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Fluorine in PDB 4d6t: Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520

Enzymatic activity of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520

All present enzymatic activity of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520:
1.10.2.2;

Protein crystallography data

The structure of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520, PDB code: 4d6t was solved by M.J.Capper, P.M.O'neill, N.Fisher, R.W.Strange, D.Moss, S.A.Ward, N.G.Berry, A.S.Lawrenson, S.S.Hasnain, G.A.Biagini, S.V.Antonyuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 3.57
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 129.896, 129.896, 722.152, 90.00, 90.00, 120.00
R / Rfree (%) 20.6 / 25.156

Other elements in 4d6t:

The structure of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 also contains other interesting chemical elements:

Iron (Fe) 8 atoms
Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 (pdb code 4d6t). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520, PDB code: 4d6t:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4d6t

Go back to Fluorine Binding Sites List in 4d6t
Fluorine binding site 1 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:0.1
occ:1.00
 F23 C:4X9503 0.0 0.1 1.0
C1 C:4X9503 1.3 0.7 1.0
F24 C:4X9503 2.2 0.1 1.0
F25 C:4X9503 2.2 0.7 1.0
O3 C:4X9503 2.2 0.7 1.0
C4 C:4X9503 3.5 0.8 1.0
CE C:MET190 3.7 0.2 1.0
CG C:MET190 3.7 0.4 1.0
CD2 C:LEU41 4.1 98.4 1.0
C5 C:4X9503 4.2 0.5 1.0
SD C:MET190 4.3 0.5 1.0
CB C:ALA193 4.4 89.3 1.0
C9 C:4X9503 4.4 0.2 1.0
O C:MET190 4.5 93.8 1.0
CB C:MET190 4.6 97.0 1.0
CA C:MET190 4.6 88.5 1.0
CE C:MET194 4.9 0.3 1.0

Fluorine binding site 2 out of 6 in 4d6t

Go back to Fluorine Binding Sites List in 4d6t
Fluorine binding site 2 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:0.1
occ:1.00
 F24 C:4X9503 0.0 0.1 1.0
C1 C:4X9503 1.3 0.7 1.0
F23 C:4X9503 2.2 0.1 1.0
F25 C:4X9503 2.2 0.7 1.0
O3 C:4X9503 2.2 0.7 1.0
C4 C:4X9503 3.2 0.8 1.0
C5 C:4X9503 3.2 0.5 1.0
CE C:MET194 3.4 0.3 1.0
CE C:MET190 4.0 0.2 1.0
CG C:MET194 4.2 0.6 1.0
C9 C:4X9503 4.5 0.2 1.0
C6 C:4X9503 4.5 0.6 1.0
SD C:MET194 4.6 0.7 1.0
CG C:MET190 4.6 0.4 1.0
O C:MET190 5.0 93.8 1.0

Fluorine binding site 3 out of 6 in 4d6t

Go back to Fluorine Binding Sites List in 4d6t
Fluorine binding site 3 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:0.7
occ:1.00
 F25 C:4X9503 0.0 0.7 1.0
C1 C:4X9503 1.3 0.7 1.0
F23 C:4X9503 2.2 0.1 1.0
F24 C:4X9503 2.2 0.1 1.0
O3 C:4X9503 2.3 0.7 1.0
C4 C:4X9503 2.8 0.8 1.0
C5 C:4X9503 2.8 0.5 1.0
C9 C:4X9503 3.9 0.2 1.0
C6 C:4X9503 4.0 0.6 1.0
CD1 C:LEU197 4.4 0.4 1.0
CB C:ALA193 4.4 89.3 1.0
C8 C:4X9503 4.8 0.7 1.0
C7 C:4X9503 4.8 0.2 1.0
CA C:GLY38 4.9 95.0 1.0

Fluorine binding site 4 out of 6 in 4d6t

Go back to Fluorine Binding Sites List in 4d6t
Fluorine binding site 4 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F503

b:0.5
occ:1.00
 F23 P:4X9503 0.0 0.5 1.0
C1 P:4X9503 1.3 0.9 1.0
F24 P:4X9503 2.2 0.3 1.0
F25 P:4X9503 2.2 0.9 1.0
O3 P:4X9503 2.2 0.4 1.0
C4 P:4X9503 2.9 0.9 1.0
C5 P:4X9503 3.1 0.8 1.0
O P:MET190 3.9 80.5 1.0
CG P:MET190 3.9 0.2 1.0
CB P:ALA193 3.9 82.0 1.0
CE P:MET194 4.0 0.7 1.0
CG P:MET194 4.0 0.8 1.0
C9 P:4X9503 4.1 0.6 1.0
CE P:MET190 4.2 0.2 1.0
C6 P:4X9503 4.3 0.9 1.0
SD P:MET194 4.6 0.9 1.0
N P:MET194 4.6 92.5 1.0
CA P:MET190 4.6 92.3 1.0
C P:MET190 4.7 86.8 1.0
SD P:MET190 4.7 0.6 1.0
CB P:MET190 4.8 95.7 1.0
C P:ALA193 4.9 89.7 1.0

Fluorine binding site 5 out of 6 in 4d6t

Go back to Fluorine Binding Sites List in 4d6t
Fluorine binding site 5 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F503

b:0.3
occ:1.00
 F24 P:4X9503 0.0 0.3 1.0
C1 P:4X9503 1.3 0.9 1.0
F23 P:4X9503 2.2 0.5 1.0
F25 P:4X9503 2.2 0.9 1.0
O3 P:4X9503 2.2 0.4 1.0
CG P:MET190 3.1 0.2 1.0
CE P:MET190 3.2 0.2 1.0
CD2 P:LEU41 3.2 91.7 1.0
SD P:MET190 3.3 0.6 1.0
C4 P:4X9503 3.4 0.9 1.0
CB P:MET190 3.8 95.7 1.0
CA P:MET190 4.0 92.3 1.0
C9 P:4X9503 4.1 0.6 1.0
CG P:LEU41 4.2 88.6 1.0
C5 P:4X9503 4.3 0.8 1.0
O P:MET190 4.5 80.5 1.0
CB P:ALA193 4.6 82.0 1.0
CB P:LEU41 4.6 87.8 1.0
C P:MET190 4.8 86.8 1.0
CG1 P:ILE42 4.8 0.2 1.0

Fluorine binding site 6 out of 6 in 4d6t

Go back to Fluorine Binding Sites List in 4d6t
Fluorine binding site 6 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F503

b:0.9
occ:1.00
 F25 P:4X9503 0.0 0.9 1.0
C1 P:4X9503 1.3 0.9 1.0
F23 P:4X9503 2.2 0.5 1.0
F24 P:4X9503 2.2 0.3 1.0
O3 P:4X9503 2.2 0.4 1.0
C4 P:4X9503 2.5 0.9 1.0
C9 P:4X9503 3.0 0.6 1.0
CE P:MET190 3.2 0.2 1.0
C5 P:4X9503 3.3 0.8 1.0
C8 P:4X9503 4.0 0.3 1.0
CD1 P:ILE42 4.1 0.1 1.0
C6 P:4X9503 4.2 0.9 1.0
CG P:MET190 4.4 0.2 1.0
SD P:MET190 4.4 0.6 1.0
C7 P:4X9503 4.5 0.5 1.0
CG1 P:ILE42 4.5 0.2 1.0
CE P:MET194 4.5 0.7 1.0

Reference:

M.J.Capper, P.M.O'neill, N.Fisher, R.W.Strange, D.Moss, S.A.Ward, N.G.Berry, A.S.Lawrenson, S.S.Hasnain, G.A.Biagini, S.V.Antonyuk. Antimalarial 4(1H)-Pyridones Bind to the Qi Site of Cytochrome BC1. Proc.Natl.Acad.Sci.Usa V. 112 755 2015.
ISSN: ISSN 0027-8424
PubMed: 25564664
DOI: 10.1073/PNAS.1416611112
Page generated: Thu Aug 1 00:51:43 2024

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