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Iron in PDB 5okd: Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911.

Enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911.

All present enzymatic activity of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911.:
1.10.2.2;

Protein crystallography data

The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911., PDB code: 5okd was solved by K.Amporndanai, P.M.O'neill, 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) 31.76 / 3.10
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 209.871, 209.871, 342.097, 90.00, 90.00, 120.00
R / Rfree (%) 20.5 / 24

Other elements in 5okd:

The structure of Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911. 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 SCR0911. (pdb code 5okd). 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 SCR0911., PDB code: 5okd:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 5okd

Go back to Iron Binding Sites List in 5okd
Iron binding site 1 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911.


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 SCR0911. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe402

b:69.0
occ:1.00
FE C:HEM402 0.0 69.0 1.0
ND C:HEM402 1.9 71.0 1.0
NA C:HEM402 2.0 70.7 1.0
NC C:HEM402 2.1 69.0 1.0
NB C:HEM402 2.1 70.0 1.0
NE2 C:HIS83 2.3 71.1 1.0
NE2 C:HIS182 2.3 76.2 1.0
C1D C:HEM402 2.9 70.8 1.0
C4D C:HEM402 2.9 71.2 1.0
C1A C:HEM402 3.0 71.9 1.0
C4A C:HEM402 3.0 71.2 1.0
C4C C:HEM402 3.1 69.3 1.0
C4B C:HEM402 3.1 69.9 1.0
C1B C:HEM402 3.1 70.7 1.0
C1C C:HEM402 3.1 69.5 1.0
CE1 C:HIS182 3.1 76.8 1.0
CE1 C:HIS83 3.1 71.6 1.0
CD2 C:HIS83 3.3 72.2 1.0
CD2 C:HIS182 3.3 76.8 1.0
CHA C:HEM402 3.4 71.9 1.0
CHD C:HEM402 3.4 70.2 1.0
CHB C:HEM402 3.4 71.1 1.0
CHC C:HEM402 3.5 69.7 1.0
C2D C:HEM402 4.2 71.6 1.0
C3D C:HEM402 4.2 72.0 1.0
C2A C:HEM402 4.2 73.0 1.0
C3A C:HEM402 4.2 72.3 1.0
ND1 C:HIS83 4.3 72.9 1.0
C3C C:HEM402 4.3 69.4 1.0
C2C C:HEM402 4.3 69.2 1.0
ND1 C:HIS182 4.3 77.8 1.0
C2B C:HEM402 4.3 70.0 1.0
C3B C:HEM402 4.3 70.2 1.0
CG C:HIS83 4.4 73.3 1.0
CG C:HIS182 4.4 76.8 1.0
CA C:GLY130 4.8 82.8 1.0

Iron binding site 2 out of 5 in 5okd

Go back to Iron Binding Sites List in 5okd
Iron binding site 2 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911.


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 SCR0911. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe403

b:63.3
occ:1.00
FE C:HEM403 0.0 63.3 1.0
ND C:HEM403 1.9 65.3 1.0
NA C:HEM403 2.0 64.5 1.0
NC C:HEM403 2.1 64.3 1.0
NB C:HEM403 2.1 64.9 1.0
NE2 C:HIS196 2.3 65.2 1.0
NE2 C:HIS97 2.3 70.7 1.0
C4D C:HEM403 2.9 64.7 1.0
C1D C:HEM403 2.9 65.2 1.0
C1A C:HEM403 3.0 64.8 1.0
C4A C:HEM403 3.0 65.0 1.0
C4B C:HEM403 3.1 65.5 1.0
C4C C:HEM403 3.1 65.0 1.0
C1B C:HEM403 3.1 64.5 1.0
C1C C:HEM403 3.1 64.9 1.0
CD2 C:HIS196 3.2 66.4 1.0
CE1 C:HIS97 3.2 71.3 1.0
CE1 C:HIS196 3.3 66.3 1.0
CD2 C:HIS97 3.3 70.8 1.0
CHA C:HEM403 3.4 64.7 1.0
CHD C:HEM403 3.4 65.3 1.0
CHB C:HEM403 3.4 65.6 1.0
CHC C:HEM403 3.4 65.5 1.0
C2A C:HEM403 4.2 65.3 1.0
C2D C:HEM403 4.2 64.7 1.0
C3D C:HEM403 4.2 64.7 1.0
C3A C:HEM403 4.2 65.3 1.0
C3C C:HEM403 4.3 65.6 1.0
C2C C:HEM403 4.3 64.9 1.0
C2B C:HEM403 4.3 63.5 1.0
CG C:HIS196 4.3 67.1 1.0
ND1 C:HIS97 4.3 72.5 1.0
C3B C:HEM403 4.3 65.1 1.0
ND1 C:HIS196 4.4 68.1 1.0
CG C:HIS97 4.4 71.3 1.0

Iron binding site 3 out of 5 in 5okd

Go back to Iron Binding Sites List in 5okd
Iron binding site 3 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911.


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 SCR0911. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe501

b:0.4
occ:1.00
FE D:HEC501 0.0 0.4 1.0
NA D:HEC501 2.1 0.1 1.0
NC D:HEC501 2.1 0.6 1.0
ND D:HEC501 2.1 0.5 1.0
NB D:HEC501 2.1 0.9 1.0
NE2 D:HIS41 2.2 0.4 1.0
SD D:MET160 2.4 0.2 1.0
CE1 D:HIS41 3.0 0.8 1.0
C1C D:HEC501 3.1 1.0 1.0
C4A D:HEC501 3.1 0.5 1.0
C1A D:HEC501 3.1 0.7 1.0
C4D D:HEC501 3.1 0.1 1.0
C4B D:HEC501 3.1 0.8 1.0
C1D D:HEC501 3.1 0.0 1.0
C4C D:HEC501 3.1 0.4 1.0
C1B D:HEC501 3.1 0.5 1.0
CD2 D:HIS41 3.4 0.4 1.0
CHC D:HEC501 3.5 0.9 1.0
CHA D:HEC501 3.5 0.6 1.0
CHB D:HEC501 3.5 0.8 1.0
CHD D:HEC501 3.5 0.1 1.0
CE D:MET160 3.7 1.0 1.0
CG D:MET160 3.7 0.0 1.0
ND1 D:HIS41 4.2 0.5 1.0
CB D:MET160 4.4 0.5 1.0
CG D:HIS41 4.4 0.4 1.0
C3C D:HEC501 4.4 0.6 1.0
C3B D:HEC501 4.4 0.1 1.0
C3A D:HEC501 4.4 0.2 1.0
C3D D:HEC501 4.4 0.9 1.0
C2C D:HEC501 4.4 0.4 1.0
C2D D:HEC501 4.4 0.4 1.0
C2A D:HEC501 4.4 0.4 1.0
C2B D:HEC501 4.5 0.6 1.0

Iron binding site 4 out of 5 in 5okd

Go back to Iron Binding Sites List in 5okd
Iron binding site 4 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911.


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 SCR0911. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:0.6
occ:1.00
FE1 E:FES201 0.0 0.6 1.0
S1 E:FES201 2.2 0.8 1.0
S2 E:FES201 2.2 0.0 1.0
SG E:CYS158 2.9 0.4 1.0
O E:HOH302 2.9 0.9 1.0
FE2 E:FES201 3.1 0.2 1.0
O E:HOH303 3.2 0.6 1.0
SG E:CYS139 3.2 0.3 1.0
CB E:CYS160 3.5 0.3 1.0
SG E:CYS144 3.8 0.9 1.0
CB E:CYS158 3.9 0.3 1.0
CB E:CYS139 4.0 0.6 1.0
N E:HIS161 4.1 0.8 1.0
SG E:CYS160 4.2 0.1 1.0
CB E:CYS144 4.4 0.6 1.0
CA E:CYS160 4.5 0.3 1.0
CB E:HIS161 4.5 0.2 1.0
ND1 E:HIS161 4.6 0.6 1.0
N E:CYS160 4.7 0.7 1.0
C E:CYS160 4.8 0.7 1.0
OG E:SER163 4.8 0.7 1.0
O E:HOH301 4.8 0.9 1.0
CB E:SER163 4.9 0.1 1.0
CG E:HIS161 4.9 0.3 1.0
CA E:HIS161 5.0 0.5 1.0

Iron binding site 5 out of 5 in 5okd

Go back to Iron Binding Sites List in 5okd
Iron binding site 5 out of 5 in the Crystal Structure of Bovine Cytochrome BC1 in Complex with Inhibitor SCR0911.


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 SCR0911. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe201

b:0.2
occ:1.00
FE2 E:FES201 0.0 0.2 1.0
S1 E:FES201 2.2 0.8 1.0
S2 E:FES201 2.2 0.0 1.0
ND1 E:HIS141 2.9 0.6 1.0
CG E:HIS161 3.0 0.3 1.0
CB E:HIS161 3.1 0.2 1.0
FE1 E:FES201 3.1 0.6 1.0
ND1 E:HIS161 3.2 0.6 1.0
CB E:HIS141 3.3 1.0 1.0
CG E:HIS141 3.5 0.4 1.0
CD2 E:HIS161 3.7 0.2 1.0
O E:HOH303 3.8 0.6 1.0
CE1 E:HIS161 3.9 0.6 1.0
CG E:PRO175 4.0 0.0 1.0
CE1 E:HIS141 4.0 0.4 1.0
NE2 E:HIS161 4.2 0.9 1.0
N E:LEU142 4.3 0.1 1.0
CA E:HIS161 4.4 0.5 1.0
O E:HOH302 4.4 0.9 1.0
N E:HIS161 4.5 0.8 1.0
CA E:HIS141 4.6 0.2 1.0
CD2 E:HIS141 4.7 0.5 1.0
CB E:LEU142 4.7 0.5 1.0
CG E:LEU142 4.7 0.8 1.0
CB E:PRO175 4.8 0.7 1.0
CD1 E:LEU142 4.8 0.8 1.0
C E:HIS141 4.8 0.3 1.0
OG E:SER163 4.9 0.7 1.0
NE2 E:HIS141 4.9 1.0 1.0

Reference:

K.Amporndanai, R.M.Johnson, P.M.O'neill, C.W.G.Fishwick, A.H.Jamson, S.Rawson, S.P.Muench, S.S.Hasnain, S.V.Antonyuk. X-Ray and Cryo-Em Structures of Inhibitor-Bound CYTOCHROMEBC1COMPLEXES For Structure-Based Drug Discovery. Iucrj V. 5 200 2018.
ISSN: ESSN 2052-2525
PubMed: 29765610
DOI: 10.1107/S2052252518001616
Page generated: Tue Aug 6 08:26:46 2024

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