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Iron in PDB 7r3v: Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.

Enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.

All present enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.:
7.1.1.8;

Protein crystallography data

The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67., PDB code: 7r3v was solved by N.Pinthong, K.Amporndanai, P.M.O'neill, S.S.Hasnain, S.Antonyuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.86 / 3.20
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 209.589, 209.589, 342.429, 90, 90, 120
R / Rfree (%) 20.5 / 25.6

Other elements in 7r3v:

The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67. also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67. (pdb code 7r3v). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67., PDB code: 7r3v:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 7r3v

Go back to Iron Binding Sites List in 7r3v
Iron binding site 1 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:62.4
occ:1.00
FE C:HEM401 0.0 62.4 1.0
ND C:HEM401 1.9 60.5 1.0
NA C:HEM401 2.0 70.5 1.0
NC C:HEM401 2.0 65.2 1.0
NB C:HEM401 2.1 63.9 1.0
NE2 C:HIS83 2.2 59.6 1.0
NE2 C:HIS182 2.2 50.9 1.0
C4D C:HEM401 2.9 67.6 1.0
C1D C:HEM401 2.9 57.0 1.0
C1A C:HEM401 3.0 69.8 1.0
CE1 C:HIS83 3.0 65.1 1.0
C4C C:HEM401 3.0 67.3 1.0
CE1 C:HIS182 3.0 58.0 1.0
C4B C:HEM401 3.1 69.1 1.0
C4A C:HEM401 3.1 72.3 1.0
C1B C:HEM401 3.1 70.3 1.0
C1C C:HEM401 3.1 67.8 1.0
CD2 C:HIS182 3.2 53.8 1.0
CD2 C:HIS83 3.2 60.3 1.0
CHA C:HEM401 3.3 71.6 1.0
CHD C:HEM401 3.4 62.0 1.0
CHC C:HEM401 3.5 71.2 1.0
CHB C:HEM401 3.5 71.7 1.0
ND1 C:HIS83 4.1 77.2 1.0
C2D C:HEM401 4.2 63.5 1.0
C2A C:HEM401 4.2 66.7 1.0
ND1 C:HIS182 4.2 65.1 1.0
C3D C:HEM401 4.2 69.4 1.0
C3A C:HEM401 4.2 68.6 1.0
C3C C:HEM401 4.2 69.7 1.0
C2C C:HEM401 4.3 73.4 1.0
CG C:HIS83 4.3 67.7 1.0
C2B C:HEM401 4.3 70.6 1.0
CG C:HIS182 4.3 57.2 1.0
C3B C:HEM401 4.3 72.3 1.0
NE2 C:GLN44 4.9 64.4 1.0
CA C:GLY130 4.9 70.0 1.0

Iron binding site 2 out of 5 in 7r3v

Go back to Iron Binding Sites List in 7r3v
Iron binding site 2 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:51.8
occ:1.00
FE C:HEM402 0.0 51.8 1.0
ND C:HEM402 1.9 56.8 1.0
NA C:HEM402 2.0 64.3 1.0
NB C:HEM402 2.0 55.8 1.0
NC C:HEM402 2.0 56.3 1.0
NE2 C:HIS196 2.2 43.8 1.0
NE2 C:HIS97 2.2 55.5 1.0
C4D C:HEM402 2.9 57.1 1.0
C1D C:HEM402 2.9 56.5 1.0
C1A C:HEM402 3.0 63.9 1.0
C4C C:HEM402 3.0 56.0 1.0
C4B C:HEM402 3.0 67.3 1.0
CE1 C:HIS97 3.0 60.5 1.0
C1B C:HEM402 3.0 58.6 1.0
C1C C:HEM402 3.1 59.5 1.0
C4A C:HEM402 3.1 63.9 1.0
CD2 C:HIS196 3.1 46.1 1.0
CE1 C:HIS196 3.2 52.9 1.0
CD2 C:HIS97 3.2 52.6 1.0
CHD C:HEM402 3.3 54.1 1.0
CHA C:HEM402 3.4 56.6 1.0
CHC C:HEM402 3.4 64.2 1.0
CHB C:HEM402 3.5 66.8 1.0
ND1 C:HIS97 4.1 63.3 1.0
C3D C:HEM402 4.2 63.3 1.0
C2A C:HEM402 4.2 56.6 1.0
C2D C:HEM402 4.2 62.5 1.0
C3C C:HEM402 4.2 60.8 1.0
CG C:HIS196 4.2 51.1 1.0
C2C C:HEM402 4.2 62.3 1.0
ND1 C:HIS196 4.2 55.0 1.0
CG C:HIS97 4.3 56.7 1.0
C3A C:HEM402 4.3 54.9 1.0
C3B C:HEM402 4.3 67.7 1.0
C2B C:HEM402 4.3 59.0 1.0
NH2 C:ARG100 5.0 68.0 1.0

Iron binding site 3 out of 5 in 7r3v

Go back to Iron Binding Sites List in 7r3v
Iron binding site 3 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:90.7
occ:1.00
FE D:HEC501 0.0 90.7 1.0
NE2 D:HIS41 1.8 120.0 1.0
NB D:HEC501 2.1 78.6 1.0
NA D:HEC501 2.1 86.1 1.0
ND D:HEC501 2.1 84.8 1.0
NC D:HEC501 2.1 102.7 1.0
SD D:MET160 2.3 107.1 1.0
CE1 D:HIS41 2.8 119.3 1.0
CD2 D:HIS41 2.9 120.0 1.0
C4B D:HEC501 3.0 85.4 1.0
C1B D:HEC501 3.1 78.4 1.0
C4A D:HEC501 3.1 92.2 1.0
C4D D:HEC501 3.1 91.3 1.0
C1A D:HEC501 3.1 83.8 1.0
C1C D:HEC501 3.1 108.2 1.0
C1D D:HEC501 3.1 79.8 1.0
C4C D:HEC501 3.1 108.5 1.0
CHC D:HEC501 3.4 100.3 1.0
CHB D:HEC501 3.4 81.2 1.0
CHA D:HEC501 3.4 93.1 1.0
CHD D:HEC501 3.5 94.3 1.0
CE D:MET160 3.6 101.7 1.0
CG D:MET160 3.7 109.9 1.0
ND1 D:HIS41 3.9 124.4 1.0
CG D:HIS41 4.0 116.8 1.0
C3B D:HEC501 4.3 85.6 1.0
C2B D:HEC501 4.4 82.1 1.0
C3A D:HEC501 4.4 94.2 1.0
C3D D:HEC501 4.4 94.6 1.0
C2D D:HEC501 4.4 89.8 1.0
C2A D:HEC501 4.5 82.4 1.0
CB D:MET160 4.5 103.8 1.0
C3C D:HEC501 4.5 107.9 1.0
C2C D:HEC501 4.5 111.1 1.0

Iron binding site 4 out of 5 in 7r3v

Go back to Iron Binding Sites List in 7r3v
Iron binding site 4 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:144.8
occ:0.50
FE1 E:FES201 0.0 144.8 0.5
S2 E:FES201 2.2 185.9 0.5
S1 E:FES201 2.2 211.0 1.0
SG E:CYS158 2.6 144.5 0.5
SG E:CYS139 2.6 192.7 1.0
CB E:CYS158 2.9 155.0 1.0
FE2 E:FES201 3.0 205.8 1.0
CB E:CYS139 3.3 149.9 1.0
CB E:CYS144 3.9 176.2 1.0
CB E:CYS160 4.0 153.7 1.0
CB E:SER163 4.2 251.9 1.0
OG E:SER163 4.2 173.0 1.0
SG E:CYS144 4.3 168.8 1.0
SG E:CYS160 4.3 162.2 1.0
CA E:CYS158 4.3 164.9 0.5
O E:CYS158 4.4 150.8 1.0
C E:CYS158 4.5 150.9 1.0
N E:HIS161 4.6 245.8 1.0
N E:CYS160 4.6 207.5 1.0
N E:CYS144 4.7 184.4 1.0
CA E:CYS139 4.7 159.3 1.0
CB E:HIS141 4.8 172.3 1.0
CA E:CYS160 4.8 188.5 1.0
CA E:CYS144 4.9 175.8 1.0

Iron binding site 5 out of 5 in 7r3v

Go back to Iron Binding Sites List in 7r3v
Iron binding site 5 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67.


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor Ck-2-67. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:205.8
occ:1.00
FE2 E:FES201 0.0 205.8 1.0
S2 E:FES201 2.2 185.9 0.5
S1 E:FES201 2.2 211.0 1.0
ND1 E:HIS161 2.7 187.5 1.0
ND1 E:HIS141 2.7 194.8 1.0
FE1 E:FES201 3.0 144.8 0.5
CB E:HIS161 3.2 236.7 1.0
CG E:HIS161 3.3 211.2 1.0
CG E:HIS141 3.5 167.4 1.0
CB E:HIS141 3.5 172.3 1.0
N E:HIS161 3.5 245.8 1.0
CE1 E:HIS141 3.7 201.4 1.0
CB E:CYS160 3.8 153.7 1.0
CE1 E:HIS161 3.8 172.4 1.0
CA E:HIS161 3.9 242.6 1.0
N E:LEU142 4.1 185.6 1.0
C E:CYS160 4.2 208.0 1.0
CB E:LEU142 4.3 150.0 1.0
SG E:CYS139 4.5 192.7 1.0
CG E:LEU142 4.5 126.9 1.0
CD2 E:HIS161 4.6 198.0 1.0
CA E:CYS160 4.6 188.5 1.0
C E:HIS161 4.7 221.6 1.0
OG E:SER163 4.7 173.0 1.0
CD2 E:HIS141 4.7 171.6 1.0
CA E:HIS141 4.7 168.1 1.0
CA E:LEU142 4.8 177.9 1.0
NE2 E:HIS161 4.8 189.0 1.0
NE2 E:HIS141 4.8 201.2 1.0
C E:HIS141 4.8 164.7 1.0
CD1 E:LEU142 4.9 107.5 1.0
O E:CYS160 5.0 191.8 1.0

Reference:

K.Amporndanai, N.Pinthong, P.M.O'neill, W.D.Hong, R.K.Amewu, C.Pidathala, N.G.Berry, S.C.Leung, S.A.Ward, G.A.Biagini, S.S.Hasnain, S.V.Antonyuk. Targeting the Ubiquinol-Reduction (Q I ) Site of the Mitochondrial Cytochrome Bc 1 Complex For the Development of Next Generation Quinolone Antimalarials. Biology (Basel) V. 11 2022.
ISSN: ESSN 2079-7737
PubMed: 35892964
DOI: 10.3390/BIOLOGY11081109
Page generated: Thu Aug 8 22:42:48 2024

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