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Iron in PDB 2a06: Bovine Cytochrome BC1 Complex with Stigmatellin Bound

Enzymatic activity of Bovine Cytochrome BC1 Complex with Stigmatellin Bound

All present enzymatic activity of Bovine Cytochrome BC1 Complex with Stigmatellin Bound:
1.10.2.2;

Protein crystallography data

The structure of Bovine Cytochrome BC1 Complex with Stigmatellin Bound, PDB code: 2a06 was solved by L.S.Huang, D.Cobessi, E.Y.Tung, E.A.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.87 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 128.252, 168.800, 230.818, 90.00, 90.00, 90.00
R / Rfree (%) 22.2 / 25.8

Iron Binding Sites:

The binding sites of Iron atom in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound (pdb code 2a06). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound, PDB code: 2a06:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 2a06

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Iron binding site 1 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

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

b:27.3
occ:1.00
FE C:HEM501 0.0 27.3 1.0
NC C:HEM501 1.9 25.5 1.0
NA C:HEM501 1.9 27.9 1.0
NB C:HEM501 2.0 29.2 1.0
NE2 C:HIS83 2.0 23.4 1.0
NE2 C:HIS182 2.0 26.8 1.0
ND C:HEM501 2.0 27.8 1.0
CE1 C:HIS83 3.0 24.7 1.0
CD2 C:HIS182 3.0 24.2 1.0
C1C C:HEM501 3.0 27.4 1.0
C4C C:HEM501 3.0 29.0 1.0
C1A C:HEM501 3.0 29.9 1.0
C4A C:HEM501 3.0 25.6 1.0
CE1 C:HIS182 3.0 23.8 1.0
CD2 C:HIS83 3.0 24.4 1.0
C1B C:HEM501 3.0 26.7 1.0
C4B C:HEM501 3.0 26.7 1.0
C4D C:HEM501 3.1 23.9 1.0
C1D C:HEM501 3.1 24.7 1.0
CHB C:HEM501 3.4 24.0 1.0
CHC C:HEM501 3.4 27.4 1.0
CHA C:HEM501 3.4 26.8 1.0
CHD C:HEM501 3.4 27.5 1.0
ND1 C:HIS83 4.1 22.0 1.0
ND1 C:HIS182 4.1 24.4 1.0
CG C:HIS182 4.1 24.5 1.0
CG C:HIS83 4.2 21.5 1.0
C3C C:HEM501 4.2 25.6 1.0
C2A C:HEM501 4.2 26.8 1.0
C2C C:HEM501 4.2 25.6 1.0
C3A C:HEM501 4.2 28.2 1.0
C2B C:HEM501 4.3 28.4 1.0
C3B C:HEM501 4.3 31.0 1.0
C3D C:HEM501 4.3 27.0 1.0
C2D C:HEM501 4.4 26.2 1.0
CA C:GLY130 4.7 29.3 1.0
NE2 C:GLN44 4.9 26.9 1.0

Iron binding site 2 out of 10 in 2a06

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Iron binding site 2 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

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

b:29.3
occ:1.00
FE C:HEM502 0.0 29.3 1.0
NC C:HEM502 1.9 25.6 1.0
ND C:HEM502 2.0 26.9 1.0
NE2 C:HIS97 2.0 28.9 1.0
NE2 C:HIS196 2.0 25.4 1.0
NB C:HEM502 2.0 25.0 1.0
NA C:HEM502 2.0 25.1 1.0
CE1 C:HIS97 2.9 36.5 1.0
CD2 C:HIS196 3.0 28.1 1.0
C4C C:HEM502 3.0 29.2 1.0
C1C C:HEM502 3.0 27.5 1.0
CE1 C:HIS196 3.0 29.6 1.0
C1D C:HEM502 3.0 28.2 1.0
C4D C:HEM502 3.0 23.1 1.0
CD2 C:HIS97 3.1 29.0 1.0
C1B C:HEM502 3.1 28.2 1.0
C4A C:HEM502 3.1 26.6 1.0
C1A C:HEM502 3.1 25.7 1.0
C4B C:HEM502 3.1 26.4 1.0
CHD C:HEM502 3.4 24.4 1.0
CHB C:HEM502 3.4 28.3 1.0
CHC C:HEM502 3.4 24.3 1.0
CHA C:HEM502 3.4 27.4 1.0
ND1 C:HIS97 4.1 33.0 1.0
ND1 C:HIS196 4.1 28.3 1.0
CG C:HIS196 4.1 25.8 1.0
CG C:HIS97 4.2 30.0 1.0
C2C C:HEM502 4.2 26.2 1.0
C3C C:HEM502 4.2 26.3 1.0
C2D C:HEM502 4.2 24.0 1.0
C3D C:HEM502 4.3 27.0 1.0
C3A C:HEM502 4.3 25.1 1.0
C2B C:HEM502 4.3 27.1 1.0
C2A C:HEM502 4.3 30.7 1.0
C3B C:HEM502 4.3 29.0 1.0
O C:HOH4105 4.9 31.2 1.0

Iron binding site 3 out of 10 in 2a06

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Iron binding site 3 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

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

b:32.1
occ:1.00
FE D:HEC501 0.0 32.1 1.0
NA D:HEC501 1.9 34.7 1.0
ND D:HEC501 1.9 34.8 1.0
NE2 D:HIS41 2.0 31.0 1.0
NB D:HEC501 2.0 34.4 1.0
NC D:HEC501 2.0 37.4 1.0
SD D:MET160 2.2 34.7 1.0
CE1 D:HIS41 2.9 26.1 1.0
C4D D:HEC501 3.0 33.8 1.0
C4A D:HEC501 3.0 35.0 1.0
C1D D:HEC501 3.0 35.2 1.0
C1A D:HEC501 3.0 34.9 1.0
CD2 D:HIS41 3.0 32.5 1.0
C1B D:HEC501 3.1 34.2 1.0
C4B D:HEC501 3.1 33.5 1.0
C1C D:HEC501 3.1 36.3 1.0
C4C D:HEC501 3.1 37.3 1.0
CHA D:HEC501 3.4 33.0 1.0
CHB D:HEC501 3.4 31.4 1.0
CHD D:HEC501 3.4 36.4 1.0
CHC D:HEC501 3.4 31.0 1.0
CG D:MET160 3.5 35.5 1.0
CE D:MET160 3.5 36.1 1.0
ND1 D:HIS41 4.1 29.0 1.0
CB D:MET160 4.1 33.7 1.0
CG D:HIS41 4.1 27.1 1.0
C3D D:HEC501 4.2 35.8 1.0
C3A D:HEC501 4.2 31.5 1.0
C2A D:HEC501 4.2 34.0 1.0
C2D D:HEC501 4.2 35.4 1.0
C2B D:HEC501 4.3 34.0 1.0
C3B D:HEC501 4.3 33.0 1.0
C2C D:HEC501 4.3 34.6 1.0
C3C D:HEC501 4.3 38.0 1.0

Iron binding site 4 out of 10 in 2a06

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Iron binding site 4 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

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

b:40.0
occ:1.00
FE1 E:FES501 0.0 40.0 1.0
SG E:CYS158 2.2 45.1 1.0
S1 E:FES501 2.2 39.8 1.0
S2 E:FES501 2.2 38.6 1.0
SG E:CYS139 2.3 39.3 1.0
FE2 E:FES501 2.7 40.3 1.0
CB E:CYS158 3.0 47.4 1.0
CB E:CYS139 3.1 37.2 1.0
CB E:HIS141 4.0 41.1 1.0
OG E:SER163 4.2 50.3 1.0
CB E:SER163 4.4 47.9 1.0
CB E:CYS160 4.4 41.5 1.0
CA E:CYS158 4.4 46.7 1.0
ND1 E:HIS141 4.4 39.4 1.0
CB E:CYS144 4.4 46.2 1.0
N E:HIS161 4.5 39.0 1.0
ND1 E:HIS161 4.6 38.6 1.0
CA E:CYS139 4.6 38.4 1.0
N E:LEU142 4.7 39.0 1.0
CG E:HIS141 4.7 42.5 1.0
O E:CYS158 4.7 49.3 1.0
C E:CYS158 4.7 46.5 1.0
N E:CYS144 4.7 39.4 1.0
N E:CYS160 4.8 38.1 1.0
N E:HIS141 5.0 38.7 1.0

Iron binding site 5 out of 10 in 2a06

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Iron binding site 5 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

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

b:40.3
occ:1.00
FE2 E:FES501 0.0 40.3 1.0
ND1 E:HIS141 2.1 39.4 1.0
ND1 E:HIS161 2.1 38.6 1.0
S2 E:FES501 2.2 38.6 1.0
S1 E:FES501 2.3 39.8 1.0
FE1 E:FES501 2.7 40.0 1.0
CG E:HIS161 3.1 36.4 1.0
CG E:HIS141 3.1 42.5 1.0
CE1 E:HIS141 3.2 36.5 1.0
CE1 E:HIS161 3.2 37.7 1.0
CB E:HIS161 3.3 36.8 1.0
CB E:HIS141 3.3 41.1 1.0
N E:HIS161 3.6 39.0 1.0
N E:LEU142 4.0 39.0 1.0
CA E:HIS161 4.0 41.9 1.0
CB E:CYS160 4.1 41.5 1.0
CD2 E:HIS161 4.2 39.1 1.0
CD2 E:HIS141 4.2 43.0 1.0
NE2 E:HIS141 4.2 37.9 1.0
NE2 E:HIS161 4.2 33.1 1.0
CB E:LEU142 4.3 35.4 1.0
C E:CYS160 4.3 41.8 1.0
SG E:CYS139 4.4 39.3 1.0
SG E:CYS158 4.6 45.1 1.0
CG E:LEU142 4.6 37.3 1.0
CA E:HIS141 4.6 40.6 1.0
CG E:PRO175 4.6 41.1 1.0
C E:HIS141 4.7 38.9 1.0
CA E:LEU142 4.7 37.2 1.0
CA E:CYS160 4.7 40.2 1.0
CD1 E:LEU142 4.7 31.6 1.0
OG E:SER163 4.8 50.3 1.0
C E:HIS161 4.8 42.9 1.0

Iron binding site 6 out of 10 in 2a06

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Iron binding site 6 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Bovine Cytochrome BC1 Complex with Stigmatellin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe501

b:28.8
occ:1.00
FE P:HEM501 0.0 28.8 1.0
NB P:HEM501 1.9 27.5 1.0
ND P:HEM501 2.0 24.8 1.0
NC P:HEM501 2.0 23.7 1.0
NE2 P:HIS182 2.0 23.8 1.0
NA P:HEM501 2.0 25.3 1.0
NE2 P:HIS83 2.0 28.4 1.0
CE1 P:HIS182 3.0 29.6 1.0
C1C P:HEM501 3.0 23.2 1.0
CD2 P:HIS83 3.0 33.6 1.0
C4B P:HEM501 3.0 27.6 1.0
C4C P:HEM501 3.0 23.5 1.0
CE1 P:HIS83 3.0 31.5 1.0
C1B P:HEM501 3.0 29.3 1.0
CD2 P:HIS182 3.0 26.7 1.0
C4D P:HEM501 3.0 27.5 1.0
C1A P:HEM501 3.0 24.8 1.0
C1D P:HEM501 3.0 26.7 1.0
C4A P:HEM501 3.1 26.5 1.0
CHC P:HEM501 3.3 25.7 1.0
CHA P:HEM501 3.4 24.4 1.0
CHD P:HEM501 3.4 26.2 1.0
CHB P:HEM501 3.4 24.9 1.0
ND1 P:HIS182 4.1 25.1 1.0
ND1 P:HIS83 4.1 28.8 1.0
CG P:HIS83 4.1 30.1 1.0
CG P:HIS182 4.1 30.8 1.0
C2B P:HEM501 4.2 27.1 1.0
C3B P:HEM501 4.2 28.8 1.0
C2D P:HEM501 4.2 26.9 1.0
C3D P:HEM501 4.3 30.4 1.0
C2C P:HEM501 4.3 30.2 1.0
C3C P:HEM501 4.3 26.0 1.0
C2A P:HEM501 4.3 25.8 1.0
C3A P:HEM501 4.3 22.2 1.0
CA P:GLY130 4.7 29.1 1.0
NE2 P:GLN44 4.9 27.7 1.0

Iron binding site 7 out of 10 in 2a06

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Iron binding site 7 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Bovine Cytochrome BC1 Complex with Stigmatellin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe502

b:29.4
occ:1.00
FE P:HEM502 0.0 29.4 1.0
NC P:HEM502 1.9 25.9 1.0
ND P:HEM502 2.0 28.1 1.0
NB P:HEM502 2.0 24.9 1.0
NA P:HEM502 2.0 25.5 1.0
NE2 P:HIS196 2.0 30.9 1.0
NE2 P:HIS97 2.0 30.9 1.0
CE1 P:HIS97 3.0 27.8 1.0
C4C P:HEM502 3.0 24.5 1.0
CE1 P:HIS196 3.0 31.2 1.0
CD2 P:HIS196 3.0 31.4 1.0
C1C P:HEM502 3.0 27.1 1.0
C4B P:HEM502 3.0 27.3 1.0
C1A P:HEM502 3.0 27.8 1.0
C4D P:HEM502 3.0 24.3 1.0
CD2 P:HIS97 3.0 26.0 1.0
C1B P:HEM502 3.0 27.2 1.0
C4A P:HEM502 3.1 28.1 1.0
C1D P:HEM502 3.1 28.8 1.0
CHD P:HEM502 3.4 25.8 1.0
CHA P:HEM502 3.4 25.5 1.0
CHB P:HEM502 3.4 25.8 1.0
CHC P:HEM502 3.4 24.1 1.0
ND1 P:HIS196 4.1 29.9 1.0
ND1 P:HIS97 4.1 24.8 1.0
CG P:HIS196 4.1 32.8 1.0
CG P:HIS97 4.2 28.2 1.0
C3C P:HEM502 4.2 24.5 1.0
C2C P:HEM502 4.2 27.9 1.0
C2A P:HEM502 4.3 28.1 1.0
C3B P:HEM502 4.3 26.4 1.0
C3D P:HEM502 4.3 29.5 1.0
C2D P:HEM502 4.3 30.1 1.0
C2B P:HEM502 4.3 28.8 1.0
C3A P:HEM502 4.3 29.1 1.0

Iron binding site 8 out of 10 in 2a06

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Iron binding site 8 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

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

b:36.1
occ:1.00
FE Q:HEC501 0.0 36.1 1.0
NA Q:HEC501 1.9 32.4 1.0
ND Q:HEC501 1.9 31.7 1.0
NC Q:HEC501 1.9 34.7 1.0
NB Q:HEC501 2.0 29.3 1.0
NE2 Q:HIS41 2.0 35.0 1.0
SD Q:MET160 2.2 39.4 1.0
CE1 Q:HIS41 3.0 32.9 1.0
C1D Q:HEC501 3.0 35.4 1.0
C1A Q:HEC501 3.0 37.1 1.0
C4C Q:HEC501 3.0 37.0 1.0
C4D Q:HEC501 3.0 36.5 1.0
C1B Q:HEC501 3.0 31.4 1.0
C4A Q:HEC501 3.0 34.5 1.0
CD2 Q:HIS41 3.0 35.6 1.0
C4B Q:HEC501 3.1 35.7 1.0
C1C Q:HEC501 3.1 35.4 1.0
CHD Q:HEC501 3.3 31.9 1.0
CHA Q:HEC501 3.4 42.0 1.0
CHB Q:HEC501 3.4 33.1 1.0
CG Q:MET160 3.4 33.0 1.0
CHC Q:HEC501 3.5 36.3 1.0
CE Q:MET160 3.5 33.8 1.0
ND1 Q:HIS41 4.1 36.1 1.0
CB Q:MET160 4.1 31.9 1.0
CG Q:HIS41 4.1 36.3 1.0
C2A Q:HEC501 4.2 32.8 1.0
C2D Q:HEC501 4.2 35.7 1.0
C3D Q:HEC501 4.2 37.1 1.0
C2B Q:HEC501 4.2 33.0 1.0
C3C Q:HEC501 4.2 38.2 1.0
C3A Q:HEC501 4.3 33.9 1.0
C3B Q:HEC501 4.3 35.9 1.0
C2C Q:HEC501 4.3 37.6 1.0

Iron binding site 9 out of 10 in 2a06

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Iron binding site 9 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

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

b:29.1
occ:1.00
FE1 R:FES501 0.0 29.1 1.0
S2 R:FES501 2.2 30.3 1.0
S1 R:FES501 2.2 27.7 1.0
SG R:CYS158 2.3 35.0 1.0
SG R:CYS139 2.3 32.2 1.0
FE2 R:FES501 2.7 30.5 1.0
CB R:CYS139 3.1 29.0 1.0
CB R:CYS158 3.1 31.9 1.0
CB R:HIS141 3.9 21.1 1.0
OG R:SER163 4.2 35.1 1.0
ND1 R:HIS141 4.3 30.7 1.0
CB R:CYS160 4.4 26.2 1.0
CB R:CYS144 4.4 35.5 1.0
CB R:SER163 4.4 31.4 1.0
CA R:CYS158 4.5 32.0 1.0
N R:LEU142 4.5 27.9 1.0
CA R:CYS139 4.5 29.3 1.0
N R:HIS161 4.5 32.6 1.0
ND1 R:HIS161 4.5 33.8 1.0
N R:CYS144 4.6 30.8 1.0
CG R:HIS141 4.6 30.4 1.0
C R:CYS158 4.8 28.9 1.0
O R:CYS158 4.9 29.7 1.0
N R:HIS141 4.9 25.5 1.0
CA R:HIS141 4.9 26.5 1.0
N R:CYS160 4.9 33.7 1.0

Iron binding site 10 out of 10 in 2a06

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Iron binding site 10 out of 10 in the Bovine Cytochrome BC1 Complex with Stigmatellin Bound


Mono view


Stereo pair view

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

b:30.5
occ:1.00
FE2 R:FES501 0.0 30.5 1.0
ND1 R:HIS161 2.1 33.8 1.0
ND1 R:HIS141 2.2 30.7 1.0
S2 R:FES501 2.2 30.3 1.0
S1 R:FES501 2.2 27.7 1.0
FE1 R:FES501 2.7 29.1 1.0
CG R:HIS161 3.0 31.9 1.0
CG R:HIS141 3.1 30.4 1.0
CE1 R:HIS161 3.2 34.4 1.0
CE1 R:HIS141 3.2 31.6 1.0
CB R:HIS161 3.3 27.6 1.0
CB R:HIS141 3.4 21.1 1.0
N R:HIS161 3.6 32.6 1.0
N R:LEU142 4.0 27.9 1.0
CA R:HIS161 4.0 33.4 1.0
CB R:CYS160 4.0 26.2 1.0
CD2 R:HIS161 4.2 33.9 1.0
NE2 R:HIS161 4.2 33.4 1.0
CB R:LEU142 4.3 25.2 1.0
CD2 R:HIS141 4.3 31.3 1.0
NE2 R:HIS141 4.3 31.8 1.0
C R:CYS160 4.3 33.9 1.0
SG R:CYS139 4.4 32.2 1.0
SG R:CYS158 4.5 35.0 1.0
CG R:LEU142 4.6 33.1 1.0
CG R:PRO175 4.6 33.1 1.0
CA R:HIS141 4.7 26.5 1.0
CA R:LEU142 4.7 31.0 1.0
CA R:CYS160 4.7 33.0 1.0
C R:HIS141 4.7 26.3 1.0
CD1 R:LEU142 4.8 30.3 1.0
OG R:SER163 4.8 35.1 1.0
C R:HIS161 4.8 36.0 1.0

Reference:

L.S.Huang, D.Cobessi, E.Y.Tung, E.A.Berry. Binding of the Respiratory Chain Inhibitor Antimycin to the Mitochondrial Bc(1) Complex: A New Crystal Structure Reveals An Altered Intramolecular Hydrogen-Bonding Pattern. J.Mol.Biol. V. 351 573 2005.
ISSN: ISSN 0022-2836
PubMed: 16024040
DOI: 10.1016/J.JMB.2005.05.053
Page generated: Sat Aug 3 18:48:11 2024

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