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Iron 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:

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 GSK932121 (pdb code 4d6u). 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 GSK932121, PDB code: 4d6u:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 4d6u

Go back to Iron Binding Sites List in 4d6u
Iron binding site 1 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:0.3
occ:1.00
 FE C:HEM501 0.0 0.3 1.0
ND C:HEM501 1.9 0.7 1.0
NA C:HEM501 2.0 0.9 1.0
NE2 C:HIS182 2.1 0.4 1.0
NC C:HEM501 2.1 0.9 1.0
NB C:HEM501 2.1 1.0 1.0
NE2 C:HIS83 2.2 0.1 1.0
C4D C:HEM501 2.9 0.5 1.0
C1D C:HEM501 2.9 0.0 1.0
CE1 C:HIS182 2.9 0.8 1.0
C1A C:HEM501 3.0 0.1 1.0
C4A C:HEM501 3.0 1.0 1.0
C4C C:HEM501 3.0 0.2 1.0
C1B C:HEM501 3.1 0.5 1.0
C4B C:HEM501 3.1 0.6 1.0
CD2 C:HIS83 3.1 0.9 1.0
C1C C:HEM501 3.1 0.2 1.0
CD2 C:HIS182 3.1 0.9 1.0
CE1 C:HIS83 3.2 0.6 1.0
CHA C:HEM501 3.3 0.4 1.0
CHD C:HEM501 3.4 0.8 1.0
CHB C:HEM501 3.5 0.7 1.0
CHC C:HEM501 3.5 0.2 1.0
ND1 C:HIS182 4.1 0.5 1.0
C2A C:HEM501 4.2 0.9 1.0
C3D C:HEM501 4.2 0.7 1.0
C2D C:HEM501 4.2 0.0 1.0
C3A C:HEM501 4.2 0.7 1.0
CG C:HIS182 4.2 0.3 1.0
ND1 C:HIS83 4.2 0.4 1.0
CG C:HIS83 4.3 0.4 1.0
C3C C:HEM501 4.3 0.9 1.0
C2C C:HEM501 4.3 1.0 1.0
C2B C:HEM501 4.3 0.1 1.0
C3B C:HEM501 4.4 0.4 1.0
CA C:GLY130 4.7 0.1 1.0
NE2 C:GLN44 4.8 0.2 1.0

Iron binding site 2 out of 8 in 4d6u

Go back to Iron Binding Sites List in 4d6u
Iron binding site 2 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:0.2
occ:1.00
 FE C:HEM502 0.0 0.2 1.0
ND C:HEM502 1.9 0.8 1.0
NA C:HEM502 2.0 0.7 1.0
NC C:HEM502 2.1 97.6 1.0
NB C:HEM502 2.1 0.1 1.0
NE2 C:HIS196 2.2 0.2 1.0
NE2 C:HIS97 2.2 0.8 1.0
C4D C:HEM502 2.8 0.2 1.0
C1D C:HEM502 2.9 0.1 1.0
C1A C:HEM502 3.0 0.8 1.0
C4C C:HEM502 3.0 98.9 1.0
C4A C:HEM502 3.0 0.2 1.0
C4B C:HEM502 3.1 0.6 1.0
CE1 C:HIS196 3.1 0.1 1.0
C1B C:HEM502 3.1 0.9 1.0
C1C C:HEM502 3.1 0.3 1.0
CD2 C:HIS97 3.2 0.7 1.0
CE1 C:HIS97 3.2 0.9 1.0
CD2 C:HIS196 3.2 0.2 1.0
CHA C:HEM502 3.3 0.7 1.0
CHD C:HEM502 3.4 0.0 1.0
CHB C:HEM502 3.5 1.0 1.0
CHC C:HEM502 3.5 0.8 1.0
C3D C:HEM502 4.1 0.8 1.0
C2D C:HEM502 4.1 0.1 1.0
C3A C:HEM502 4.2 0.7 1.0
C2A C:HEM502 4.2 0.2 1.0
ND1 C:HIS196 4.2 0.1 1.0
C3C C:HEM502 4.2 100.0 1.0
C2C C:HEM502 4.3 0.2 1.0
ND1 C:HIS97 4.3 0.2 1.0
CG C:HIS97 4.3 0.9 1.0
CG C:HIS196 4.3 0.4 1.0
C2B C:HEM502 4.3 0.0 1.0
C3B C:HEM502 4.4 0.6 1.0
NH2 C:ARG100 4.8 0.4 1.0

Iron binding site 3 out of 8 in 4d6u

Go back to Iron Binding Sites List in 4d6u
Iron binding site 3 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:0.6
occ:1.00
 FE D:HEC501 0.0 0.6 1.0
NE2 D:HIS41 2.0 0.4 1.0
NA D:HEC501 2.1 0.8 1.0
NC D:HEC501 2.1 0.4 1.0
NB D:HEC501 2.1 0.4 1.0
ND D:HEC501 2.1 0.0 1.0
SD D:MET160 2.3 0.1 1.0
CE1 D:HIS41 2.9 0.8 1.0
CD2 D:HIS41 3.0 0.5 1.0
C4A D:HEC501 3.1 0.8 1.0
C4C D:HEC501 3.1 0.4 1.0
C1B D:HEC501 3.1 0.2 1.0
C1D D:HEC501 3.1 0.5 1.0
C1C D:HEC501 3.1 0.3 1.0
C1A D:HEC501 3.1 0.8 1.0
C4B D:HEC501 3.1 0.9 1.0
C4D D:HEC501 3.1 0.1 1.0
CHB D:HEC501 3.5 0.1 1.0
CHD D:HEC501 3.5 0.6 1.0
CHC D:HEC501 3.5 0.7 1.0
CHA D:HEC501 3.5 0.9 1.0
CG D:MET160 3.6 0.4 1.0
CE D:MET160 3.7 0.2 1.0
ND1 D:HIS41 4.0 0.8 1.0
CG D:HIS41 4.1 0.1 1.0
CB D:MET160 4.3 0.6 1.0
C3C D:HEC501 4.4 0.6 1.0
C3A D:HEC501 4.4 0.7 1.0
C3B D:HEC501 4.4 0.2 1.0
C2A D:HEC501 4.4 0.9 1.0
C2D D:HEC501 4.4 0.8 1.0
C3D D:HEC501 4.4 0.7 1.0
C2C D:HEC501 4.4 0.1 1.0
C2B D:HEC501 4.5 0.2 1.0

Iron binding site 4 out of 8 in 4d6u

Go back to Iron Binding Sites List in 4d6u
Iron binding site 4 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe501

b:0.9
occ:1.00
 FE P:HEM501 0.0 0.9 1.0
ND P:HEM501 1.9 0.2 1.0
NA P:HEM501 2.0 0.5 1.0
NC P:HEM501 2.1 0.6 1.0
NE2 P:HIS83 2.1 0.6 1.0
NB P:HEM501 2.1 0.3 1.0
NE2 P:HIS182 2.1 0.4 1.0
C4D P:HEM501 2.9 0.8 1.0
C1D P:HEM501 2.9 0.5 1.0
CE1 P:HIS182 3.0 0.6 1.0
C1A P:HEM501 3.0 0.9 1.0
C4A P:HEM501 3.0 0.8 1.0
C4C P:HEM501 3.0 0.7 1.0
C4B P:HEM501 3.1 0.3 1.0
CE1 P:HIS83 3.1 0.2 1.0
C1B P:HEM501 3.1 0.5 1.0
CD2 P:HIS83 3.1 0.5 1.0
C1C P:HEM501 3.1 1.0 1.0
CD2 P:HIS182 3.2 0.1 1.0
CHA P:HEM501 3.3 0.1 1.0
CHD P:HEM501 3.4 0.6 1.0
CHB P:HEM501 3.5 0.9 1.0
CHC P:HEM501 3.5 0.7 1.0
ND1 P:HIS182 4.1 0.7 1.0
ND1 P:HIS83 4.2 0.2 1.0
C3D P:HEM501 4.2 0.4 1.0
C2D P:HEM501 4.2 0.6 1.0
C2A P:HEM501 4.2 0.2 1.0
CG P:HIS83 4.2 0.5 1.0
C3A P:HEM501 4.2 0.1 1.0
C3C P:HEM501 4.3 0.4 1.0
C2C P:HEM501 4.3 0.6 1.0
CG P:HIS182 4.3 0.7 1.0
C2B P:HEM501 4.3 0.6 1.0
C3B P:HEM501 4.3 0.9 1.0
NE2 P:GLN44 4.8 0.4 1.0
CA P:GLY130 4.8 0.2 1.0

Iron binding site 5 out of 8 in 4d6u

Go back to Iron Binding Sites List in 4d6u
Iron binding site 5 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe502

b:0.4
occ:1.00
 FE P:HEM502 0.0 0.4 1.0
ND P:HEM502 1.9 1.0 1.0
NA P:HEM502 2.0 0.6 1.0
NC P:HEM502 2.1 0.5 1.0
NB P:HEM502 2.1 0.7 1.0
NE2 P:HIS97 2.3 0.4 1.0
NE2 P:HIS196 2.3 0.3 1.0
C4D P:HEM502 2.9 0.1 1.0
C1D P:HEM502 2.9 0.7 1.0
C1A P:HEM502 3.0 0.6 1.0
C4A P:HEM502 3.1 0.3 1.0
C4C P:HEM502 3.1 0.8 1.0
C1B P:HEM502 3.1 0.7 1.0
C4B P:HEM502 3.1 0.6 1.0
CD2 P:HIS97 3.1 0.8 1.0
C1C P:HEM502 3.1 0.6 1.0
CD2 P:HIS196 3.2 0.9 1.0
CHA P:HEM502 3.3 0.8 1.0
CE1 P:HIS196 3.3 0.9 1.0
CHD P:HEM502 3.4 0.5 1.0
CE1 P:HIS97 3.4 0.6 1.0
CHB P:HEM502 3.5 0.2 1.0
CHC P:HEM502 3.5 0.0 1.0
C2D P:HEM502 4.1 0.8 1.0
C3D P:HEM502 4.1 0.5 1.0
C2A P:HEM502 4.2 0.2 1.0
C3A P:HEM502 4.2 0.3 1.0
C2C P:HEM502 4.3 0.7 1.0
C3C P:HEM502 4.3 1.0 1.0
CG P:HIS97 4.3 0.9 1.0
C2B P:HEM502 4.3 0.8 1.0
C3B P:HEM502 4.4 0.5 1.0
CG P:HIS196 4.4 0.6 1.0
ND1 P:HIS196 4.4 0.1 1.0
ND1 P:HIS97 4.4 0.9 1.0

Iron binding site 6 out of 8 in 4d6u

Go back to Iron Binding Sites List in 4d6u
Iron binding site 6 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe501

b:0.0
occ:1.00
 FE Q:HEC501 0.0 0.0 1.0
NB Q:HEC501 2.1 0.4 1.0
ND Q:HEC501 2.1 0.9 1.0
NA Q:HEC501 2.1 0.5 1.0
NC Q:HEC501 2.1 0.6 1.0
NE2 Q:HIS41 2.1 0.7 1.0
SD Q:MET160 2.3 0.9 1.0
CE1 Q:HIS41 3.1 1.0 1.0
CD2 Q:HIS41 3.1 1.0 1.0
C1B Q:HEC501 3.1 0.1 1.0
C1A Q:HEC501 3.1 0.8 1.0
C4B Q:HEC501 3.1 0.4 1.0
C4D Q:HEC501 3.1 0.2 1.0
C4C Q:HEC501 3.1 0.3 1.0
C1D Q:HEC501 3.1 0.1 1.0
C4A Q:HEC501 3.1 0.6 1.0
C1C Q:HEC501 3.1 0.2 1.0
CHB Q:HEC501 3.5 0.7 1.0
CHA Q:HEC501 3.5 0.8 1.0
CHC Q:HEC501 3.5 0.8 1.0
CHD Q:HEC501 3.5 0.8 1.0
CG Q:MET160 3.5 0.7 1.0
CE Q:MET160 3.9 0.2 1.0
ND1 Q:HIS41 4.2 0.6 1.0
CG Q:HIS41 4.2 0.4 1.0
CB Q:MET160 4.4 0.6 1.0
C3B Q:HEC501 4.4 0.9 1.0
C3C Q:HEC501 4.4 0.7 1.0
C2B Q:HEC501 4.4 0.7 1.0
C3D Q:HEC501 4.4 0.5 1.0
C2A Q:HEC501 4.4 0.5 1.0
C2D Q:HEC501 4.4 0.8 1.0
C3A Q:HEC501 4.4 0.5 1.0
C2C Q:HEC501 4.4 0.5 1.0

Iron binding site 7 out of 8 in 4d6u

Go back to Iron Binding Sites List in 4d6u
Iron binding site 7 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:0.1
occ:1.00
 FE1 R:FES501 0.0 0.1 1.0
S2 R:FES501 2.2 1.0 1.0
S1 R:FES501 2.2 0.3 1.0
ND1 R:HIS141 3.0 0.2 1.0
CB R:HIS141 3.1 0.5 1.0
FE2 R:FES501 3.1 0.1 1.0
CG R:HIS141 3.2 0.2 1.0
CB R:HIS161 3.7 0.2 1.0
N R:LEU142 3.8 0.0 1.0
CE1 R:HIS141 4.0 0.5 1.0
ND1 R:HIS161 4.2 0.4 1.0
O R:LEU142 4.2 0.3 1.0
N R:HIS161 4.2 0.1 1.0
CD2 R:HIS141 4.2 0.9 1.0
CA R:HIS141 4.2 0.3 1.0
C R:HIS141 4.3 0.5 1.0
CG R:HIS161 4.4 0.1 1.0
CB R:CYS160 4.4 0.3 1.0
CA R:HIS161 4.5 0.1 1.0
SG R:CYS144 4.6 0.3 1.0
NE2 R:HIS141 4.6 0.6 1.0
SG R:CYS160 4.7 0.1 1.0
CB R:LEU142 4.7 1.0 1.0
CA R:LEU142 4.7 0.4 1.0
N R:HIS141 4.9 0.4 1.0
C R:CYS160 4.9 0.5 1.0
CB R:CYS144 4.9 0.5 1.0
SG R:CYS158 4.9 0.5 1.0
C R:LEU142 5.0 0.8 1.0

Iron binding site 8 out of 8 in 4d6u

Go back to Iron Binding Sites List in 4d6u
Iron binding site 8 out of 8 in the Cytochrome BC1 Bound to the 4(1H)-Pyridone GSK932121


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 GSK932121 within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:0.1
occ:1.00
 FE2 R:FES501 0.0 0.1 1.0
S2 R:FES501 2.2 1.0 1.0
S1 R:FES501 2.2 0.3 1.0
SG R:CYS158 2.3 0.5 1.0
FE1 R:FES501 3.1 0.1 1.0
OG R:SER163 3.3 0.1 1.0
CB R:CYS158 3.4 1.0 1.0
N R:HIS161 3.6 0.1 1.0
CB R:SER163 3.7 1.0 1.0
SG R:CYS139 3.8 0.7 1.0
N R:SER163 4.0 0.2 1.0
C R:HIS161 4.1 0.3 1.0
CB R:CYS160 4.1 0.3 1.0
CA R:HIS161 4.2 0.1 1.0
N R:GLY162 4.3 0.1 1.0
O R:HIS161 4.3 0.3 1.0
CA R:SER163 4.5 0.4 1.0
CB R:HIS161 4.5 0.2 1.0
C R:CYS160 4.6 0.5 1.0
CD R:PRO175 4.6 0.2 1.0
CB R:HIS141 4.6 0.5 1.0
N R:CYS160 4.7 0.2 1.0
CA R:CYS160 4.7 0.0 1.0
CA R:CYS158 4.8 0.5 1.0
CB R:CYS139 4.8 0.9 1.0
O R:CYS158 4.9 0.2 1.0
C R:CYS158 4.9 0.2 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 01:10:10 2024

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