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Iron in PDB 6zfs: Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4

Enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4

All present enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4:
7.1.1.8;

Protein crystallography data

The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4, PDB code: 6zfs was solved by K.Amporndanai, P.M.O'neill, W.D.Hong, R.K.Amewu, C.Pidathala, N.G.Berry, G.A.Biagini, S.C.Leung, S.S.Hasnain, S.V.Antonyuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 90.74 / 3.50
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 209.56, 209.56, 343.348, 90, 90, 120
R / Rfree (%) 21.7 / 24.6

Other elements in 6zfs:

The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4 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 Quinolone Inhibitor Wdh-1U-4 (pdb code 6zfs). 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 Quinolone Inhibitor Wdh-1U-4, PDB code: 6zfs:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 6zfs

Go back to Iron Binding Sites List in 6zfs
Iron binding site 1 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4


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 Quinolone Inhibitor Wdh-1U-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe401

b:107.7
occ:1.00
FE C:HEM401 0.0 107.7 1.0
ND C:HEM401 1.9 109.3 1.0
NA C:HEM401 2.0 109.0 1.0
NC C:HEM401 2.1 108.0 1.0
NB C:HEM401 2.1 107.9 1.0
NE2 C:HIS83 2.2 108.7 1.0
NE2 C:HIS182 2.2 108.5 1.0
C4D C:HEM401 2.9 110.0 1.0
C1D C:HEM401 2.9 109.3 1.0
C1A C:HEM401 3.0 109.8 1.0
C4C C:HEM401 3.0 108.7 1.0
CE1 C:HIS83 3.1 109.0 1.0
C4A C:HEM401 3.1 109.2 1.0
CE1 C:HIS182 3.1 109.0 1.0
C4B C:HEM401 3.1 107.9 1.0
C1B C:HEM401 3.1 108.2 1.0
C1C C:HEM401 3.1 108.2 1.0
CD2 C:HIS83 3.2 110.0 1.0
CD2 C:HIS182 3.3 108.6 1.0
CHA C:HEM401 3.3 110.1 1.0
CHD C:HEM401 3.4 109.0 1.0
CHB C:HEM401 3.5 108.7 1.0
CHC C:HEM401 3.5 107.9 1.0
C3D C:HEM401 4.2 110.2 1.0
C2D C:HEM401 4.2 109.7 1.0
C2A C:HEM401 4.2 110.4 1.0
ND1 C:HIS83 4.2 110.0 1.0
ND1 C:HIS182 4.2 109.0 1.0
C3A C:HEM401 4.2 110.1 1.0
C3C C:HEM401 4.3 109.0 1.0
C2C C:HEM401 4.3 108.7 1.0
CG C:HIS83 4.3 110.4 1.0
C2B C:HEM401 4.3 108.0 1.0
CG C:HIS182 4.3 108.4 1.0
C3B C:HEM401 4.4 107.7 1.0
CA C:GLY130 4.9 117.0 1.0

Iron binding site 2 out of 5 in 6zfs

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Iron binding site 2 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4


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 Quinolone Inhibitor Wdh-1U-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:95.9
occ:1.00
FE C:HEM402 0.0 95.9 1.0
ND C:HEM402 1.9 96.6 1.0
NA C:HEM402 2.0 96.6 1.0
NC C:HEM402 2.1 96.6 1.0
NB C:HEM402 2.1 96.3 1.0
NE2 C:HIS196 2.2 96.8 1.0
NE2 C:HIS97 2.2 97.7 1.0
C4D C:HEM402 2.9 96.8 1.0
C1D C:HEM402 2.9 96.8 1.0
C1A C:HEM402 3.0 96.7 1.0
CD2 C:HIS196 3.0 97.2 1.0
C4C C:HEM402 3.0 96.9 1.0
C4A C:HEM402 3.1 96.7 1.0
CE1 C:HIS97 3.1 98.3 1.0
C4B C:HEM402 3.1 96.5 1.0
C1B C:HEM402 3.1 96.6 1.0
C1C C:HEM402 3.1 96.9 1.0
CD2 C:HIS97 3.2 98.7 1.0
CE1 C:HIS196 3.2 98.1 1.0
CHA C:HEM402 3.3 96.7 1.0
CHD C:HEM402 3.4 96.9 1.0
CHB C:HEM402 3.5 96.9 1.0
CHC C:HEM402 3.5 96.9 1.0
C2D C:HEM402 4.2 96.9 1.0
C3D C:HEM402 4.2 97.1 1.0
CG C:HIS196 4.2 98.1 1.0
C2A C:HEM402 4.2 96.9 1.0
ND1 C:HIS97 4.2 98.9 1.0
ND1 C:HIS196 4.2 98.5 1.0
C3A C:HEM402 4.2 96.6 1.0
C3C C:HEM402 4.3 97.5 1.0
C2C C:HEM402 4.3 97.1 1.0
CG C:HIS97 4.3 99.1 1.0
C2B C:HEM402 4.3 96.5 1.0
C3B C:HEM402 4.4 96.5 1.0

Iron binding site 3 out of 5 in 6zfs

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Iron binding site 3 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4


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 Quinolone Inhibitor Wdh-1U-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:151.6
occ:1.00
FE D:HEC501 0.0 151.6 1.0
NE2 D:HIS41 2.1 150.8 1.0
NB D:HEC501 2.1 150.0 1.0
NA D:HEC501 2.1 149.5 1.0
NC D:HEC501 2.1 155.8 1.0
ND D:HEC501 2.1 152.9 1.0
SD D:MET160 2.4 163.4 1.0
CE1 D:HIS41 2.8 149.1 1.0
C1B D:HEC501 3.1 148.5 1.0
C4A D:HEC501 3.1 148.8 1.0
C4B D:HEC501 3.1 151.8 1.0
C4C D:HEC501 3.1 157.8 1.0
C1C D:HEC501 3.1 157.9 1.0
C1D D:HEC501 3.1 155.3 1.0
C1A D:HEC501 3.1 149.1 1.0
C4D D:HEC501 3.1 152.1 1.0
CD2 D:HIS41 3.2 150.0 1.0
CHB D:HEC501 3.4 147.9 1.0
CHC D:HEC501 3.5 155.2 1.0
CHD D:HEC501 3.5 156.6 1.0
CHA D:HEC501 3.5 150.0 1.0
CE D:MET160 3.7 167.8 1.0
CG D:MET160 3.7 167.1 1.0
ND1 D:HIS41 4.0 148.0 1.0
CG D:HIS41 4.2 148.1 1.0
CB D:MET160 4.4 166.5 1.0
C3B D:HEC501 4.4 151.3 1.0
C3C D:HEC501 4.4 160.7 1.0
C2B D:HEC501 4.4 149.4 1.0
C3A D:HEC501 4.4 147.9 1.0
C2A D:HEC501 4.5 147.5 1.0
C2C D:HEC501 4.5 161.0 1.0
C2D D:HEC501 4.5 156.0 1.0
C3D D:HEC501 4.5 153.3 1.0

Iron binding site 4 out of 5 in 6zfs

Go back to Iron Binding Sites List in 6zfs
Iron binding site 4 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4


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 Quinolone Inhibitor Wdh-1U-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:254.2
occ:1.00
FE1 E:FES201 0.0 254.2 1.0
S1 E:FES201 2.2 258.3 1.0
S2 E:FES201 2.2 263.4 1.0
SG E:CYS158 2.7 200.3 1.0
SG E:CYS139 3.0 218.7 1.0
FE2 E:FES201 3.1 267.9 1.0
CB E:CYS160 3.6 218.2 1.0
CB E:CYS139 3.6 214.8 1.0
CB E:CYS158 3.8 199.5 1.0
SG E:CYS144 3.9 223.3 1.0
N E:HIS161 4.1 215.7 1.0
SG E:CYS160 4.4 221.7 1.0
CB E:CYS144 4.4 219.8 1.0
CA E:CYS160 4.6 215.5 1.0
CB E:HIS161 4.6 216.7 1.0
ND1 E:HIS161 4.6 214.5 1.0
OG E:SER163 4.7 205.2 1.0
N E:CYS160 4.8 211.9 1.0
C E:CYS160 4.8 216.6 1.0
CB E:HIS141 4.9 241.5 1.0
CB E:SER163 4.9 202.7 1.0
CA E:HIS161 4.9 215.3 1.0

Iron binding site 5 out of 5 in 6zfs

Go back to Iron Binding Sites List in 6zfs
Iron binding site 5 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Quinolone Inhibitor Wdh-1U-4


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 Quinolone Inhibitor Wdh-1U-4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:267.9
occ:1.00
FE2 E:FES201 0.0 267.9 1.0
S1 E:FES201 2.2 258.3 1.0
S2 E:FES201 2.2 263.4 1.0
ND1 E:HIS141 2.8 251.9 1.0
CB E:HIS161 2.9 216.7 1.0
CG E:HIS161 3.1 216.8 1.0
FE1 E:FES201 3.1 254.2 1.0
ND1 E:HIS161 3.2 214.5 1.0
CB E:HIS141 3.3 241.5 1.0
CG E:HIS141 3.4 248.9 1.0
CD2 E:HIS161 3.9 216.9 1.0
CE1 E:HIS141 3.9 254.1 1.0
CG E:PRO175 4.0 199.7 1.0
CE1 E:HIS161 4.1 213.8 1.0
CA E:HIS161 4.2 215.3 1.0
N E:LEU142 4.3 225.2 1.0
N E:HIS161 4.3 215.7 1.0
NE2 E:HIS161 4.4 215.5 1.0
CB E:LEU142 4.6 220.4 1.0
CD2 E:HIS141 4.6 252.5 1.0
CA E:HIS141 4.6 232.8 1.0
CB E:PRO175 4.7 199.8 1.0
NE2 E:HIS141 4.8 255.0 1.0
C E:HIS141 4.8 230.0 1.0
OG E:SER163 4.9 205.2 1.0
N E:GLY162 4.9 206.2 1.0
C E:HIS161 5.0 211.4 1.0

Reference:

K.Amporndanai, P.M.O'neill, W.D.Hong, R.K.Amewu, C.Pidathala, N.Berry, G.A.Biangini, S.C.Leung, S.S.Hasnain, S.V.Antonyuk. Targeting the Ubiquinol-Reduction (Qi) Site of the Mitochondrial Cytochrome BC1 Complex For the Development of Next Generation Quinolone Antimalarials To Be Published.
Page generated: Sat Jul 10 15:08:29 2021

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