Atomistry » Fluorine » PDB 5ci0-5dde » 5cic
Atomistry »
  Fluorine »
    PDB 5ci0-5dde »
      5cic »

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

Go back to Fluorine Binding Sites List in 5cic
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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy