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Iron in PDB 3h1k: Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound

Enzymatic activity of Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound

All present enzymatic activity of Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound:
1.10.2.2;

Protein crystallography data

The structure of Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound, PDB code: 3h1k was solved by E.A.Berry, Z.Zhang, H.D.Bellamy, L.S.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 18.00 / 3.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 171.717, 181.297, 241.288, 90.00, 90.00, 90.00
R / Rfree (%) 23.9 / 28.4

Other elements in 3h1k:

The structure of Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound also contains other interesting chemical elements:

Iodine (I) 2 atoms
Zinc (Zn) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound (pdb code 3h1k). 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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound, PDB code: 3h1k:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 3h1k

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Iron binding site 1 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound 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
NC C:HEM501 1.9 49.5 1.0
NA C:HEM501 1.9 50.3 1.0
NB C:HEM501 1.9 51.8 1.0
ND C:HEM501 1.9 49.8 1.0
NE2 C:HIS183 2.0 47.1 1.0
NE2 C:HIS84 2.0 49.6 1.0
C1C C:HEM501 2.9 51.4 1.0
CE1 C:HIS84 2.9 49.7 1.0
C4C C:HEM501 2.9 49.9 1.0
CD2 C:HIS183 2.9 46.1 1.0
C4A C:HEM501 2.9 51.7 1.0
C4B C:HEM501 3.0 53.4 1.0
C4D C:HEM501 3.0 50.4 1.0
C1A C:HEM501 3.0 51.1 1.0
C1D C:HEM501 3.0 50.0 1.0
CE1 C:HIS183 3.0 46.9 1.0
C1B C:HEM501 3.0 53.9 1.0
CD2 C:HIS84 3.1 49.8 1.0
CHC C:HEM501 3.3 52.6 1.0
CHD C:HEM501 3.3 49.5 1.0
CHA C:HEM501 3.3 51.1 1.0
CHB C:HEM501 3.4 53.1 1.0
ND1 C:HIS84 4.1 51.2 1.0
ND1 C:HIS183 4.1 47.9 1.0
CG C:HIS183 4.1 46.2 1.0
C2C C:HEM501 4.1 52.1 1.0
C3A C:HEM501 4.1 51.9 1.0
C3C C:HEM501 4.2 51.6 1.0
CG C:HIS84 4.2 49.9 1.0
C3D C:HEM501 4.2 50.8 1.0
C3B C:HEM501 4.2 54.5 1.0
C2A C:HEM501 4.2 52.0 1.0
C2D C:HEM501 4.2 49.8 1.0
C2B C:HEM501 4.3 54.2 1.0
CA C:GLY49 4.7 48.1 1.0
CA C:GLY131 5.0 55.4 1.0

Iron binding site 2 out of 10 in 3h1k

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Iron binding site 2 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe502

b:45.4
occ:1.00
 FE C:HEM502 0.0 45.4 1.0
ND C:HEM502 1.9 45.9 1.0
NB C:HEM502 1.9 45.1 1.0
NC C:HEM502 1.9 45.6 1.0
NA C:HEM502 1.9 45.5 1.0
NE2 C:HIS197 2.0 46.2 1.0
NE2 C:HIS98 2.0 47.6 1.0
CE1 C:HIS98 2.9 50.8 1.0
C1D C:HEM502 2.9 47.7 1.0
CE1 C:HIS197 2.9 48.4 1.0
C4B C:HEM502 2.9 45.4 1.0
C4D C:HEM502 2.9 46.9 1.0
C1C C:HEM502 2.9 44.8 1.0
C4C C:HEM502 3.0 46.5 1.0
C1B C:HEM502 3.0 45.4 1.0
C1A C:HEM502 3.0 46.7 1.0
CD2 C:HIS197 3.0 49.5 1.0
C4A C:HEM502 3.0 44.8 1.0
CD2 C:HIS98 3.1 48.2 1.0
CHC C:HEM502 3.3 45.1 1.0
CHD C:HEM502 3.3 48.3 1.0
CHA C:HEM502 3.3 47.2 1.0
CHB C:HEM502 3.4 45.3 1.0
ND1 C:HIS197 4.0 52.5 1.0
ND1 C:HIS98 4.0 52.0 1.0
CG C:HIS197 4.1 52.5 1.0
C2D C:HEM502 4.2 48.3 1.0
CG C:HIS98 4.2 49.3 1.0
C3D C:HEM502 4.2 47.9 1.0
C3B C:HEM502 4.2 46.1 1.0
C2C C:HEM502 4.2 44.5 1.0
C3C C:HEM502 4.2 45.4 1.0
C2A C:HEM502 4.2 46.6 1.0
C3A C:HEM502 4.3 45.2 1.0
C2B C:HEM502 4.3 46.2 1.0

Iron binding site 3 out of 10 in 3h1k

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Iron binding site 3 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:60.8
occ:1.00
 FE D:HEC501 0.0 60.8 1.0
NC D:HEC501 1.9 59.5 1.0
ND D:HEC501 1.9 57.9 1.0
NA D:HEC501 1.9 58.9 1.0
NB D:HEC501 1.9 59.9 1.0
NE2 D:HIS41 2.0 60.6 1.0
SD D:MET160 2.1 57.1 1.0
C4C D:HEC501 2.9 60.1 1.0
C1D D:HEC501 2.9 57.4 1.0
CD2 D:HIS41 2.9 61.3 1.0
C4A D:HEC501 2.9 59.3 1.0
C1B D:HEC501 2.9 59.5 1.0
C1C D:HEC501 3.0 60.6 1.0
C4D D:HEC501 3.0 58.4 1.0
C1A D:HEC501 3.0 59.6 1.0
C4B D:HEC501 3.0 60.3 1.0
CE1 D:HIS41 3.0 61.6 1.0
CHD D:HEC501 3.2 58.6 1.0
CHB D:HEC501 3.3 59.2 1.0
CE D:MET160 3.3 56.6 1.0
CHC D:HEC501 3.4 60.4 1.0
CHA D:HEC501 3.4 59.3 1.0
CG D:MET160 3.5 60.4 1.0
CG D:HIS41 4.1 62.5 1.0
ND1 D:HIS41 4.1 61.2 1.0
C2D D:HEC501 4.1 57.6 1.0
C3C D:HEC501 4.2 61.7 1.0
CB D:MET160 4.2 62.5 1.0
C2B D:HEC501 4.2 60.3 1.0
C2C D:HEC501 4.2 61.4 1.0
C3A D:HEC501 4.2 59.8 1.0
C3D D:HEC501 4.2 58.8 1.0
C2A D:HEC501 4.2 60.0 1.0
C3B D:HEC501 4.2 60.9 1.0

Iron binding site 4 out of 10 in 3h1k

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Iron binding site 4 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.0
occ:0.79
 FE1 E:FES501 0.0 0.0 0.8
S2 E:FES501 2.2 0.5 0.8
S1 E:FES501 2.2 0.5 0.8
SG E:CYS139 2.3 0.7 0.8
SG E:CYS158 2.3 0.6 0.8
FE2 E:FES501 2.7 0.7 0.8
CB E:CYS139 3.1 0.2 0.8
CB E:CYS158 3.1 0.8 0.8
CB E:CYS144 4.0 0.8 0.8
CB E:HIS141 4.1 0.3 0.8
CB E:CYS160 4.3 0.2 0.8
ND1 E:HIS161 4.5 1.0 0.8
ND1 E:HIS141 4.5 0.2 0.8
CA E:CYS139 4.5 0.9 0.8
CA E:CYS158 4.6 0.7 0.8
O E:CYS158 4.6 0.6 0.8
CB E:SER163 4.6 0.9 0.8
OH E:TYR165 4.7 0.1 0.8
OG E:SER163 4.7 0.3 0.8
N E:HIS161 4.8 0.4 0.8
CG E:HIS141 4.8 0.8 0.8
CE1 E:TYR165 4.9 0.5 0.8
SG E:CYS144 4.9 0.4 0.8
C E:CYS158 4.9 0.7 0.8

Iron binding site 5 out of 10 in 3h1k

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Iron binding site 5 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe501

b:0.7
occ:0.79
 FE2 E:FES501 0.0 0.7 0.8
ND1 E:HIS161 2.1 1.0 0.8
ND1 E:HIS141 2.1 0.2 0.8
S2 E:FES501 2.2 0.5 0.8
S1 E:FES501 2.2 0.5 0.8
FE1 E:FES501 2.7 0.0 0.8
CG E:HIS141 3.0 0.8 0.8
CG E:HIS161 3.0 0.2 0.8
CE1 E:HIS161 3.1 1.0 0.8
CE1 E:HIS141 3.1 0.0 0.8
CB E:HIS141 3.2 0.3 0.8
CB E:HIS161 3.3 0.8 0.8
N E:HIS161 4.2 0.4 0.8
CD2 E:HIS141 4.2 0.6 0.8
CD2 E:HIS161 4.2 0.9 0.8
NE2 E:HIS161 4.2 0.9 0.8
NE2 E:HIS141 4.2 0.6 0.8
CB E:CYS160 4.3 0.2 0.8
CA E:HIS161 4.4 0.2 0.8
N E:LEU142 4.5 0.4 0.8
SG E:CYS139 4.5 0.7 0.8
SG E:CYS158 4.5 0.6 0.8
CA E:HIS141 4.7 0.8 0.8
OG E:SER163 4.7 0.3 0.8
C E:CYS160 4.8 0.4 0.8
CG E:LEU142 4.9 0.9 0.8

Iron binding site 6 out of 10 in 3h1k

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Iron binding site 6 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe501

b:68.2
occ:1.00
 FE P:HEM501 0.0 68.2 1.0
NC P:HEM501 1.9 70.0 1.0
NA P:HEM501 1.9 71.2 1.0
NB P:HEM501 1.9 71.4 1.0
ND P:HEM501 1.9 70.7 1.0
NE2 P:HIS183 2.0 64.3 1.0
NE2 P:HIS84 2.0 67.1 1.0
C1C P:HEM501 2.9 72.5 1.0
CE1 P:HIS84 2.9 66.3 1.0
C4A P:HEM501 3.0 72.3 1.0
C4B P:HEM501 3.0 73.5 1.0
CD2 P:HIS183 3.0 62.4 1.0
C1A P:HEM501 3.0 73.0 1.0
CE1 P:HIS183 3.0 61.8 1.0
C4D P:HEM501 3.0 72.0 1.0
C4C P:HEM501 3.0 69.1 1.0
C1B P:HEM501 3.0 73.4 1.0
C1D P:HEM501 3.0 70.5 1.0
CD2 P:HIS84 3.0 66.0 1.0
CHC P:HEM501 3.3 73.6 1.0
CHB P:HEM501 3.3 73.5 1.0
CHA P:HEM501 3.4 72.3 1.0
CHD P:HEM501 3.4 69.4 1.0
ND1 P:HIS84 4.1 67.1 1.0
ND1 P:HIS183 4.1 63.3 1.0
CG P:HIS183 4.1 62.5 1.0
C3A P:HEM501 4.1 72.6 1.0
CG P:HIS84 4.2 66.5 1.0
C2C P:HEM501 4.2 71.8 1.0
C2A P:HEM501 4.2 74.0 1.0
C3B P:HEM501 4.2 74.2 1.0
C3D P:HEM501 4.2 71.5 1.0
C3C P:HEM501 4.2 69.1 1.0
C2D P:HEM501 4.3 70.7 1.0
C2B P:HEM501 4.3 73.9 1.0
CA P:GLY49 4.8 65.0 1.0
CA P:GLY131 5.0 69.2 1.0

Iron binding site 7 out of 10 in 3h1k

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Iron binding site 7 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
P:Fe502

b:72.6
occ:1.00
 FE P:HEM502 0.0 72.6 1.0
NC P:HEM502 1.9 73.2 1.0
NB P:HEM502 1.9 73.1 1.0
ND P:HEM502 1.9 74.3 1.0
NA P:HEM502 2.0 72.6 1.0
NE2 P:HIS197 2.0 74.1 1.0
NE2 P:HIS98 2.0 74.7 1.0
CE1 P:HIS197 2.9 75.7 1.0
C1C P:HEM502 2.9 74.1 1.0
C4B P:HEM502 2.9 72.8 1.0
CE1 P:HIS98 3.0 75.8 1.0
C1D P:HEM502 3.0 75.0 1.0
C4C P:HEM502 3.0 73.4 1.0
C4D P:HEM502 3.0 74.4 1.0
C1B P:HEM502 3.0 72.9 1.0
C4A P:HEM502 3.0 72.2 1.0
CD2 P:HIS197 3.0 75.1 1.0
C1A P:HEM502 3.0 72.8 1.0
CD2 P:HIS98 3.0 76.0 1.0
CHC P:HEM502 3.3 73.7 1.0
CHD P:HEM502 3.4 73.9 1.0
CHB P:HEM502 3.4 72.4 1.0
CHA P:HEM502 3.4 72.4 1.0
ND1 P:HIS197 4.0 77.5 1.0
ND1 P:HIS98 4.1 76.0 1.0
CG P:HIS197 4.1 76.3 1.0
CG P:HIS98 4.2 77.2 1.0
C2C P:HEM502 4.2 74.1 1.0
C3C P:HEM502 4.2 73.7 1.0
C3D P:HEM502 4.2 76.1 1.0
C3B P:HEM502 4.2 71.5 1.0
C2D P:HEM502 4.2 76.1 1.0
C2A P:HEM502 4.2 74.2 1.0
C3A P:HEM502 4.2 73.4 1.0
C2B P:HEM502 4.3 72.4 1.0
O P:HOH383 4.6 73.6 1.0
CD1 P:LEU38 5.0 70.4 1.0

Iron binding site 8 out of 10 in 3h1k

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Iron binding site 8 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
Q:Fe501

b:96.4
occ:1.00
 FE Q:HEC501 0.0 96.4 1.0
NC Q:HEC501 1.9 93.4 1.0
ND Q:HEC501 1.9 93.2 1.0
NB Q:HEC501 2.0 91.8 1.0
NA Q:HEC501 2.0 91.7 1.0
NE2 Q:HIS41 2.0 97.3 1.0
SD Q:MET160 2.1 98.6 1.0
C4C Q:HEC501 2.8 93.7 1.0
C1D Q:HEC501 2.9 92.8 1.0
CD2 Q:HIS41 2.9 98.8 1.0
C1C Q:HEC501 3.0 91.9 1.0
C1B Q:HEC501 3.0 88.9 1.0
C4A Q:HEC501 3.0 89.1 1.0
C4D Q:HEC501 3.0 92.2 1.0
CE1 Q:HIS41 3.0 99.2 1.0
C4B Q:HEC501 3.0 90.2 1.0
C1A Q:HEC501 3.1 90.1 1.0
CHD Q:HEC501 3.2 92.9 1.0
CHB Q:HEC501 3.4 87.9 1.0
CHC Q:HEC501 3.4 90.3 1.0
CE Q:MET160 3.4 99.1 1.0
CHA Q:HEC501 3.5 90.1 1.0
CG Q:MET160 3.5 0.5 1.0
CG Q:HIS41 4.1 99.3 1.0
C3C Q:HEC501 4.1 95.3 1.0
ND1 Q:HIS41 4.1 99.2 1.0
C2C Q:HEC501 4.1 92.8 1.0
C2D Q:HEC501 4.1 93.5 1.0
CB Q:MET160 4.2 0.8 1.0
C2B Q:HEC501 4.2 88.7 1.0
C3B Q:HEC501 4.2 90.1 1.0
C3A Q:HEC501 4.2 89.4 1.0
C3D Q:HEC501 4.2 93.7 1.0
C2A Q:HEC501 4.3 89.5 1.0

Iron binding site 9 out of 10 in 3h1k

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Iron binding site 9 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:0.7
occ:0.94
 FE1 R:FES501 0.0 0.7 0.9
S2 R:FES501 2.2 0.3 0.9
S1 R:FES501 2.2 0.9 0.9
SG R:CYS139 2.3 0.3 0.9
SG R:CYS158 2.3 0.8 0.9
FE2 R:FES501 2.7 1.0 0.9
CB R:CYS139 3.1 0.0 0.9
CB R:CYS158 3.1 0.4 0.9
O R:CYS139 4.1 0.4 0.9
CB R:HIS141 4.2 0.9 0.9
CB R:CYS144 4.3 0.5 0.9
CB R:CYS160 4.3 0.1 0.9
O R:GLY143 4.4 0.2 0.9
ND1 R:HIS161 4.4 0.6 0.9
ND1 R:HIS141 4.4 0.7 0.9
CA R:CYS139 4.5 1.0 0.9
CA R:CYS158 4.6 0.4 0.9
O R:CYS158 4.6 0.2 0.9
CB R:SER163 4.6 1.0 0.9
C R:CYS139 4.7 0.4 0.9
OH R:TYR165 4.7 0.9 0.9
OG R:SER163 4.8 0.4 0.9
CG R:HIS141 4.8 0.3 0.9
N R:HIS161 4.8 0.1 0.9
CB R:ALA176 4.8 0.2 0.9
CE1 R:TYR165 4.9 0.2 0.9
C R:CYS158 4.9 0.8 0.9
SG R:CYS144 4.9 0.9 0.9

Iron binding site 10 out of 10 in 3h1k

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Iron binding site 10 out of 10 in the Chicken Cytochrome BC1 Complex with Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound


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 Zn++ and An Iodinated Derivative of Kresoxim-Methyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
R:Fe501

b:1.0
occ:0.94
 FE2 R:FES501 0.0 1.0 0.9
ND1 R:HIS161 2.1 0.6 0.9
ND1 R:HIS141 2.1 0.7 0.9
S1 R:FES501 2.2 0.9 0.9
S2 R:FES501 2.2 0.3 0.9
FE1 R:FES501 2.7 0.7 0.9
CG R:HIS161 3.1 0.6 0.9
CG R:HIS141 3.1 0.3 0.9
CE1 R:HIS161 3.1 0.8 0.9
CE1 R:HIS141 3.1 0.5 0.9
CB R:HIS141 3.3 0.9 0.9
CB R:HIS161 3.3 0.2 0.9
N R:HIS161 4.2 0.1 0.9
CD2 R:HIS161 4.2 0.7 0.9
CD2 R:HIS141 4.2 0.0 0.9
NE2 R:HIS161 4.2 1.0 0.9
NE2 R:HIS141 4.2 0.9 0.9
CB R:CYS160 4.4 0.1 0.9
CA R:HIS161 4.4 0.1 0.9
SG R:CYS139 4.5 0.3 0.9
N R:LEU142 4.5 0.9 0.9
SG R:CYS158 4.5 0.8 0.9
OG R:SER163 4.7 0.4 0.9
CB R:ALA176 4.7 0.2 0.9
CA R:HIS141 4.8 0.3 0.9
C R:CYS160 4.8 0.4 0.9
CG R:PRO175 4.9 0.2 0.9

Reference:

E.A.Berry, Z.Zhang, H.D.Bellamy, L.Huang. Crystallographic Location of Two Zn(2+)-Binding Sites in the Avian Cytochrome Bc(1) Complex Biochim.Biophys.Acta V.1459 440 2000.
ISSN: ISSN 0006-3002
PubMed: 11004461
Page generated: Sun Aug 4 11:03:06 2024

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