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Iron in PDB 5nmi: Cytochrome BC1 Bound to the Inhibitor MJM170

Enzymatic activity of Cytochrome BC1 Bound to the Inhibitor MJM170

All present enzymatic activity of Cytochrome BC1 Bound to the Inhibitor MJM170:
1.10.2.2;

Protein crystallography data

The structure of Cytochrome BC1 Bound to the Inhibitor MJM170, PDB code: 5nmi was solved by N.J.Capper, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.74 / 3.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 129.477, 129.477, 720.294, 90.00, 90.00, 120.00
R / Rfree (%) 24.8 / 26.8

Iron Binding Sites:

The binding sites of Iron atom in the Cytochrome BC1 Bound to the Inhibitor MJM170 (pdb code 5nmi). 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 Inhibitor MJM170, PDB code: 5nmi:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 in 5nmi

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Iron binding site 1 out of 8 in the Cytochrome BC1 Bound to the Inhibitor MJM170


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 Inhibitor MJM170 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:55.6
occ:1.00
 FE C:HEM501 0.0 55.6 1.0
NE2 C:HIS182 1.9 59.6 1.0
ND C:HEM501 1.9 54.5 1.0
NE2 C:HIS83 1.9 55.3 1.0
NA C:HEM501 2.0 60.9 1.0
NC C:HEM501 2.1 53.4 1.0
NB C:HEM501 2.1 59.3 1.0
CE1 C:HIS83 2.8 57.5 1.0
CE1 C:HIS182 2.8 56.4 1.0
C4D C:HEM501 2.9 56.6 1.0
CD2 C:HIS182 2.9 54.9 1.0
C1D C:HEM501 3.0 57.5 1.0
C1A C:HEM501 3.0 62.1 1.0
CD2 C:HIS83 3.0 56.5 1.0
C4A C:HEM501 3.0 58.0 1.0
C4B C:HEM501 3.1 56.0 1.0
C4C C:HEM501 3.1 52.9 1.0
C1C C:HEM501 3.1 59.0 1.0
C1B C:HEM501 3.1 63.2 1.0
CHA C:HEM501 3.4 60.1 1.0
CHD C:HEM501 3.4 54.8 1.0
CHB C:HEM501 3.4 63.4 1.0
CHC C:HEM501 3.5 58.0 1.0
ND1 C:HIS83 3.9 56.1 1.0
ND1 C:HIS182 4.0 48.5 1.0
CG C:HIS182 4.0 51.6 1.0
CG C:HIS83 4.1 59.1 1.0
C3D C:HEM501 4.2 58.9 1.0
C2D C:HEM501 4.2 62.1 1.0
C2A C:HEM501 4.2 62.0 1.0
C3A C:HEM501 4.2 54.4 1.0
C2C C:HEM501 4.3 64.2 1.0
C3C C:HEM501 4.3 55.1 1.0
C2B C:HEM501 4.3 62.5 1.0
C3B C:HEM501 4.4 59.0 1.0
NE2 C:GLN44 4.6 57.2 1.0
CA C:GLY130 4.8 68.2 1.0

Iron binding site 2 out of 8 in 5nmi

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Iron binding site 2 out of 8 in the Cytochrome BC1 Bound to the Inhibitor MJM170


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 Inhibitor MJM170 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:54.7
occ:1.00
 FE C:HEM502 0.0 54.7 1.0
NE2 C:HIS97 1.9 63.0 1.0
ND C:HEM502 1.9 57.0 1.0
NE2 C:HIS196 1.9 58.5 1.0
NA C:HEM502 2.0 52.1 1.0
NC C:HEM502 2.1 45.0 1.0
NB C:HEM502 2.1 50.0 1.0
CE1 C:HIS97 2.8 59.4 1.0
CE1 C:HIS196 2.9 60.9 1.0
C1D C:HEM502 2.9 54.0 1.0
C4D C:HEM502 2.9 55.2 1.0
CD2 C:HIS196 3.0 54.9 1.0
CD2 C:HIS97 3.0 61.5 1.0
C1A C:HEM502 3.0 50.0 1.0
C4A C:HEM502 3.0 53.2 1.0
C4C C:HEM502 3.1 47.1 1.0
C1B C:HEM502 3.1 54.1 1.0
C4B C:HEM502 3.1 49.5 1.0
C1C C:HEM502 3.1 47.1 1.0
CHD C:HEM502 3.4 47.7 1.0
CHA C:HEM502 3.4 49.7 1.0
CHB C:HEM502 3.4 51.2 1.0
CHC C:HEM502 3.5 45.6 1.0
ND1 C:HIS97 3.9 53.7 1.0
ND1 C:HIS196 4.0 57.6 1.0
CG C:HIS97 4.1 54.0 1.0
CG C:HIS196 4.1 57.2 1.0
C2D C:HEM502 4.2 63.6 1.0
C3D C:HEM502 4.2 64.7 1.0
C2A C:HEM502 4.2 53.9 1.0
C3A C:HEM502 4.2 52.3 1.0
C3C C:HEM502 4.3 49.3 1.0
C2C C:HEM502 4.3 48.1 1.0
C2B C:HEM502 4.3 57.5 1.0
C3B C:HEM502 4.4 53.7 1.0
NH2 C:ARG100 4.9 98.3 1.0

Iron binding site 3 out of 8 in 5nmi

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Iron binding site 3 out of 8 in the Cytochrome BC1 Bound to the Inhibitor MJM170


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 Inhibitor MJM170 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:86.6
occ:1.00
 FE D:HEC501 0.0 86.6 1.0
NE2 D:HIS41 1.8 0.5 1.0
NB D:HEC501 2.1 88.9 1.0
ND D:HEC501 2.1 75.2 1.0
NA D:HEC501 2.1 77.3 1.0
NC D:HEC501 2.1 73.6 1.0
SD D:MET160 2.3 0.4 1.0
CE1 D:HIS41 2.7 0.9 1.0
CD2 D:HIS41 3.0 0.1 1.0
C4B D:HEC501 3.0 86.9 1.0
C4D D:HEC501 3.1 72.8 1.0
C1C D:HEC501 3.1 83.2 1.0
C1A D:HEC501 3.1 74.4 1.0
C1D D:HEC501 3.1 74.7 1.0
C1B D:HEC501 3.1 98.9 1.0
C4A D:HEC501 3.1 80.8 1.0
C4C D:HEC501 3.1 72.1 1.0
CHC D:HEC501 3.4 79.5 1.0
CHA D:HEC501 3.4 69.0 1.0
CHD D:HEC501 3.5 66.3 1.0
CHB D:HEC501 3.5 94.5 1.0
CG D:MET160 3.6 0.6 1.0
CE D:MET160 3.7 0.4 1.0
ND1 D:HIS41 3.8 0.5 1.0
CG D:HIS41 4.0 0.5 1.0
C3B D:HEC501 4.4 0.4 1.0
C3D D:HEC501 4.4 77.5 1.0
C2A D:HEC501 4.4 76.5 1.0
C2D D:HEC501 4.4 80.0 1.0
C2B D:HEC501 4.4 0.6 1.0
C2C D:HEC501 4.4 94.8 1.0
C3A D:HEC501 4.4 78.8 1.0
C3C D:HEC501 4.4 88.8 1.0
CB D:MET160 4.5 0.7 1.0

Iron binding site 4 out of 8 in 5nmi

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Iron binding site 4 out of 8 in the Cytochrome BC1 Bound to the Inhibitor MJM170


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 Inhibitor MJM170 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.1
occ:1.00
 FE1 E:FES501 0.0 0.1 1.0
S1 E:FES501 2.2 0.4 1.0
S2 E:FES501 2.2 0.1 1.0
SG E:CYS139 2.3 0.6 1.0
SG E:CYS158 2.3 93.1 1.0
FE2 E:FES501 3.2 0.3 1.0
CB E:CYS139 3.3 0.9 1.0
CB E:CYS158 3.7 96.3 1.0
CB E:HIS141 4.0 0.8 1.0
O E:LEU142 4.0 0.8 1.0
CB E:CYS144 4.1 0.3 1.0
CB E:CYS160 4.3 0.3 1.0
ND1 E:HIS141 4.3 0.3 1.0
OG E:SER163 4.3 0.1 1.0
ND1 E:HIS161 4.4 0.2 1.0
N E:LEU142 4.4 0.7 1.0
SG E:CYS144 4.5 0.4 1.0
N E:HIS161 4.6 0.7 1.0
CB E:SER163 4.6 0.3 1.0
CG E:HIS141 4.7 0.9 1.0
CA E:CYS139 4.7 0.1 1.0
N E:HIS141 4.9 0.6 1.0
CA E:HIS141 4.9 0.8 1.0
CA E:CYS158 5.0 0.2 1.0

Iron binding site 5 out of 8 in 5nmi

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Iron binding site 5 out of 8 in the Cytochrome BC1 Bound to the Inhibitor MJM170


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 Inhibitor MJM170 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.3
occ:1.00
 FE2 E:FES501 0.0 0.3 1.0
ND1 E:HIS161 1.9 0.2 1.0
ND1 E:HIS141 1.9 0.3 1.0
S2 E:FES501 2.2 0.1 1.0
S1 E:FES501 2.2 0.4 1.0
CE1 E:HIS141 2.7 0.6 1.0
CE1 E:HIS161 2.8 0.7 1.0
CG E:HIS161 2.9 0.8 1.0
CG E:HIS141 3.0 0.9 1.0
FE1 E:FES501 3.2 0.1 1.0
CB E:HIS161 3.3 0.3 1.0
CB E:HIS141 3.6 0.8 1.0
NE2 E:HIS141 3.9 0.8 1.0
NE2 E:HIS161 3.9 0.8 1.0
CD2 E:HIS161 3.9 0.8 1.0
N E:HIS161 4.0 0.7 1.0
CD2 E:HIS141 4.1 0.6 1.0
CA E:HIS161 4.2 0.1 1.0
N E:LEU142 4.5 0.7 1.0
CB E:CYS160 4.5 0.3 1.0
CG E:PRO175 4.7 0.1 1.0
C E:CYS160 4.7 0.8 1.0
SG E:CYS139 4.8 0.6 1.0
CA E:HIS141 4.8 0.8 1.0
C E:HIS141 4.9 0.8 1.0
C E:HIS161 4.9 0.6 1.0
OG E:SER163 5.0 0.1 1.0
SG E:CYS158 5.0 93.1 1.0
CB E:LEU142 5.0 0.2 1.0

Iron binding site 6 out of 8 in 5nmi

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Iron binding site 6 out of 8 in the Cytochrome BC1 Bound to the Inhibitor MJM170


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 Inhibitor MJM170 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe402

b:53.9
occ:1.00
 FE P:HEM402 0.0 53.9 1.0
NE2 P:HIS182 1.8 52.6 1.0
NE2 P:HIS83 1.8 42.3 1.0
ND P:HEM402 1.9 54.5 1.0
NA P:HEM402 2.0 53.5 1.0
NB P:HEM402 2.1 56.9 1.0
NC P:HEM402 2.1 55.0 1.0
CE1 P:HIS182 2.3 50.6 1.0
CE1 P:HIS83 2.7 40.9 1.0
CD2 P:HIS83 2.9 46.3 1.0
C4D P:HEM402 2.9 53.3 1.0
C1D P:HEM402 2.9 56.2 1.0
C1A P:HEM402 3.0 51.4 1.0
CD2 P:HIS182 3.0 56.1 1.0
C4A P:HEM402 3.0 54.6 1.0
C4B P:HEM402 3.0 56.3 1.0
C1B P:HEM402 3.1 58.1 1.0
C1C P:HEM402 3.1 59.4 1.0
C4C P:HEM402 3.1 52.9 1.0
CHA P:HEM402 3.3 48.0 1.0
CHD P:HEM402 3.4 55.2 1.0
CHB P:HEM402 3.4 53.8 1.0
CHC P:HEM402 3.4 58.2 1.0
ND1 P:HIS182 3.5 52.8 1.0
ND1 P:HIS83 3.8 45.6 1.0
CG P:HIS182 3.9 55.8 1.0
CG P:HIS83 3.9 49.1 1.0
C3D P:HEM402 4.2 57.1 1.0
C2D P:HEM402 4.2 56.2 1.0
C2A P:HEM402 4.2 56.5 1.0
C3A P:HEM402 4.2 58.7 1.0
C2C P:HEM402 4.3 58.6 1.0
C2B P:HEM402 4.3 60.4 1.0
C3C P:HEM402 4.3 53.9 1.0
C3B P:HEM402 4.3 56.1 1.0
NE2 P:GLN44 4.5 64.1 1.0
CA P:GLY130 4.8 59.3 1.0

Iron binding site 7 out of 8 in 5nmi

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Iron binding site 7 out of 8 in the Cytochrome BC1 Bound to the Inhibitor MJM170


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 Inhibitor MJM170 within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe403

b:54.9
occ:1.00
 FE P:HEM403 0.0 54.9 1.0
ND P:HEM403 1.9 54.0 1.0
NE2 P:HIS196 1.9 58.8 1.0
NE2 P:HIS97 1.9 62.5 1.0
NA P:HEM403 2.0 55.8 1.0
NC P:HEM403 2.1 53.7 1.0
NB P:HEM403 2.1 54.8 1.0
CE1 P:HIS196 2.9 55.9 1.0
CE1 P:HIS97 2.9 64.6 1.0
C4D P:HEM403 2.9 54.5 1.0
C1D P:HEM403 2.9 53.8 1.0
CD2 P:HIS196 2.9 57.6 1.0
C1A P:HEM403 3.0 56.1 1.0
CD2 P:HIS97 3.0 60.6 1.0
C4A P:HEM403 3.0 56.3 1.0
C4B P:HEM403 3.0 54.6 1.0
C1B P:HEM403 3.1 55.3 1.0
C4C P:HEM403 3.1 53.5 1.0
C1C P:HEM403 3.1 53.3 1.0
CHA P:HEM403 3.3 55.1 1.0
CHD P:HEM403 3.4 53.6 1.0
CHB P:HEM403 3.4 55.5 1.0
CHC P:HEM403 3.4 53.9 1.0
ND1 P:HIS196 4.0 48.7 1.0
ND1 P:HIS97 4.0 59.2 1.0
CG P:HIS196 4.0 54.9 1.0
CG P:HIS97 4.1 58.2 1.0
C3D P:HEM403 4.2 55.1 1.0
C2D P:HEM403 4.2 54.3 1.0
C3A P:HEM403 4.2 57.0 1.0
C2A P:HEM403 4.2 57.9 1.0
C2C P:HEM403 4.3 52.8 1.0
C3C P:HEM403 4.3 53.0 1.0
C2B P:HEM403 4.3 55.9 1.0
C3B P:HEM403 4.3 55.2 1.0
NH2 P:ARG100 5.0 59.4 1.0

Iron binding site 8 out of 8 in 5nmi

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Iron binding site 8 out of 8 in the Cytochrome BC1 Bound to the Inhibitor MJM170


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 Inhibitor MJM170 within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe501

b:76.2
occ:1.00
 FE Q:HEC501 0.0 76.2 1.0
NE2 Q:HIS41 1.9 0.1 1.0
ND Q:HEC501 2.1 64.0 1.0
NA Q:HEC501 2.1 77.3 1.0
NB Q:HEC501 2.1 82.2 1.0
NC Q:HEC501 2.1 85.2 1.0
SD Q:MET160 2.2 68.0 1.0
CE1 Q:HIS41 2.7 0.3 1.0
CD2 Q:HIS41 3.0 0.9 1.0
C1B Q:HEC501 3.1 95.8 1.0
C1D Q:HEC501 3.1 67.9 1.0
C4A Q:HEC501 3.1 79.3 1.0
C4B Q:HEC501 3.1 84.0 1.0
C4C Q:HEC501 3.1 73.6 1.0
C1C Q:HEC501 3.1 0.2 1.0
C1A Q:HEC501 3.1 74.6 1.0
C4D Q:HEC501 3.1 59.0 1.0
CHB Q:HEC501 3.4 86.0 1.0
CHD Q:HEC501 3.4 69.2 1.0
CHC Q:HEC501 3.4 92.5 1.0
CG Q:MET160 3.5 61.1 1.0
CHA Q:HEC501 3.5 60.5 1.0
CE Q:MET160 3.7 73.8 1.0
ND1 Q:HIS41 3.9 0.1 1.0
CG Q:HIS41 4.0 95.5 1.0
C3B Q:HEC501 4.4 94.2 1.0
C2D Q:HEC501 4.4 67.7 1.0
C2A Q:HEC501 4.4 76.2 1.0
C2B Q:HEC501 4.4 99.8 1.0
C3A Q:HEC501 4.4 78.2 1.0
C3D Q:HEC501 4.4 62.7 1.0
C2C Q:HEC501 4.4 0.6 1.0
CB Q:MET160 4.4 63.1 1.0
C3C Q:HEC501 4.4 92.9 1.0

Reference:

M.Mcphillie, Y.Zhou, K.El Bissati, J.Dubey, H.Lorenzi, M.Capper, A.K.Lukens, M.Hickman, S.Muench, S.K.Verma, C.R.Weber, K.Wheeler, J.Gordon, J.Sanders, H.Moulton, K.Wang, T.K.Kim, Y.He, T.Santos, S.Woods, P.Lee, D.Donkin, E.Kim, L.Fraczek, J.Lykins, F.Esaa, F.Alibana-Clouser, S.Dovgin, L.Weiss, G.Brasseur, D.Wirth, M.Kent, L.Hood, B.Meunieur, C.W.Roberts, S.S.Hasnain, S.V.Antonyuk, C.Fishwick, R.Mcleod. New Paradigms For Understanding and Step Changes in Treating Active and Chronic, Persistent Apicomplexan Infections. Sci Rep V. 6 29179 2016.
ISSN: ESSN 2045-2322
PubMed: 27412848
DOI: 10.1038/SREP29179
Page generated: Tue Aug 6 06:13:54 2024

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