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Iron 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:

Fluorine (F) 6 atoms
Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron 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 Iron atom.
In total 8 binding sites of Iron where determined in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520, PDB code: 4d6t:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4d6t

Go back to Iron Binding Sites List in 4d6t
Iron binding site 1 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe501

b:91.6
occ:1.00
 FE C:HEM501 0.0 91.6 1.0
ND C:HEM501 1.9 98.5 1.0
NA C:HEM501 2.0 95.6 1.0
NC C:HEM501 2.1 97.1 1.0
NB C:HEM501 2.1 95.9 1.0
NE2 C:HIS182 2.2 89.6 1.0
NE2 C:HIS83 2.2 86.6 1.0
C4D C:HEM501 2.9 97.4 1.0
C1D C:HEM501 2.9 0.5 1.0
C1A C:HEM501 3.0 99.9 1.0
CE1 C:HIS182 3.0 95.4 1.0
C4A C:HEM501 3.0 95.2 1.0
C1B C:HEM501 3.0 0.5 1.0
C4C C:HEM501 3.0 1.0 1.0
C4B C:HEM501 3.1 97.4 1.0
C1C C:HEM501 3.1 0.4 1.0
CE1 C:HIS83 3.1 87.6 1.0
CD2 C:HIS83 3.2 94.6 1.0
CD2 C:HIS182 3.3 95.8 1.0
CHA C:HEM501 3.3 0.0 1.0
CHD C:HEM501 3.4 0.4 1.0
CHB C:HEM501 3.4 0.7 1.0
CHC C:HEM501 3.5 0.1 1.0
ND1 C:HIS182 4.2 99.2 1.0
C2D C:HEM501 4.2 93.7 1.0
C2A C:HEM501 4.2 99.8 1.0
C3D C:HEM501 4.2 93.4 1.0
C3A C:HEM501 4.2 97.2 1.0
C2B C:HEM501 4.3 0.2 1.0
ND1 C:HIS83 4.3 92.1 1.0
C3C C:HEM501 4.3 0.4 1.0
C2C C:HEM501 4.3 0.4 1.0
C3B C:HEM501 4.3 95.7 1.0
CG C:HIS83 4.3 92.6 1.0
CG C:HIS182 4.3 93.8 1.0
CA C:GLY130 4.7 95.2 1.0
NE2 C:GLN44 4.8 0.1 1.0

Iron binding site 2 out of 8 in 4d6t

Go back to Iron Binding Sites List in 4d6t
Iron binding site 2 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe502

b:83.1
occ:1.00
 FE C:HEM502 0.0 83.1 1.0
ND C:HEM502 1.9 78.6 1.0
NA C:HEM502 2.0 81.1 1.0
NC C:HEM502 2.1 74.9 1.0
NB C:HEM502 2.1 87.5 1.0
NE2 C:HIS196 2.3 91.6 1.0
NE2 C:HIS97 2.3 99.7 1.0
C4D C:HEM502 2.9 74.1 1.0
C1D C:HEM502 2.9 81.7 1.0
C1A C:HEM502 3.0 78.8 1.0
C4A C:HEM502 3.0 80.7 1.0
C4C C:HEM502 3.0 77.7 1.0
C4B C:HEM502 3.0 95.3 1.0
C1B C:HEM502 3.0 87.9 1.0
C1C C:HEM502 3.1 77.1 1.0
CE1 C:HIS196 3.2 94.9 1.0
CD2 C:HIS196 3.3 93.0 1.0
CE1 C:HIS97 3.3 99.3 1.0
CD2 C:HIS97 3.3 94.8 1.0
CHA C:HEM502 3.3 71.8 1.0
CHD C:HEM502 3.4 83.2 1.0
CHB C:HEM502 3.4 81.2 1.0
CHC C:HEM502 3.4 86.9 1.0
C2A C:HEM502 4.2 84.7 1.0
C2D C:HEM502 4.2 85.7 1.0
C3D C:HEM502 4.2 84.6 1.0
C3A C:HEM502 4.2 83.1 1.0
C3C C:HEM502 4.2 77.5 1.0
C2C C:HEM502 4.2 76.4 1.0
C2B C:HEM502 4.3 97.0 1.0
C3B C:HEM502 4.3 99.8 1.0
ND1 C:HIS196 4.4 93.3 1.0
CG C:HIS196 4.4 99.7 1.0
ND1 C:HIS97 4.4 0.6 1.0
CG C:HIS97 4.4 0.3 1.0

Iron binding site 3 out of 8 in 4d6t

Go back to Iron Binding Sites List in 4d6t
Iron binding site 3 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
D:Fe501

b:1.0
occ:1.00
 FE D:HEC501 0.0 1.0 1.0
NE2 D:HIS41 2.0 0.9 1.0
NB D:HEC501 2.1 99.2 1.0
NA D:HEC501 2.1 96.8 1.0
NC D:HEC501 2.1 0.6 1.0
ND D:HEC501 2.1 0.1 1.0
SD D:MET160 2.3 0.0 1.0
CD2 D:HIS41 2.9 0.9 1.0
CE1 D:HIS41 3.0 0.9 1.0
C1A D:HEC501 3.1 97.7 1.0
C1B D:HEC501 3.1 96.5 1.0
C4C D:HEC501 3.1 0.7 1.0
C4A D:HEC501 3.1 88.9 1.0
C4B D:HEC501 3.1 0.4 1.0
C1C D:HEC501 3.1 0.8 1.0
C1D D:HEC501 3.1 0.8 1.0
C4D D:HEC501 3.1 0.2 1.0
CG D:MET160 3.4 97.6 1.0
CHB D:HEC501 3.4 93.6 1.0
CHA D:HEC501 3.4 0.8 1.0
CHD D:HEC501 3.5 0.0 1.0
CHC D:HEC501 3.5 0.8 1.0
CE D:MET160 3.7 0.7 1.0
CG D:HIS41 4.1 0.9 1.0
ND1 D:HIS41 4.1 0.4 1.0
CB D:MET160 4.3 96.9 1.0
C2A D:HEC501 4.4 95.1 1.0
C3C D:HEC501 4.4 0.9 1.0
C3B D:HEC501 4.4 0.2 1.0
C3A D:HEC501 4.4 86.6 1.0
C2B D:HEC501 4.4 0.4 1.0
C2C D:HEC501 4.4 0.8 1.0
C2D D:HEC501 4.4 0.0 1.0
C3D D:HEC501 4.4 0.9 1.0
CB D:PRO110 4.8 0.8 1.0

Iron binding site 4 out of 8 in 4d6t

Go back to Iron Binding Sites List in 4d6t
Iron binding site 4 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe501

b:88.4
occ:1.00
 FE P:HEM501 0.0 88.4 1.0
ND P:HEM501 1.9 0.2 1.0
NA P:HEM501 2.0 0.7 1.0
NC P:HEM501 2.1 96.0 1.0
NB P:HEM501 2.1 94.9 1.0
NE2 P:HIS182 2.1 89.3 1.0
NE2 P:HIS83 2.2 96.4 1.0
C1D P:HEM501 2.9 99.2 1.0
C4D P:HEM501 2.9 0.7 1.0
CE1 P:HIS182 3.0 96.7 1.0
C4C P:HEM501 3.0 98.3 1.0
C1A P:HEM501 3.0 0.8 1.0
C4B P:HEM501 3.1 95.1 1.0
C1B P:HEM501 3.1 0.5 1.0
C4A P:HEM501 3.1 0.9 1.0
C1C P:HEM501 3.1 95.7 1.0
CE1 P:HIS83 3.1 0.6 1.0
CD2 P:HIS83 3.2 94.5 1.0
CD2 P:HIS182 3.2 89.5 1.0
CHD P:HEM501 3.4 0.1 1.0
CHA P:HEM501 3.4 0.1 1.0
CHB P:HEM501 3.5 0.7 1.0
CHC P:HEM501 3.5 97.2 1.0
ND1 P:HIS182 4.2 94.4 1.0
C3D P:HEM501 4.2 0.4 1.0
C2D P:HEM501 4.2 98.0 1.0
C3C P:HEM501 4.3 91.9 1.0
C3A P:HEM501 4.3 98.0 1.0
ND1 P:HIS83 4.3 0.8 1.0
C2A P:HEM501 4.3 98.8 1.0
C2C P:HEM501 4.3 94.3 1.0
CG P:HIS182 4.3 95.7 1.0
C2B P:HEM501 4.3 0.6 1.0
C3B P:HEM501 4.3 0.2 1.0
CG P:HIS83 4.3 96.8 1.0
CA P:GLY130 4.7 0.4 1.0
NE2 P:GLN44 4.9 93.5 1.0

Iron binding site 5 out of 8 in 4d6t

Go back to Iron Binding Sites List in 4d6t
Iron binding site 5 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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:Fe502

b:81.7
occ:1.00
 FE P:HEM502 0.0 81.7 1.0
ND P:HEM502 1.9 83.9 1.0
NA P:HEM502 2.0 85.1 1.0
NC P:HEM502 2.1 84.4 1.0
NB P:HEM502 2.1 86.8 1.0
NE2 P:HIS196 2.3 91.8 1.0
NE2 P:HIS97 2.4 0.5 1.0
C1D P:HEM502 2.9 89.8 1.0
C4D P:HEM502 2.9 80.9 1.0
C1A P:HEM502 3.0 77.4 1.0
C4A P:HEM502 3.0 86.8 1.0
C4C P:HEM502 3.1 84.0 1.0
C1B P:HEM502 3.1 91.1 1.0
C4B P:HEM502 3.1 91.8 1.0
C1C P:HEM502 3.1 91.8 1.0
CD2 P:HIS196 3.2 85.3 1.0
CE1 P:HIS196 3.3 95.2 1.0
CD2 P:HIS97 3.3 0.1 1.0
CHA P:HEM502 3.3 74.3 1.0
CE1 P:HIS97 3.3 0.7 1.0
CHD P:HEM502 3.4 86.1 1.0
CHB P:HEM502 3.5 89.6 1.0
CHC P:HEM502 3.5 93.5 1.0
C2D P:HEM502 4.1 98.3 1.0
C2A P:HEM502 4.2 81.6 1.0
C3D P:HEM502 4.2 91.6 1.0
C3A P:HEM502 4.2 78.0 1.0
C2C P:HEM502 4.3 90.9 1.0
C3C P:HEM502 4.3 86.2 1.0
C2B P:HEM502 4.3 97.4 1.0
C3B P:HEM502 4.3 97.4 1.0
ND1 P:HIS196 4.4 95.6 1.0
CG P:HIS196 4.4 94.0 1.0
ND1 P:HIS97 4.4 0.3 1.0
CG P:HIS97 4.4 99.7 1.0

Iron binding site 6 out of 8 in 4d6t

Go back to Iron Binding Sites List in 4d6t
Iron binding site 6 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe 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
Q:Fe501

b:0.1
occ:1.00
 FE Q:HEC501 0.0 0.1 1.0
NB Q:HEC501 2.1 0.9 1.0
ND Q:HEC501 2.1 0.1 1.0
NA Q:HEC501 2.1 0.5 1.0
NC Q:HEC501 2.1 0.9 1.0
SD Q:MET160 2.2 0.2 1.0
NE2 Q:HIS41 2.2 0.4 1.0
CD2 Q:HIS41 3.1 0.8 1.0
C4B Q:HEC501 3.1 0.2 1.0
C1B Q:HEC501 3.1 0.9 1.0
C1A Q:HEC501 3.1 0.1 1.0
C1D Q:HEC501 3.1 0.3 1.0
C4D Q:HEC501 3.1 0.4 1.0
C4C Q:HEC501 3.1 0.5 1.0
C4A Q:HEC501 3.1 0.7 1.0
C1C Q:HEC501 3.1 0.5 1.0
CE1 Q:HIS41 3.2 0.8 1.0
CG Q:MET160 3.3 0.2 1.0
CHC Q:HEC501 3.5 0.7 1.0
CHA Q:HEC501 3.5 0.1 1.0
CHB Q:HEC501 3.5 0.6 1.0
CHD Q:HEC501 3.5 0.3 1.0
CE Q:MET160 3.6 0.8 1.0
CB Q:MET160 4.2 0.5 1.0
CG Q:HIS41 4.2 0.6 1.0
ND1 Q:HIS41 4.3 0.1 1.0
C3B Q:HEC501 4.4 0.0 1.0
C3D Q:HEC501 4.4 0.1 1.0
C2B Q:HEC501 4.4 1.0 1.0
C3C Q:HEC501 4.4 0.8 1.0
C2D Q:HEC501 4.4 0.3 1.0
C2A Q:HEC501 4.4 0.5 1.0
C3A Q:HEC501 4.4 0.6 1.0
C2C Q:HEC501 4.5 0.0 1.0

Iron binding site 7 out of 8 in 4d6t

Go back to Iron Binding Sites List in 4d6t
Iron binding site 7 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:0.2
occ:1.00
 FE1 R:FES501 0.0 0.2 1.0
S1 R:FES501 2.2 0.4 1.0
S2 R:FES501 2.3 0.2 1.0
FE2 R:FES501 3.2 0.0 1.0
ND1 R:HIS141 3.2 0.0 1.0
CB R:HIS141 3.3 0.0 1.0
CG R:HIS141 3.5 0.2 1.0
CB R:HIS161 3.6 0.8 1.0
N R:LEU142 3.8 0.8 1.0
O R:LEU142 3.9 0.7 1.0
C R:HIS141 4.1 0.8 1.0
ND1 R:HIS161 4.1 0.8 1.0
CG R:HIS161 4.2 0.1 1.0
N R:HIS161 4.2 0.4 1.0
CE1 R:HIS141 4.2 1.0 1.0
CA R:HIS141 4.4 0.6 1.0
CA R:HIS161 4.4 0.1 1.0
CD2 R:HIS141 4.6 0.8 1.0
CA R:LEU142 4.6 0.7 1.0
O R:HIS141 4.6 0.3 1.0
C R:LEU142 4.7 0.4 1.0
CB R:CYS160 4.7 0.9 1.0
SG R:CYS144 4.7 0.5 1.0
CB R:LEU142 4.7 0.7 1.0
N R:HIS141 4.9 0.0 1.0
CG R:PRO175 5.0 0.8 1.0
C R:CYS160 5.0 0.5 1.0
NE2 R:HIS141 5.0 0.0 1.0

Iron binding site 8 out of 8 in 4d6t

Go back to Iron Binding Sites List in 4d6t
Iron binding site 8 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cytochrome BC1 Bound to the 4(1H)-Pyridone GW844520 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:0.0
occ:1.00
 FE2 R:FES501 0.0 0.0 1.0
S1 R:FES501 2.2 0.4 1.0
S2 R:FES501 2.2 0.2 1.0
SG R:CYS158 2.5 0.2 1.0
SG R:CYS139 3.2 0.3 1.0
FE1 R:FES501 3.2 0.2 1.0
OG R:SER163 3.4 0.5 1.0
CB R:CYS158 3.4 0.3 1.0
CB R:SER163 4.0 0.8 1.0
N R:HIS161 4.1 0.4 1.0
N R:SER163 4.3 0.7 1.0
CB R:CYS139 4.3 0.9 1.0
N R:GLY162 4.4 0.7 1.0
C R:HIS161 4.5 0.7 1.0
CB R:CYS160 4.6 0.9 1.0
CB R:HIS141 4.6 0.0 1.0
CA R:HIS161 4.6 0.1 1.0
CG R:PRO175 4.6 0.8 1.0
CA R:SER163 4.8 0.6 1.0
CA R:CYS158 4.8 0.1 1.0
CB R:HIS161 4.8 0.8 1.0
O R:CYS158 4.9 0.3 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 Aug 5 01:10:09 2024

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