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Fluorine 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:

Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 6 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5cic

Go back to Fluorine Binding Sites List in 5cic
Fluorine binding site 1 out of 6 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 Fluorine with other atoms in the F 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:F302

b:58.3
occ:1.00
 F3 A:51R302 0.0 58.3 1.0
CM A:51R302 1.3 56.9 1.0
F2 A:51R302 2.2 57.7 1.0
F1 A:51R302 2.2 55.4 1.0
CD2 A:51R302 2.3 48.8 1.0
O A:HIS175 2.7 36.1 1.0
CE2 A:51R302 2.8 45.5 1.0
CA A:GLY191 3.2 44.1 1.0
CG A:51R302 3.4 38.0 1.0
N A:GLY191 3.5 43.2 1.0
O A:MET230 3.6 36.9 1.0
C A:HIS175 3.9 36.8 1.0
O A:HOH420 4.1 45.7 1.0
CB A:HIS175 4.2 32.1 1.0
CZ A:51R302 4.2 41.9 1.0
C A:PRO190 4.4 42.1 1.0
OD2 A:ASP235 4.5 42.5 1.0
C A:GLY191 4.5 45.5 1.0
CA A:HIS175 4.5 32.5 1.0
SD A:MET231 4.6 43.3 1.0
CD1 A:51R302 4.6 37.5 1.0
SD A:MET230 4.6 42.1 1.0
CE A:MET231 4.7 40.6 1.0
C A:MET230 4.8 40.4 1.0
CE1 A:51R302 4.8 43.0 1.0
CD1 A:PHE202 4.8 35.0 1.0
CG A:HIS175 4.9 33.3 1.0
O A:PRO190 4.9 40.7 1.0
O A:GLY191 4.9 41.5 1.0
N A:ALA176 5.0 35.4 1.0

Fluorine binding site 2 out of 6 in 5cic

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Fluorine binding site 2 out of 6 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 Fluorine with other atoms in the F 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
A:F302

b:55.4
occ:1.00
 F1 A:51R302 0.0 55.4 1.0
CM A:51R302 1.3 56.9 1.0
F2 A:51R302 2.2 57.7 1.0
CD2 A:51R302 2.2 48.8 1.0
F3 A:51R302 2.2 58.3 1.0
N A:GLY191 2.7 43.2 1.0
CE2 A:51R302 2.8 45.5 1.0
C A:PRO190 3.1 42.1 1.0
CA A:GLY191 3.3 44.1 1.0
CG A:51R302 3.3 38.0 1.0
O A:GLY189 3.3 37.7 1.0
O A:HOH420 3.4 45.7 1.0
CA A:PRO190 3.5 38.7 1.0
O A:PRO190 3.7 40.7 1.0
SD A:MET230 3.7 42.1 1.0
O A:MET230 3.9 36.9 1.0
CZ A:51R302 4.1 41.9 1.0
C A:GLY189 4.1 39.2 1.0
CG A:MET230 4.2 35.2 1.0
CA A:LYS179 4.2 37.0 1.0
O A:HIS175 4.3 36.1 1.0
N A:PRO190 4.3 39.4 1.0
CD1 A:51R302 4.4 37.5 1.0
N A:THR180 4.4 36.4 1.0
O A:GLY178 4.5 30.1 1.0
C A:LYS179 4.7 33.3 1.0
CE1 A:51R302 4.7 43.0 1.0
C A:GLY191 4.7 45.5 1.0
C A:MET230 4.8 40.4 1.0
CB A:PRO190 4.8 39.8 1.0
CG2 A:THR180 5.0 35.1 1.0
OG1 A:THR180 5.0 34.1 1.0
N A:LYS179 5.0 33.7 1.0

Fluorine binding site 3 out of 6 in 5cic

Go back to Fluorine Binding Sites List in 5cic
Fluorine binding site 3 out of 6 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 Fluorine with other atoms in the F 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
A:F302

b:57.7
occ:1.00
 F2 A:51R302 0.0 57.7 1.0
CM A:51R302 1.3 56.9 1.0
O A:HOH420 2.0 45.7 1.0
F1 A:51R302 2.2 55.4 1.0
F3 A:51R302 2.2 58.3 1.0
CD2 A:51R302 2.3 48.8 1.0
O A:HIS175 2.6 36.1 1.0
CG A:51R302 2.6 38.0 1.0
N A:GLY191 2.8 43.2 1.0
CA A:GLY191 3.2 44.1 1.0
CE2 A:51R302 3.6 45.5 1.0
C A:HIS175 3.6 36.8 1.0
O A:GLY178 3.7 30.1 1.0
C A:PRO190 3.8 42.1 1.0
O A:LEU177 3.9 31.6 1.0
O A:ALA176 3.9 38.7 1.0
C A:ALA176 4.0 34.8 1.0
CD1 A:51R302 4.0 37.5 1.0
CA A:ALA176 4.2 37.8 1.0
C A:GLY191 4.3 45.5 1.0
CA A:PRO190 4.3 38.7 1.0
N A:ALA176 4.4 35.4 1.0
C A:GLY178 4.4 31.5 1.0
N A:LEU177 4.4 33.3 1.0
C A:LEU177 4.5 37.5 1.0
CA A:HIS175 4.6 32.5 1.0
OD1 A:ASN195 4.7 77.5 1.0
N A:GLY192 4.7 45.1 1.0
CZ A:51R302 4.7 41.9 1.0
CA A:LYS179 4.7 37.0 1.0
O A:PRO190 4.8 40.7 1.0
CE1 A:51R302 4.8 43.0 1.0
N A:LYS179 4.9 33.7 1.0
CB A:HIS175 4.9 32.1 1.0

Fluorine binding site 4 out of 6 in 5cic

Go back to Fluorine Binding Sites List in 5cic
Fluorine binding site 4 out of 6 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 Fluorine with other atoms in the F 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
C:F302

b:52.9
occ:1.00
 F3 C:51R302 0.0 52.9 1.0
CM C:51R302 1.3 45.4 1.0
O C:HOH404 1.9 43.1 1.0
F2 C:51R302 2.2 48.6 1.0
F1 C:51R302 2.2 57.4 1.0
CD2 C:51R302 2.3 51.4 1.0
OD2 C:ASP235 2.4 36.4 1.0
CE2 C:51R302 2.7 32.9 1.0
SD C:MET231 3.2 33.0 1.0
CG C:ASP235 3.5 34.9 1.0
CG C:51R302 3.5 39.3 1.0
CA C:MET231 3.8 30.4 1.0
O C:MET230 3.8 31.9 1.0
O C:HIS175 3.8 41.5 1.0
CE1 C:PHE202 3.9 33.1 1.0
N C:LEU232 4.0 24.8 1.0
CB C:HIS175 4.0 32.2 1.0
CB C:ASP235 4.0 32.1 1.0
CZ C:51R302 4.1 39.6 1.0
CE C:MET231 4.2 38.5 1.0
CG C:MET231 4.3 36.1 1.0
ND1 C:HIS175 4.3 30.0 1.0
CB C:MET231 4.3 29.7 1.0
CD1 C:PHE202 4.4 30.2 1.0
C C:MET231 4.4 31.8 1.0
CG C:HIS175 4.5 33.8 1.0
OD1 C:ASP235 4.5 38.3 1.0
SD C:MET230 4.5 29.7 1.0
C C:MET230 4.6 33.7 1.0
N C:MET231 4.6 34.0 1.0
CD1 C:51R302 4.7 42.3 1.0
C C:HIS175 4.8 32.1 1.0
CE1 C:51R302 4.9 35.2 1.0
CG C:LEU232 5.0 32.3 1.0
CA C:GLY191 5.0 36.3 1.0
NH2 C:51R302 5.0 39.5 1.0

Fluorine binding site 5 out of 6 in 5cic

Go back to Fluorine Binding Sites List in 5cic
Fluorine binding site 5 out of 6 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 Fluorine with other atoms in the F binding site number 5 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:F302

b:57.4
occ:1.00
 F1 C:51R302 0.0 57.4 1.0
CM C:51R302 1.3 45.4 1.0
F3 C:51R302 2.2 52.9 1.0
F2 C:51R302 2.2 48.6 1.0
O C:MET230 2.2 31.9 1.0
CD2 C:51R302 2.3 51.4 1.0
SD C:MET230 2.6 29.7 1.0
O C:HOH404 2.8 43.1 1.0
C C:MET230 3.0 33.7 1.0
CE2 C:51R302 3.1 32.9 1.0
CA C:MET231 3.2 30.4 1.0
CG C:51R302 3.2 39.3 1.0
N C:MET231 3.4 34.0 1.0
CG C:MET230 3.6 31.3 1.0
N C:LEU232 4.0 24.8 1.0
CA C:GLY191 4.0 36.3 1.0
C C:MET231 4.0 31.8 1.0
SD C:MET231 4.1 33.0 1.0
CA C:MET230 4.1 31.7 1.0
CE C:MET230 4.1 25.8 1.0
N C:GLY191 4.3 31.8 1.0
OD2 C:ASP235 4.3 36.4 1.0
CB C:MET230 4.3 29.3 1.0
CB C:MET231 4.3 29.7 1.0
CZ C:51R302 4.3 39.6 1.0
CG C:MET231 4.4 36.1 1.0
CD1 C:51R302 4.5 42.3 1.0
O C:PRO190 4.5 30.8 1.0
C C:PRO190 4.5 34.8 1.0
N C:MET230 4.5 28.3 1.0
O C:GLY189 4.8 25.9 1.0
O C:HIS175 4.9 41.5 1.0
CE1 C:51R302 4.9 35.2 1.0
CE C:MET231 4.9 38.5 1.0

Fluorine binding site 6 out of 6 in 5cic

Go back to Fluorine Binding Sites List in 5cic
Fluorine binding site 6 out of 6 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 Fluorine with other atoms in the F binding site number 6 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:F302

b:48.6
occ:1.00
 F2 C:51R302 0.0 48.6 1.0
CM C:51R302 1.3 45.4 1.0
F3 C:51R302 2.2 52.9 1.0
F1 C:51R302 2.2 57.4 1.0
CD2 C:51R302 2.3 51.4 1.0
CG C:51R302 2.7 39.3 1.0
CA C:GLY191 2.9 36.3 1.0
O C:MET230 3.1 31.9 1.0
O C:HIS175 3.1 41.5 1.0
SD C:MET231 3.5 33.0 1.0
CE2 C:51R302 3.6 32.9 1.0
CE C:MET231 3.6 38.5 1.0
N C:GLY191 3.6 31.8 1.0
O C:HOH404 3.9 43.1 1.0
C C:GLY191 4.0 38.0 1.0
CD1 C:51R302 4.1 42.3 1.0
O C:GLY191 4.2 33.2 1.0
C C:MET230 4.2 33.7 1.0
O C:HOH432 4.3 40.2 1.0
C C:HIS175 4.3 32.1 1.0
CG C:MET231 4.5 36.1 1.0
CD1 C:PHE202 4.5 30.2 1.0
C C:PRO190 4.5 34.8 1.0
OD2 C:ASP235 4.5 36.4 1.0
CA C:MET231 4.5 30.4 1.0
CE1 C:PHE202 4.6 33.1 1.0
SD C:MET230 4.7 29.7 1.0
CB C:HIS175 4.7 32.2 1.0
CZ C:51R302 4.7 39.6 1.0
O C:PRO190 4.7 30.8 1.0
N C:MET231 4.9 34.0 1.0
CE1 C:51R302 5.0 35.2 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: Thu Aug 1 08:33:40 2024

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