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Fluorine in PDB 4d6u: Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121

Enzymatic activity of Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121

All present enzymatic activity of Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121:
1.10.2.2;

Protein crystallography data

The structure of Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121, PDB code: 4d6u 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 / 4.09
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 129.490, 129.490, 719.936, 90.00, 90.00, 120.00
R / Rfree (%) 22.33 / 27.106

Other elements in 4d6u:

The structure of Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121 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 GSK932121 (pdb code 4d6u). 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 GSK932121, PDB code: 4d6u:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4d6u

Go back to Fluorine Binding Sites List in 4d6u
Fluorine binding site 1 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:0.6
occ:1.00
 F1 C:G8U503 0.0 0.6 1.0
C1 C:G8U503 1.3 0.3 1.0
F3 C:G8U503 2.1 0.7 1.0
F2 C:G8U503 2.1 0.1 1.0
O29 C:G8U503 2.3 0.3 1.0
C4 C:G8U503 2.7 1.0 1.0
C9 C:G8U503 2.9 0.4 1.0
C5 C:G8U503 3.7 0.3 1.0
C8 C:G8U503 4.0 0.1 1.0
CE C:MET194 4.1 0.7 1.0
CE C:MET190 4.5 0.8 1.0
C6 C:G8U503 4.6 0.7 1.0
CG C:MET194 4.7 0.3 1.0
C7 C:G8U503 4.7 1.0 1.0
CD1 C:LEU197 4.9 0.4 1.0

Fluorine binding site 2 out of 6 in 4d6u

Go back to Fluorine Binding Sites List in 4d6u
Fluorine binding site 2 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:0.1
occ:1.00
 F2 C:G8U503 0.0 0.1 1.0
C1 C:G8U503 1.3 0.3 1.0
F1 C:G8U503 2.1 0.6 1.0
F3 C:G8U503 2.1 0.7 1.0
O29 C:G8U503 2.2 0.3 1.0
C4 C:G8U503 3.1 1.0 1.0
C9 C:G8U503 3.2 0.4 1.0
CB C:ALA193 3.8 0.6 1.0
C5 C:G8U503 4.4 0.3 1.0
CD2 C:LEU41 4.5 95.1 1.0
CG C:MET190 4.5 0.7 1.0
C8 C:G8U503 4.5 0.1 1.0
O C:MET190 4.7 0.0 1.0
CE C:MET190 5.0 0.8 1.0

Fluorine binding site 3 out of 6 in 4d6u

Go back to Fluorine Binding Sites List in 4d6u
Fluorine binding site 3 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F503

b:0.7
occ:1.00
 F3 C:G8U503 0.0 0.7 1.0
C1 C:G8U503 1.3 0.3 1.0
F1 C:G8U503 2.1 0.6 1.0
F2 C:G8U503 2.1 0.1 1.0
O29 C:G8U503 2.2 0.3 1.0
C4 C:G8U503 3.4 1.0 1.0
CD1 C:LEU197 3.6 0.4 1.0
CB C:ALA193 3.7 0.6 1.0
CG C:MET194 3.8 0.3 1.0
N C:MET194 4.0 0.3 1.0
C C:ALA193 4.0 0.1 1.0
C9 C:G8U503 4.2 0.4 1.0
O C:ALA193 4.3 0.0 1.0
CA C:MET194 4.3 0.9 1.0
C5 C:G8U503 4.3 0.3 1.0
CG C:LEU197 4.4 0.4 1.0
CA C:ALA193 4.5 0.2 1.0
O C:MET190 4.5 0.0 1.0
CE C:MET194 4.6 0.7 1.0
CB C:MET194 4.7 0.9 1.0

Fluorine binding site 4 out of 6 in 4d6u

Go back to Fluorine Binding Sites List in 4d6u
Fluorine binding site 4 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F503

b:0.0
occ:1.00
 F1 P:G8U503 0.0 0.0 1.0
C1 P:G8U503 1.3 0.8 1.0
F2 P:G8U503 2.1 0.6 1.0
F3 P:G8U503 2.1 0.5 1.0
O29 P:G8U503 2.2 1.0 1.0
C9 P:G8U503 2.5 0.6 1.0
C4 P:G8U503 2.7 0.6 1.0
C8 P:G8U503 3.7 0.5 1.0
CG P:MET190 4.0 0.7 1.0
C5 P:G8U503 4.0 0.5 1.0
CB P:ALA193 4.2 0.7 1.0
CD2 P:LEU41 4.4 0.7 1.0
SD P:MET190 4.6 0.3 1.0
O P:MET190 4.7 0.0 1.0
C7 P:G8U503 4.8 0.8 1.0
C6 P:G8U503 4.9 0.6 1.0
CB P:MET190 4.9 0.3 1.0

Fluorine binding site 5 out of 6 in 4d6u

Go back to Fluorine Binding Sites List in 4d6u
Fluorine binding site 5 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F503

b:0.6
occ:1.00
 F2 P:G8U503 0.0 0.6 1.0
C1 P:G8U503 1.3 0.8 1.0
F1 P:G8U503 2.1 0.0 1.0
F3 P:G8U503 2.1 0.5 1.0
O29 P:G8U503 2.2 1.0 1.0
CB P:ALA193 2.4 0.7 1.0
C P:ALA193 3.5 0.3 1.0
C4 P:G8U503 3.5 0.6 1.0
CA P:ALA193 3.5 0.8 1.0
N P:MET194 3.7 0.3 1.0
O P:ALA193 3.8 0.6 1.0
O P:MET190 3.9 0.0 1.0
C9 P:G8U503 4.0 0.6 1.0
CG P:MET194 4.4 0.9 1.0
CD1 P:LEU197 4.5 0.9 1.0
CA P:MET194 4.5 0.1 1.0
CG P:MET190 4.6 0.7 1.0
C5 P:G8U503 4.6 0.5 1.0
N P:ALA193 4.6 1.0 1.0
C P:MET190 4.7 0.8 1.0
CA P:MET190 4.8 0.3 1.0
CMB P:HEM502 4.8 0.7 1.0
CD2 P:LEU41 5.0 0.7 1.0

Fluorine binding site 6 out of 6 in 4d6u

Go back to Fluorine Binding Sites List in 4d6u
Fluorine binding site 6 out of 6 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:F503

b:0.5
occ:1.00
 F3 P:G8U503 0.0 0.5 1.0
C1 P:G8U503 1.3 0.8 1.0
F2 P:G8U503 2.1 0.6 1.0
F1 P:G8U503 2.1 0.0 1.0
O29 P:G8U503 2.2 1.0 1.0
C4 P:G8U503 3.0 0.6 1.0
CG P:MET194 3.6 0.9 1.0
C9 P:G8U503 3.6 0.6 1.0
C5 P:G8U503 3.9 0.5 1.0
CD1 P:LEU197 4.2 0.9 1.0
CB P:ALA193 4.4 0.7 1.0
O P:MET190 4.4 0.0 1.0
N P:MET194 4.4 0.3 1.0
SD P:MET194 4.5 0.8 1.0
CG P:MET190 4.5 0.7 1.0
CA P:MET194 4.6 0.1 1.0
C P:ALA193 4.7 0.3 1.0
CB P:MET194 4.7 0.0 1.0
C8 P:G8U503 4.8 0.5 1.0
O P:ALA193 5.0 0.6 1.0
C6 P:G8U503 5.0 0.6 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: Mon Jul 14 21:05:39 2025

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