7 69.0 1.0
CE1 a:HIS376 2.9 38.9 1.0
C1C a:HEA602 3.1 31.8 1.0
C1A a:HEA602 3.1 32.2 1.0
C4A a:HEA602 3.1 31.5 1.0
CD2 a:HIS376 3.1 38.7 1.0
C4C a:HEA602 3.1 31.4 1.0
C4B a:HEA602 3.1 29.9 1.0
C1B a:HEA602 3.1 31.0 1.0
C1D a:HEA602 3.1 30.8 1.0
C4D a:HEA602 3.2 30.4 1.0
CHC a:HEA602 3.5 30.9 1.0
CHD a:HEA602 3.5 31.3 1.0
CHB a:HEA602 3.5 31.9 1.0
CHA a:HEA602 3.5 31.6 1.0
C a:CMO608 3.6 65.8 1.0
ND1 a:HIS376 4.1 36.1 1.0
CG a:HIS376 4.2 35.8 1.0
C3A a:HEA602 4.3 32.4 1.0
C2A a:HEA602 4.3 33.3 1.0
C3C a:HEA602 4.4 30.1 1.0
C2C a:HEA602 4.4 31.3 1.0
C2B a:HEA602 4.4 30.5 1.0
C3B a:HEA602 4.4 29.5 1.0
C2D a:HEA602 4.5 30.9 1.0
C3D a:HEA602 4.5 32.2 1.0
CG2 a:VAL380 4.8 43.8 1.0
CU a:CU603 4.9 34.7 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: Sun Dec 13 16:16:02 2020

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