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Iron in PDB 4u3f: Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound

Enzymatic activity of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound

All present enzymatic activity of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound:
1.10.2.2;

Protein crystallography data

The structure of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound, PDB code: 4u3f was solved by L.-S.Huang, X.-L.Zhu, G.F.Yang, E.A.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 3.23
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 167.251, 181.483, 239.631, 90.00, 90.00, 90.00
R / Rfree (%) 23.6 / 28.4

Iron Binding Sites:

The binding sites of Iron atom in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound (pdb code 4u3f). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound, PDB code: 4u3f:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 4u3f

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Iron binding site 1 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe501

b:19.5
occ:1.00
FE C:HEM501 0.0 19.5 1.0
NE2 C:HIS84 2.0 26.4 1.0
NE2 C:HIS183 2.0 25.4 1.0
NB C:HEM501 2.0 24.2 1.0
NC C:HEM501 2.0 21.4 1.0
NA C:HEM501 2.1 22.2 1.0
ND C:HEM501 2.1 26.5 1.0
CE1 C:HIS84 2.7 28.7 1.0
CE1 C:HIS183 2.9 28.9 1.0
C1C C:HEM501 3.1 24.2 1.0
C4B C:HEM501 3.1 25.2 1.0
C1B C:HEM501 3.1 24.3 1.0
C4A C:HEM501 3.1 23.7 1.0
C4D C:HEM501 3.1 24.4 1.0
C4C C:HEM501 3.1 22.7 1.0
C1A C:HEM501 3.1 22.9 1.0
CD2 C:HIS183 3.1 24.3 1.0
C1D C:HEM501 3.1 24.1 1.0
CD2 C:HIS84 3.2 28.1 1.0
CHC C:HEM501 3.4 25.2 1.0
CHA C:HEM501 3.4 24.1 1.0
CHB C:HEM501 3.4 21.9 1.0
CHD C:HEM501 3.4 22.2 1.0
ND1 C:HIS84 3.9 31.1 1.0
ND1 C:HIS183 4.0 29.4 1.0
CG C:HIS183 4.2 25.2 1.0
CG C:HIS84 4.2 28.5 1.0
C2C C:HEM501 4.3 24.9 1.0
C3A C:HEM501 4.3 24.3 1.0
C2B C:HEM501 4.3 28.2 1.0
C3D C:HEM501 4.3 24.1 1.0
C2D C:HEM501 4.3 23.2 1.0
C3C C:HEM501 4.3 26.0 1.0
C3B C:HEM501 4.3 27.6 1.0
C2A C:HEM501 4.3 23.1 1.0
CA C:GLY49 5.0 26.4 1.0

Iron binding site 2 out of 10 in 4u3f

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Iron binding site 2 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:23.0
occ:1.00
FE C:HEM502 0.0 23.0 1.0
NB C:HEM502 2.0 22.2 1.0
ND C:HEM502 2.0 21.9 1.0
NC C:HEM502 2.0 22.5 1.0
NA C:HEM502 2.1 24.4 1.0
NE2 C:HIS197 2.1 24.8 1.0
NE2 C:HIS98 2.1 28.1 1.0
CD2 C:HIS197 3.0 24.1 1.0
CE1 C:HIS197 3.0 27.4 1.0
C1C C:HEM502 3.0 21.9 1.0
CD2 C:HIS98 3.0 25.3 1.0
C4C C:HEM502 3.0 25.0 1.0
C4B C:HEM502 3.1 24.3 1.0
CE1 C:HIS98 3.1 28.0 1.0
C1D C:HEM502 3.1 21.2 1.0
C1B C:HEM502 3.1 24.1 1.0
C4D C:HEM502 3.1 26.2 1.0
C4A C:HEM502 3.1 22.8 1.0
C1A C:HEM502 3.1 24.7 1.0
CHC C:HEM502 3.4 24.2 1.0
CHD C:HEM502 3.4 23.9 1.0
CHB C:HEM502 3.4 21.6 1.0
CHA C:HEM502 3.4 25.9 1.0
ND1 C:HIS197 4.1 25.7 1.0
ND1 C:HIS98 4.1 30.3 1.0
CG C:HIS197 4.1 26.5 1.0
CG C:HIS98 4.2 25.3 1.0
C2C C:HEM502 4.2 20.8 1.0
C3C C:HEM502 4.3 23.0 1.0
C3B C:HEM502 4.3 25.7 1.0
C2B C:HEM502 4.3 26.8 1.0
C2D C:HEM502 4.3 23.3 1.0
C3D C:HEM502 4.3 25.1 1.0
C3A C:HEM502 4.3 23.5 1.0
C2A C:HEM502 4.3 26.7 1.0

Iron binding site 3 out of 10 in 4u3f

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Iron binding site 3 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:29.5
occ:1.00
FE D:HEC501 0.0 29.5 1.0
NE2 D:HIS41 2.0 31.2 1.0
NA D:HEC501 2.0 36.5 1.0
ND D:HEC501 2.0 33.1 1.0
NB D:HEC501 2.1 29.4 1.0
NC D:HEC501 2.1 36.5 1.0
SD D:MET160 2.3 27.1 1.0
CD2 D:HIS41 2.9 34.1 1.0
CE1 D:HIS41 3.0 30.3 1.0
C4D D:HEC501 3.1 32.3 1.0
C4B D:HEC501 3.1 32.1 1.0
C4A D:HEC501 3.1 35.7 1.0
C1A D:HEC501 3.1 36.4 1.0
C1C D:HEC501 3.1 42.0 1.0
C1B D:HEC501 3.1 32.9 1.0
C1D D:HEC501 3.1 38.9 1.0
C4C D:HEC501 3.1 31.6 1.0
CHA D:HEC501 3.4 33.4 1.0
CHC D:HEC501 3.4 38.2 1.0
CHB D:HEC501 3.4 33.5 1.0
CHD D:HEC501 3.5 35.0 1.0
CG D:MET160 3.6 33.4 1.0
CE D:MET160 3.7 32.9 1.0
CG D:HIS41 4.0 34.9 1.0
ND1 D:HIS41 4.0 33.6 1.0
C3B D:HEC501 4.3 29.7 1.0
C3A D:HEC501 4.3 33.6 1.0
C3D D:HEC501 4.3 38.5 1.0
C2A D:HEC501 4.3 29.7 1.0
C2B D:HEC501 4.3 34.6 1.0
C2D D:HEC501 4.3 40.0 1.0
C2C D:HEC501 4.3 38.9 1.0
C3C D:HEC501 4.3 40.0 1.0
CB D:MET160 4.4 31.9 1.0

Iron binding site 4 out of 10 in 4u3f

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Iron binding site 4 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:92.1
occ:0.81
FE1 E:FES501 0.0 92.1 0.8
SG E:CYS158 2.2 0.2 0.8
SG E:CYS139 2.2 0.6 1.0
S2 E:FES501 2.2 0.1 0.8
S1 E:FES501 2.2 1.0 0.8
CB E:CYS139 2.8 0.4 1.0
FE2 E:FES501 3.1 0.6 0.8
CB E:CYS158 3.2 0.2 0.8
OG E:SER163 4.3 0.6 0.8
CA E:CYS139 4.3 0.1 1.0
CB E:HIS141 4.4 0.1 1.0
CB E:SER163 4.4 0.7 0.8
CB E:CYS160 4.5 0.0 1.0
CA E:CYS158 4.6 0.5 0.8
CB E:CYS144 4.8 96.0 1.0
ND1 E:HIS161 4.8 0.6 1.0
O E:CYS144 4.8 0.8 1.0
N E:HIS161 4.8 0.7 1.0
OH E:TYR165 4.8 0.2 1.0
N E:CYS144 4.9 95.4 1.0
N E:LEU142 5.0 99.8 1.0

Iron binding site 5 out of 10 in 4u3f

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Iron binding site 5 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.6
occ:0.81
FE2 E:FES501 0.0 0.6 0.8
ND1 E:HIS161 2.2 0.6 1.0
ND1 E:HIS141 2.2 0.8 1.0
S1 E:FES501 2.2 1.0 0.8
S2 E:FES501 2.2 0.1 0.8
CG E:HIS161 3.0 0.1 1.0
CG E:HIS141 3.0 0.1 1.0
FE1 E:FES501 3.1 92.1 0.8
CB E:HIS161 3.2 0.7 1.0
CB E:HIS141 3.2 0.1 1.0
CE1 E:HIS161 3.2 0.5 1.0
CE1 E:HIS141 3.3 0.3 1.0
N E:LEU142 3.9 99.8 1.0
N E:HIS161 3.9 0.7 1.0
CA E:HIS161 4.1 0.3 1.0
CD2 E:HIS161 4.2 0.8 1.0
CD2 E:HIS141 4.2 0.9 1.0
NE2 E:HIS161 4.2 0.4 1.0
SG E:CYS139 4.3 0.6 1.0
CB E:LEU142 4.3 86.6 1.0
NE2 E:HIS141 4.3 96.9 1.0
CB E:CYS160 4.4 0.0 1.0
CA E:HIS141 4.4 0.0 1.0
C E:HIS141 4.6 100.0 1.0
CG E:LEU142 4.6 86.0 1.0
CG E:PRO175 4.6 0.5 1.0
CA E:LEU142 4.7 87.6 1.0
SG E:CYS158 4.7 0.2 0.8
OG E:SER163 4.7 0.6 0.8
C E:CYS160 4.8 0.2 1.0
C E:HIS161 4.8 0.8 1.0

Iron binding site 6 out of 10 in 4u3f

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Iron binding site 6 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe402

b:31.1
occ:1.00
FE P:HEM402 0.0 31.1 1.0
NE2 P:HIS84 2.0 34.2 1.0
NE2 P:HIS183 2.0 30.7 1.0
NC P:HEM402 2.0 32.2 1.0
NB P:HEM402 2.1 31.8 1.0
ND P:HEM402 2.1 32.2 1.0
NA P:HEM402 2.1 31.3 1.0
CE1 P:HIS84 2.8 35.3 1.0
CE1 P:HIS183 2.9 32.7 1.0
C1C P:HEM402 3.1 34.1 1.0
C4D P:HEM402 3.1 32.6 1.0
C1B P:HEM402 3.1 31.0 1.0
C4A P:HEM402 3.1 33.2 1.0
CD2 P:HIS183 3.1 31.0 1.0
C4B P:HEM402 3.1 30.8 1.0
C1A P:HEM402 3.1 31.0 1.0
C4C P:HEM402 3.1 31.3 1.0
C1D P:HEM402 3.1 32.6 1.0
CD2 P:HIS84 3.2 34.9 1.0
CHC P:HEM402 3.4 32.0 1.0
CHA P:HEM402 3.4 32.6 1.0
CHB P:HEM402 3.4 30.9 1.0
CHD P:HEM402 3.4 32.4 1.0
ND1 P:HIS84 4.0 34.7 1.0
ND1 P:HIS183 4.0 34.2 1.0
CG P:HIS183 4.1 32.7 1.0
CG P:HIS84 4.2 35.0 1.0
C2C P:HEM402 4.3 35.5 1.0
C3D P:HEM402 4.3 29.0 1.0
C3A P:HEM402 4.3 31.5 1.0
C2D P:HEM402 4.3 30.6 1.0
C2B P:HEM402 4.3 32.7 1.0
C3C P:HEM402 4.3 34.4 1.0
C2A P:HEM402 4.3 32.4 1.0
C3B P:HEM402 4.3 32.1 1.0
CA P:GLY49 5.0 35.1 1.0

Iron binding site 7 out of 10 in 4u3f

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Iron binding site 7 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe403

b:30.2
occ:1.00
FE P:HEM403 0.0 30.2 1.0
ND P:HEM403 2.0 33.3 1.0
NB P:HEM403 2.0 27.8 1.0
NC P:HEM403 2.0 28.5 1.0
NA P:HEM403 2.1 31.4 1.0
NE2 P:HIS197 2.1 32.9 1.0
NE2 P:HIS98 2.1 42.3 1.0
CD2 P:HIS197 3.0 36.5 1.0
CE1 P:HIS197 3.0 34.0 1.0
CD2 P:HIS98 3.0 45.9 1.0
C1C P:HEM403 3.0 31.2 1.0
C4C P:HEM403 3.0 30.2 1.0
CE1 P:HIS98 3.1 42.6 1.0
C4B P:HEM403 3.1 29.6 1.0
C1D P:HEM403 3.1 32.9 1.0
C1B P:HEM403 3.1 31.0 1.0
C4D P:HEM403 3.1 33.4 1.0
C4A P:HEM403 3.1 31.3 1.0
C1A P:HEM403 3.1 32.6 1.0
CHC P:HEM403 3.4 30.8 1.0
CHD P:HEM403 3.4 34.8 1.0
CHB P:HEM403 3.4 32.8 1.0
CHA P:HEM403 3.4 35.6 1.0
ND1 P:HIS197 4.1 34.8 1.0
ND1 P:HIS98 4.1 42.8 1.0
CG P:HIS197 4.1 40.9 1.0
CG P:HIS98 4.1 43.9 1.0
C2C P:HEM403 4.2 31.4 1.0
C3C P:HEM403 4.2 30.0 1.0
C3B P:HEM403 4.3 29.8 1.0
C2B P:HEM403 4.3 28.6 1.0
C2D P:HEM403 4.3 32.6 1.0
C3D P:HEM403 4.3 34.0 1.0
C3A P:HEM403 4.3 35.0 1.0
C2A P:HEM403 4.3 38.9 1.0

Iron binding site 8 out of 10 in 4u3f

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Iron binding site 8 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe501

b:62.2
occ:1.00
FE Q:HEC501 0.0 62.2 1.0
NE2 Q:HIS41 2.0 54.3 1.0
NA Q:HEC501 2.0 50.8 1.0
ND Q:HEC501 2.0 53.6 1.0
NB Q:HEC501 2.1 48.5 1.0
NC Q:HEC501 2.1 46.6 1.0
SD Q:MET160 2.3 60.2 1.0
CD2 Q:HIS41 2.9 57.1 1.0
CE1 Q:HIS41 3.0 54.6 1.0
C4D Q:HEC501 3.1 50.8 1.0
C4B Q:HEC501 3.1 48.0 1.0
C1A Q:HEC501 3.1 50.9 1.0
C4A Q:HEC501 3.1 50.1 1.0
C1C Q:HEC501 3.1 53.2 1.0
C1B Q:HEC501 3.1 53.3 1.0
C1D Q:HEC501 3.1 48.7 1.0
C4C Q:HEC501 3.1 44.5 1.0
CHA Q:HEC501 3.4 50.7 1.0
CHC Q:HEC501 3.4 52.2 1.0
CHB Q:HEC501 3.4 53.5 1.0
CHD Q:HEC501 3.5 46.0 1.0
CG Q:MET160 3.6 60.9 1.0
CE Q:MET160 3.7 59.2 1.0
CG Q:HIS41 4.0 57.8 1.0
ND1 Q:HIS41 4.0 57.2 1.0
C3B Q:HEC501 4.3 49.3 1.0
C3A Q:HEC501 4.3 45.1 1.0
C3D Q:HEC501 4.3 53.6 1.0
C2A Q:HEC501 4.3 49.0 1.0
C2D Q:HEC501 4.3 48.8 1.0
C2B Q:HEC501 4.3 52.2 1.0
C2C Q:HEC501 4.3 51.5 1.0
C3C Q:HEC501 4.3 49.8 1.0
CB Q:MET160 4.4 63.3 1.0

Iron binding site 9 out of 10 in 4u3f

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Iron binding site 9 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:0.5
occ:1.00
FE1 R:FES501 0.0 0.5 1.0
SG R:CYS139 2.2 72.5 1.0
SG R:CYS158 2.2 67.7 1.0
S1 R:FES501 2.2 71.1 1.0
S2 R:FES501 2.2 84.9 1.0
CB R:CYS139 3.0 69.2 1.0
FE2 R:FES501 3.1 92.9 1.0
CB R:CYS158 3.1 84.4 1.0
CB R:HIS141 4.0 81.3 1.0
OG R:SER163 4.3 77.8 0.9
CB R:SER163 4.4 86.1 0.9
CA R:CYS139 4.4 67.7 1.0
CB R:CYS160 4.5 77.3 1.0
CB R:CYS144 4.5 70.6 1.0
CA R:CYS158 4.6 94.6 1.0
N R:CYS144 4.7 66.9 1.0
N R:LEU142 4.7 71.5 1.0
ND1 R:HIS141 4.7 88.1 1.0
ND1 R:HIS161 4.8 84.0 1.0
N R:HIS161 4.8 83.4 1.0
OH R:TYR165 4.9 89.5 1.0
CG R:HIS141 4.9 83.9 1.0
N R:HIS141 4.9 79.4 1.0

Iron binding site 10 out of 10 in 4u3f

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Iron binding site 10 out of 10 in the Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Cytochrome BC1 Complex From Chicken with Designed Inhibitor Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:92.9
occ:1.00
FE2 R:FES501 0.0 92.9 1.0
ND1 R:HIS141 2.2 88.1 1.0
ND1 R:HIS161 2.2 84.0 1.0
S1 R:FES501 2.2 71.1 1.0
S2 R:FES501 2.2 84.9 1.0
CG R:HIS161 3.0 84.7 1.0
CG R:HIS141 3.0 83.9 1.0
FE1 R:FES501 3.1 0.5 1.0
CB R:HIS161 3.2 84.7 1.0
CE1 R:HIS141 3.2 87.0 1.0
CB R:HIS141 3.2 81.3 1.0
CE1 R:HIS161 3.2 83.1 1.0
N R:LEU142 3.9 71.5 1.0
N R:HIS161 3.9 83.4 1.0
CA R:HIS161 4.1 86.8 1.0
CD2 R:HIS141 4.1 81.7 1.0
CD2 R:HIS161 4.1 81.5 1.0
NE2 R:HIS141 4.2 81.5 1.0
NE2 R:HIS161 4.2 78.4 1.0
CB R:LEU142 4.2 68.5 1.0
CB R:CYS160 4.4 77.3 1.0
CA R:HIS141 4.5 79.4 1.0
SG R:CYS139 4.5 72.5 1.0
C R:HIS141 4.6 76.8 1.0
CG R:LEU142 4.6 62.7 1.0
CA R:LEU142 4.7 63.1 1.0
SG R:CYS158 4.7 67.7 1.0
OG R:SER163 4.7 77.8 0.9
C R:CYS160 4.8 79.7 1.0
C R:HIS161 4.8 90.9 1.0
CD1 R:LEU142 4.9 54.1 1.0
CG R:PRO175 5.0 81.6 1.0

Reference:

G.-F.Hao, S.-G.Yang, W.Huang, L.Wang, Y.-Q.Shen, W.-L.Tu, H.Li, L.-S.Huang, J.-W.Wu, E.A.Berry, G.-F.Yang. Rational Design of Highly Potent and Slow-Binding Cytochrome BC1 Inhibitor As Fungicide By Computational Substitution Optimization Sci Rep V. 5 2015.
ISSN: ESSN 2045-2322
DOI: 10.1038/SREP13471
Page generated: Tue Aug 5 15:15:24 2025

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