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Iron in PDB 3h1l: Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites

Enzymatic activity of Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites

All present enzymatic activity of Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites:
1.10.2.2;

Protein crystallography data

The structure of Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites, PDB code: 3h1l was solved by E.A.Berry, L.S.Huang, N.Minagawa, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.99 / 3.21
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 174.139, 182.364, 241.626, 90.00, 90.00, 90.00
R / Rfree (%) 26.7 / 29.5

Other elements in 3h1l:

The structure of Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites (pdb code 3h1l). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites, PDB code: 3h1l:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 3h1l

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Iron binding site 1 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

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

b:48.1
occ:1.00
 FE C:HEM501 0.0 48.1 1.0
NB C:HEM501 1.9 50.8 1.0
NA C:HEM501 1.9 52.3 1.0
ND C:HEM501 1.9 52.5 1.0
NC C:HEM501 2.0 51.4 1.0
NE2 C:HIS84 2.0 51.5 1.0
NE2 C:HIS183 2.0 50.4 1.0
CE1 C:HIS183 2.9 51.9 1.0
C1B C:HEM501 2.9 53.7 1.0
C4A C:HEM501 2.9 54.5 1.0
CE1 C:HIS84 2.9 54.3 1.0
C4B C:HEM501 2.9 52.5 1.0
C1A C:HEM501 3.0 53.2 1.0
C4D C:HEM501 3.0 54.6 1.0
C1C C:HEM501 3.0 51.7 1.0
C1D C:HEM501 3.0 53.8 1.0
C4C C:HEM501 3.0 51.4 1.0
CD2 C:HIS84 3.1 52.8 1.0
CD2 C:HIS183 3.1 49.4 1.0
CHB C:HEM501 3.3 55.0 1.0
CHA C:HEM501 3.3 54.6 1.0
CHC C:HEM501 3.4 52.0 1.0
CHD C:HEM501 3.4 52.2 1.0
ND1 C:HIS183 4.0 51.2 1.0
ND1 C:HIS84 4.1 53.8 1.0
CG C:HIS84 4.2 51.8 1.0
C3A C:HEM501 4.2 54.5 1.0
CG C:HIS183 4.2 48.4 1.0
C2A C:HEM501 4.2 53.0 1.0
C3B C:HEM501 4.2 53.2 1.0
C2C C:HEM501 4.2 53.4 1.0
C2B C:HEM501 4.2 53.5 1.0
C3C C:HEM501 4.2 52.8 1.0
C3D C:HEM501 4.2 56.0 1.0
C2D C:HEM501 4.3 55.0 1.0
CA C:GLY131 4.8 52.3 1.0

Iron binding site 2 out of 10 in 3h1l

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Iron binding site 2 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

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

b:44.3
occ:1.00
 FE C:HEM502 0.0 44.3 1.0
NB C:HEM502 1.9 42.0 1.0
ND C:HEM502 1.9 40.5 1.0
NA C:HEM502 1.9 42.6 1.0
NC C:HEM502 2.0 40.8 1.0
NE2 C:HIS197 2.0 43.0 1.0
NE2 C:HIS98 2.0 46.5 1.0
C4B C:HEM502 2.9 43.2 1.0
C1D C:HEM502 3.0 40.5 1.0
CD2 C:HIS197 3.0 44.3 1.0
C4D C:HEM502 3.0 40.7 1.0
C4C C:HEM502 3.0 39.9 1.0
C4A C:HEM502 3.0 42.9 1.0
C1B C:HEM502 3.0 42.6 1.0
C1A C:HEM502 3.0 41.4 1.0
CE1 C:HIS197 3.0 44.9 1.0
CD2 C:HIS98 3.0 48.8 1.0
CE1 C:HIS98 3.0 49.6 1.0
C1C C:HEM502 3.0 39.5 1.0
CHD C:HEM502 3.3 39.4 1.0
CHC C:HEM502 3.3 41.1 1.0
CHB C:HEM502 3.4 42.9 1.0
CHA C:HEM502 3.4 40.4 1.0
ND1 C:HIS197 4.1 46.0 1.0
CG C:HIS197 4.1 45.4 1.0
ND1 C:HIS98 4.1 51.2 1.0
CG C:HIS98 4.1 50.6 1.0
C2D C:HEM502 4.2 42.2 1.0
C2A C:HEM502 4.2 42.0 1.0
C3A C:HEM502 4.2 42.0 1.0
C3B C:HEM502 4.2 43.3 1.0
C2C C:HEM502 4.2 38.8 1.0
C3D C:HEM502 4.2 42.0 1.0
C3C C:HEM502 4.2 39.4 1.0
C2B C:HEM502 4.3 42.1 1.0

Iron binding site 3 out of 10 in 3h1l

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Iron binding site 3 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

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

b:48.7
occ:1.00
 FE D:HEC501 0.0 48.7 1.0
NC D:HEC501 1.9 48.5 1.0
ND D:HEC501 1.9 46.5 1.0
NA D:HEC501 2.0 45.1 1.0
NB D:HEC501 2.0 47.5 1.0
NE2 D:HIS41 2.0 54.0 1.0
SD D:MET160 2.2 50.7 1.0
C4C D:HEC501 2.9 50.4 1.0
C1D D:HEC501 2.9 47.1 1.0
C4D D:HEC501 3.0 46.8 1.0
C1B D:HEC501 3.0 46.0 1.0
C1C D:HEC501 3.0 49.9 1.0
CE1 D:HIS41 3.0 57.4 1.0
CD2 D:HIS41 3.0 56.3 1.0
C4A D:HEC501 3.0 43.6 1.0
C1A D:HEC501 3.0 43.9 1.0
C4B D:HEC501 3.0 47.6 1.0
CHD D:HEC501 3.2 49.3 1.0
CHA D:HEC501 3.3 45.0 1.0
CHB D:HEC501 3.4 42.8 1.0
CHC D:HEC501 3.4 48.5 1.0
CE D:MET160 3.5 45.0 1.0
CG D:MET160 3.5 49.6 1.0
ND1 D:HIS41 4.1 57.1 1.0
CG D:HIS41 4.1 56.6 1.0
CB D:MET160 4.2 51.3 1.0
C3C D:HEC501 4.2 52.9 1.0
C2D D:HEC501 4.2 47.8 1.0
C2B D:HEC501 4.2 47.3 1.0
C3D D:HEC501 4.2 48.3 1.0
C2C D:HEC501 4.2 50.8 1.0
C3B D:HEC501 4.3 48.2 1.0
C3A D:HEC501 4.3 43.7 1.0
C2A D:HEC501 4.3 44.2 1.0

Iron binding site 4 out of 10 in 3h1l

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Iron binding site 4 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

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

b:0.4
occ:0.96
 FE1 E:FES501 0.0 0.4 1.0
S2 E:FES501 2.2 0.6 1.0
S1 E:FES501 2.2 0.6 1.0
SG E:CYS158 2.3 0.1 1.0
SG E:CYS139 2.3 0.0 1.0
FE2 E:FES501 2.6 0.3 1.0
CB E:CYS158 3.0 0.3 1.0
CB E:CYS139 3.1 0.1 1.0
CB E:HIS141 3.9 0.5 1.0
OG E:SER163 4.3 0.8 1.0
ND1 E:HIS141 4.3 0.4 1.0
ND1 E:HIS161 4.4 0.2 1.0
CB E:CYS160 4.4 0.9 1.0
CA E:CYS158 4.5 0.9 1.0
CB E:CYS144 4.5 0.4 1.0
N E:HIS161 4.5 0.5 1.0
CB E:SER163 4.5 0.9 1.0
CA E:CYS139 4.5 1.0 1.0
CG E:HIS141 4.6 0.8 1.0
N E:LEU142 4.7 0.2 1.0
N E:CYS144 4.7 0.3 1.0
O E:CYS158 4.8 0.7 1.0
C E:CYS158 4.9 0.3 1.0
SG E:CYS144 5.0 0.8 1.0
CA E:HIS141 5.0 0.4 1.0

Iron binding site 5 out of 10 in 3h1l

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Iron binding site 5 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

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

b:0.3
occ:0.96
 FE2 E:FES501 0.0 0.3 1.0
ND1 E:HIS161 2.1 0.2 1.0
ND1 E:HIS141 2.1 0.4 1.0
S1 E:FES501 2.2 0.6 1.0
S2 E:FES501 2.2 0.6 1.0
FE1 E:FES501 2.6 0.4 1.0
CG E:HIS161 3.0 0.4 1.0
CG E:HIS141 3.0 0.8 1.0
CE1 E:HIS161 3.1 0.7 1.0
CE1 E:HIS141 3.1 0.8 1.0
CB E:HIS161 3.2 1.0 1.0
CB E:HIS141 3.3 0.5 1.0
N E:HIS161 3.8 0.5 1.0
CA E:HIS161 4.1 0.7 1.0
N E:LEU142 4.1 0.2 1.0
CD2 E:HIS161 4.1 0.8 1.0
CB E:CYS160 4.2 0.9 1.0
NE2 E:HIS161 4.2 1.0 1.0
CD2 E:HIS141 4.2 0.6 1.0
NE2 E:HIS141 4.2 0.8 1.0
SG E:CYS139 4.3 0.0 1.0
SG E:CYS158 4.4 0.1 1.0
CB E:LEU142 4.5 0.9 1.0
C E:CYS160 4.6 0.1 1.0
CA E:HIS141 4.7 0.4 1.0
C E:HIS141 4.8 0.4 1.0
CG E:LEU142 4.8 0.2 1.0
CA E:LEU142 4.8 0.3 1.0
C E:HIS161 4.9 0.6 1.0
CG E:PRO175 4.9 0.0 1.0
OG E:SER163 4.9 0.8 1.0
CA E:CYS160 5.0 0.1 1.0

Iron binding site 6 out of 10 in 3h1l

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Iron binding site 6 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe501

b:73.9
occ:1.00
 FE P:HEM501 0.0 73.9 1.0
NA P:HEM501 1.9 77.4 1.0
NB P:HEM501 1.9 75.8 1.0
NC P:HEM501 1.9 76.7 1.0
ND P:HEM501 2.0 77.3 1.0
NE2 P:HIS183 2.0 72.1 1.0
NE2 P:HIS84 2.0 74.9 1.0
CE1 P:HIS183 2.9 70.9 1.0
CE1 P:HIS84 2.9 74.1 1.0
C1B P:HEM501 2.9 76.9 1.0
C4A P:HEM501 3.0 78.8 1.0
C1A P:HEM501 3.0 79.3 1.0
C4B P:HEM501 3.0 77.1 1.0
C1C P:HEM501 3.0 78.5 1.0
C4D P:HEM501 3.0 78.6 1.0
C4C P:HEM501 3.0 76.8 1.0
C1D P:HEM501 3.1 77.5 1.0
CD2 P:HIS84 3.1 74.8 1.0
CD2 P:HIS183 3.1 70.4 1.0
CHB P:HEM501 3.3 78.8 1.0
CHC P:HEM501 3.4 78.5 1.0
CHA P:HEM501 3.4 79.3 1.0
CHD P:HEM501 3.4 77.3 1.0
ND1 P:HIS183 4.1 70.8 1.0
ND1 P:HIS84 4.1 74.2 1.0
C2B P:HEM501 4.2 76.8 1.0
CG P:HIS84 4.2 75.7 1.0
CG P:HIS183 4.2 70.0 1.0
C3B P:HEM501 4.2 76.2 1.0
C2A P:HEM501 4.2 79.9 1.0
C3A P:HEM501 4.2 78.4 1.0
C2C P:HEM501 4.2 78.5 1.0
C3D P:HEM501 4.3 79.1 1.0
C3C P:HEM501 4.3 76.8 1.0
C2D P:HEM501 4.3 78.0 1.0
CA P:GLY131 4.8 79.2 1.0

Iron binding site 7 out of 10 in 3h1l

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Iron binding site 7 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites 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
NC P:HEM502 1.9 81.3 1.0
NB P:HEM502 1.9 80.8 1.0
ND P:HEM502 1.9 83.2 1.0
NA P:HEM502 2.0 81.1 1.0
NE2 P:HIS197 2.0 80.1 1.0
NE2 P:HIS98 2.0 83.4 1.0
C1C P:HEM502 2.9 81.3 1.0
C4B P:HEM502 2.9 81.2 1.0
C4C P:HEM502 2.9 82.3 1.0
C1D P:HEM502 3.0 83.9 1.0
CD2 P:HIS197 3.0 79.7 1.0
CE1 P:HIS197 3.0 79.8 1.0
CD2 P:HIS98 3.0 84.1 1.0
CE1 P:HIS98 3.0 83.8 1.0
C1B P:HEM502 3.0 80.1 1.0
C4A P:HEM502 3.0 80.3 1.0
C4D P:HEM502 3.0 84.1 1.0
C1A P:HEM502 3.1 81.5 1.0
CHC P:HEM502 3.3 81.6 1.0
CHD P:HEM502 3.3 83.4 1.0
CHB P:HEM502 3.4 80.1 1.0
CHA P:HEM502 3.5 81.9 1.0
ND1 P:HIS197 4.1 80.1 1.0
CG P:HIS197 4.1 79.6 1.0
ND1 P:HIS98 4.1 84.0 1.0
CG P:HIS98 4.1 85.8 1.0
C2C P:HEM502 4.2 81.7 1.0
C3C P:HEM502 4.2 82.1 1.0
C3B P:HEM502 4.2 80.9 1.0
C2D P:HEM502 4.2 84.6 1.0
C3A P:HEM502 4.3 80.8 1.0
C2B P:HEM502 4.3 80.2 1.0
C3D P:HEM502 4.3 85.7 1.0
C2A P:HEM502 4.3 82.2 1.0

Iron binding site 8 out of 10 in 3h1l

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Iron binding site 8 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

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

b:0.6
occ:1.00
 FE Q:HEC501 0.0 0.6 1.0
NC Q:HEC501 1.9 0.1 1.0
NB Q:HEC501 2.0 99.1 1.0
ND Q:HEC501 2.0 98.9 1.0
NA Q:HEC501 2.0 99.3 1.0
NE2 Q:HIS41 2.0 0.4 1.0
SD Q:MET160 2.1 0.2 1.0
C4C Q:HEC501 2.9 1.0 1.0
CD2 Q:HIS41 3.0 0.1 1.0
C1D Q:HEC501 3.0 97.5 1.0
C1B Q:HEC501 3.0 97.2 1.0
C1C Q:HEC501 3.0 0.0 1.0
C4B Q:HEC501 3.0 99.2 1.0
C4A Q:HEC501 3.0 97.2 1.0
C4D Q:HEC501 3.0 97.0 1.0
CE1 Q:HIS41 3.0 0.3 1.0
C1A Q:HEC501 3.1 97.1 1.0
CHD Q:HEC501 3.3 98.3 1.0
CHB Q:HEC501 3.3 96.5 1.0
CHC Q:HEC501 3.4 0.2 1.0
CHA Q:HEC501 3.4 96.4 1.0
CE Q:MET160 3.5 0.1 1.0
CG Q:MET160 3.5 0.3 1.0
CG Q:HIS41 4.1 0.9 1.0
ND1 Q:HIS41 4.1 0.1 1.0
C3C Q:HEC501 4.2 0.4 1.0
C2B Q:HEC501 4.2 98.0 1.0
C2D Q:HEC501 4.2 97.5 1.0
CB Q:MET160 4.2 0.6 1.0
C2C Q:HEC501 4.2 0.7 1.0
C3B Q:HEC501 4.2 99.3 1.0
C3D Q:HEC501 4.2 97.5 1.0
C3A Q:HEC501 4.3 96.5 1.0
C2A Q:HEC501 4.3 96.4 1.0

Iron binding site 9 out of 10 in 3h1l

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Iron binding site 9 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

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

b:69.0
occ:1.00
 FE1 R:FES501 0.0 69.0 1.0
S1 R:FES501 2.2 69.7 1.0
S2 R:FES501 2.2 69.0 1.0
SG R:CYS158 2.2 70.2 1.0
SG R:CYS139 2.3 71.2 1.0
FE2 R:FES501 2.6 69.4 1.0
CB R:CYS158 3.0 67.4 1.0
CB R:CYS139 3.1 71.2 1.0
CB R:HIS141 3.9 70.8 1.0
OG R:SER163 4.2 75.0 1.0
ND1 R:HIS141 4.3 69.6 1.0
ND1 R:HIS161 4.4 66.6 1.0
CA R:CYS158 4.5 67.3 1.0
CB R:CYS160 4.5 66.6 1.0
CB R:SER163 4.5 73.6 1.0
CA R:CYS139 4.5 72.5 1.0
CG R:HIS141 4.6 69.5 1.0
N R:HIS161 4.6 67.9 1.0
CB R:CYS144 4.6 68.9 1.0
N R:LEU142 4.7 68.9 1.0
N R:CYS144 4.8 66.7 1.0
O R:CYS158 4.9 67.2 1.0
C R:CYS158 4.9 66.6 1.0
CA R:HIS141 5.0 71.6 1.0
N R:HIS141 5.0 73.7 1.0

Iron binding site 10 out of 10 in 3h1l

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Iron binding site 10 out of 10 in the Chicken Cytochrome BC1 Complex with Ascochlorin Bound at Qo and Qi Sites


Mono view


Stereo pair view

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

b:69.4
occ:1.00
 FE2 R:FES501 0.0 69.4 1.0
ND1 R:HIS161 2.1 66.6 1.0
ND1 R:HIS141 2.1 69.6 1.0
S2 R:FES501 2.2 69.0 1.0
S1 R:FES501 2.2 69.7 1.0
FE1 R:FES501 2.6 69.0 1.0
CG R:HIS161 3.0 65.6 1.0
CG R:HIS141 3.0 69.5 1.0
CE1 R:HIS161 3.1 66.8 1.0
CE1 R:HIS141 3.1 69.0 1.0
CB R:HIS161 3.2 66.0 1.0
CB R:HIS141 3.3 70.8 1.0
N R:HIS161 3.8 67.9 1.0
N R:LEU142 4.0 68.9 1.0
CA R:HIS161 4.1 67.9 1.0
CD2 R:HIS161 4.2 65.7 1.0
CD2 R:HIS141 4.2 69.6 1.0
NE2 R:HIS161 4.2 66.0 1.0
NE2 R:HIS141 4.2 67.8 1.0
CB R:CYS160 4.2 66.6 1.0
SG R:CYS139 4.3 71.2 1.0
CB R:LEU142 4.4 63.7 1.0
SG R:CYS158 4.4 70.2 1.0
CA R:HIS141 4.6 71.6 1.0
C R:CYS160 4.7 67.0 1.0
CG R:LEU142 4.7 60.3 1.0
C R:HIS141 4.7 70.8 1.0
CA R:LEU142 4.7 66.7 1.0
CG R:PRO175 4.8 83.9 1.0
C R:HIS161 4.9 68.7 1.0
OG R:SER163 4.9 75.0 1.0

Reference:

E.A.Berry, L.S.Huang, D.W.Lee, F.Daldal, K.Nagai, N.Minagawa. Ascochlorin Is A Novel, Specific Inhibitor of the Mitochondrial Cytochrome Bc(1) Complex. Biochim.Biophys.Acta V.1797 360 2010.
ISSN: ISSN 0006-3002
PubMed: 20025846
DOI: 10.1016/J.BBABIO.2009.12.003
Page generated: Sun Dec 13 15:07:17 2020

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