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Iron in PDB 5cic: Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C

Enzymatic activity of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C

All present enzymatic activity of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C:
1.11.1.5;

Protein crystallography data

The structure of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C, PDB code: 5cic was solved by B.R.Crane, T.M.Payne, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.84 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.257, 117.531, 88.446, 90.00, 104.37, 90.00
R / Rfree (%) 19.2 / 22.8

Other elements in 5cic:

The structure of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C (pdb code 5cic). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C, PDB code: 5cic:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in 5cic

Go back to Iron Binding Sites List in 5cic
Iron binding site 1 out of 4 in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe301

b:32.1
occ:1.00
 FE A:HEM301 0.0 32.1 1.0
NE2 A:HIS175 2.0 30.9 1.0
NC A:HEM301 2.1 26.2 1.0
NA A:HEM301 2.1 33.6 1.0
NB A:HEM301 2.1 32.2 1.0
ND A:HEM301 2.1 28.9 1.0
CD2 A:HIS175 3.0 34.2 1.0
CE1 A:HIS175 3.1 36.1 1.0
C4C A:HEM301 3.1 30.1 1.0
C1D A:HEM301 3.1 30.2 1.0
C4B A:HEM301 3.1 37.7 1.0
C1C A:HEM301 3.1 31.0 1.0
C4D A:HEM301 3.1 33.7 1.0
C1B A:HEM301 3.1 35.0 1.0
C1A A:HEM301 3.1 35.3 1.0
C4A A:HEM301 3.1 35.2 1.0
CHD A:HEM301 3.4 28.5 1.0
CHC A:HEM301 3.5 32.8 1.0
CHA A:HEM301 3.5 32.5 1.0
CHB A:HEM301 3.5 34.3 1.0
ND1 A:HIS175 4.2 30.9 1.0
CG A:HIS175 4.2 33.3 1.0
CE1 A:51R302 4.2 43.0 1.0
NE1 A:TRP51 4.2 31.5 1.0
C3B A:HEM301 4.3 40.1 1.0
C2D A:HEM301 4.3 31.6 1.0
C2B A:HEM301 4.3 37.1 1.0
C3D A:HEM301 4.3 33.6 1.0
C3C A:HEM301 4.3 29.9 1.0
C2C A:HEM301 4.3 30.6 1.0
C2A A:HEM301 4.3 36.3 1.0
C3A A:HEM301 4.3 34.3 1.0
CD1 A:TRP51 4.5 32.0 1.0
NH2 A:51R302 4.6 51.7 1.0
CZ A:51R302 4.8 41.9 1.0
CD1 A:51R302 5.0 37.5 1.0

Iron binding site 2 out of 4 in 5cic

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Iron binding site 2 out of 4 in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe201

b:35.1
occ:1.00
 FE B:HEM201 0.0 35.1 1.0
NE2 B:HIS18 2.0 37.5 1.0
NC B:HEM201 2.0 34.2 1.0
NB B:HEM201 2.0 34.9 1.0
NA B:HEM201 2.0 37.6 1.0
ND B:HEM201 2.1 36.9 1.0
SD B:MET80 2.3 33.2 1.0
CE1 B:HIS18 2.8 40.7 1.0
C4C B:HEM201 3.0 35.7 1.0
C1A B:HEM201 3.0 36.8 1.0
C1C B:HEM201 3.0 32.3 1.0
C4B B:HEM201 3.1 36.9 1.0
C4A B:HEM201 3.1 38.4 1.0
C1B B:HEM201 3.1 38.0 1.0
C4D B:HEM201 3.1 40.5 1.0
C1D B:HEM201 3.1 38.1 1.0
CD2 B:HIS18 3.1 34.8 1.0
CG B:MET80 3.4 36.8 1.0
CHA B:HEM201 3.4 37.4 1.0
CHD B:HEM201 3.4 38.0 1.0
CHC B:HEM201 3.4 34.9 1.0
CHB B:HEM201 3.4 33.7 1.0
CE B:MET80 3.5 33.7 1.0
ND1 B:HIS18 4.0 38.2 1.0
CG B:HIS18 4.2 38.5 1.0
CB B:MET80 4.2 35.9 1.0
C2A B:HEM201 4.3 42.2 1.0
C2C B:HEM201 4.3 37.8 1.0
C3C B:HEM201 4.3 37.9 1.0
C3A B:HEM201 4.3 40.3 1.0
C3B B:HEM201 4.3 32.3 1.0
C2B B:HEM201 4.3 37.6 1.0
C3D B:HEM201 4.3 41.9 1.0
C2D B:HEM201 4.3 43.7 1.0
OH B:TYR67 4.8 37.0 1.0

Iron binding site 3 out of 4 in 5cic

Go back to Iron Binding Sites List in 5cic
Iron binding site 3 out of 4 in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:25.5
occ:1.00
 FE C:HEM301 0.0 25.5 1.0
NC C:HEM301 2.0 29.0 1.0
NE2 C:HIS175 2.0 31.0 1.0
NB C:HEM301 2.1 29.9 1.0
ND C:HEM301 2.1 32.0 1.0
NA C:HEM301 2.1 28.9 1.0
CD2 C:HIS175 3.0 30.9 1.0
C1C C:HEM301 3.0 33.2 1.0
C4C C:HEM301 3.0 29.0 1.0
CE1 C:HIS175 3.0 32.3 1.0
C4B C:HEM301 3.1 30.2 1.0
C1D C:HEM301 3.1 29.1 1.0
C4D C:HEM301 3.1 33.8 1.0
C1A C:HEM301 3.1 34.7 1.0
C1B C:HEM301 3.1 31.2 1.0
C4A C:HEM301 3.1 31.4 1.0
CHC C:HEM301 3.4 28.9 1.0
CHD C:HEM301 3.4 26.5 1.0
CHA C:HEM301 3.4 27.1 1.0
CHB C:HEM301 3.5 29.2 1.0
NH2 C:51R302 4.1 39.5 1.0
NE1 C:TRP51 4.1 30.8 1.0
ND1 C:HIS175 4.2 30.0 1.0
CG C:HIS175 4.2 33.8 1.0
C3B C:HEM301 4.3 31.0 1.0
C2C C:HEM301 4.3 32.1 1.0
C3C C:HEM301 4.3 31.1 1.0
C2D C:HEM301 4.3 28.9 1.0
C2B C:HEM301 4.3 30.3 1.0
C3D C:HEM301 4.3 31.3 1.0
C2A C:HEM301 4.3 32.6 1.0
C3A C:HEM301 4.4 34.7 1.0
CD1 C:TRP51 4.4 35.1 1.0
CD C:ARG48 4.8 39.4 1.0

Iron binding site 4 out of 4 in 5cic

Go back to Iron Binding Sites List in 5cic
Iron binding site 4 out of 4 in the Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex of Yeast Cytochrome C Peroxidase (W191G) Bound to 3- Aminobenzotrifluoride with Iso-1 Cytochrome C within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe201

b:37.0
occ:1.00
 FE D:HEM201 0.0 37.0 1.0
NE2 D:HIS18 2.0 40.2 1.0
NA D:HEM201 2.0 50.4 1.0
NB D:HEM201 2.0 44.4 1.0
ND D:HEM201 2.1 53.8 1.0
NC D:HEM201 2.1 47.0 1.0
SD D:MET80 2.3 49.3 1.0
CE1 D:HIS18 2.9 49.2 1.0
C1A D:HEM201 3.0 48.5 1.0
C4A D:HEM201 3.0 47.0 1.0
C1B D:HEM201 3.1 46.8 1.0
C4B D:HEM201 3.1 42.9 1.0
C4D D:HEM201 3.1 52.8 1.0
CD2 D:HIS18 3.1 42.0 1.0
C1D D:HEM201 3.1 51.8 1.0
C1C D:HEM201 3.1 46.4 1.0
C4C D:HEM201 3.1 43.6 1.0
CE D:MET80 3.3 47.1 1.0
CHA D:HEM201 3.4 49.7 1.0
CHB D:HEM201 3.4 45.4 1.0
CHC D:HEM201 3.4 39.2 1.0
CHD D:HEM201 3.4 48.6 1.0
CG D:MET80 3.5 45.3 1.0
ND1 D:HIS18 4.1 42.2 1.0
CG D:HIS18 4.2 41.4 1.0
C2A D:HEM201 4.2 48.9 1.0
C3A D:HEM201 4.3 51.1 1.0
C2B D:HEM201 4.3 43.3 1.0
C3B D:HEM201 4.3 41.7 1.0
C3D D:HEM201 4.3 54.1 1.0
C2D D:HEM201 4.3 52.1 1.0
CB D:MET80 4.3 46.9 1.0
C2C D:HEM201 4.3 46.7 1.0
C3C D:HEM201 4.3 46.7 1.0
OH D:TYR67 4.9 48.3 1.0

Reference:

T.M.Payne, E.F.Yee, B.Dzikovski, B.R.Crane. Constraints on the Radical Cation Center of Cytochrome C Peroxidase For Electron Transfer From Cytochrome C. Biochemistry V. 55 4807 2016.
ISSN: ISSN 0006-2960
PubMed: 27499202
DOI: 10.1021/ACS.BIOCHEM.6B00262
Page generated: Mon Aug 5 21:01:03 2024

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