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Iron in PDB 5klv: Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited

Enzymatic activity of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited

All present enzymatic activity of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited:
1.10.2.2;

Protein crystallography data

The structure of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited, PDB code: 5klv was solved by D.Xia, L.Esser, F.Zhou, Y.Zhou, Y.Xiao, W.K.Tang, C.A.Yu, Z.Qin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.68 / 2.65
Space group I 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 153.986, 153.986, 592.713, 90.00, 90.00, 90.00
R / Rfree (%) 22.8 / 26.9

Other elements in 5klv:

The structure of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited (pdb code 5klv). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 5 binding sites of Iron where determined in the Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited, PDB code: 5klv:
Jump to Iron binding site number: 1; 2; 3; 4; 5;

Iron binding site 1 out of 5 in 5klv

Go back to Iron Binding Sites List in 5klv
Iron binding site 1 out of 5 in the Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1001

b:73.8
occ:1.00
FE C:HEM1001 0.0 73.8 1.0
NE2 C:HIS83 1.9 68.5 1.0
NE2 C:HIS182 2.0 58.3 1.0
ND C:HEM1001 2.0 73.6 1.0
NA C:HEM1001 2.0 76.2 1.0
NC C:HEM1001 2.1 77.8 1.0
NB C:HEM1001 2.1 75.7 1.0
CE1 C:HIS182 2.8 58.0 1.0
CE1 C:HIS83 2.8 68.2 1.0
HE1 C:HIS182 2.9 68.4 1.0
HE1 C:HIS83 3.0 82.1 1.0
CD2 C:HIS83 3.0 64.0 1.0
C1D C:HEM1001 3.0 73.2 1.0
C4D C:HEM1001 3.0 73.9 1.0
C1A C:HEM1001 3.1 77.1 1.0
C4C C:HEM1001 3.1 76.2 1.0
C4A C:HEM1001 3.1 78.0 1.0
CD2 C:HIS182 3.1 59.1 1.0
C1C C:HEM1001 3.1 79.1 1.0
C1B C:HEM1001 3.1 77.1 1.0
C4B C:HEM1001 3.1 76.5 1.0
HD2 C:HIS83 3.3 75.7 1.0
HD2 C:HIS182 3.4 69.8 1.0
CHD C:HEM1001 3.4 74.0 1.0
CHA C:HEM1001 3.4 75.3 1.0
CHB C:HEM1001 3.4 78.0 1.0
CHC C:HEM1001 3.5 76.8 1.0
ND1 C:HIS83 4.0 62.7 1.0
ND1 C:HIS182 4.0 58.5 1.0
CG C:HIS83 4.1 69.5 1.0
HA3 C:GLY130 4.1 96.6 1.0
CG C:HIS182 4.1 59.2 1.0
C2D C:HEM1001 4.2 72.2 1.0
C3D C:HEM1001 4.3 73.4 1.0
C2A C:HEM1001 4.3 80.4 1.0
C3A C:HEM1001 4.3 79.5 1.0
C3C C:HEM1001 4.3 77.7 1.0
C2C C:HEM1001 4.3 79.4 1.0
C2B C:HEM1001 4.3 79.0 1.0
C3B C:HEM1001 4.3 77.8 1.0
HHD C:HEM1001 4.4 89.0 1.0
HHA C:HEM1001 4.4 90.6 1.0
HHB C:HEM1001 4.4 93.8 1.0
HHC C:HEM1001 4.4 91.0 1.0
HA2 C:GLY48 4.5 84.2 1.0
HA3 C:GLY48 4.5 84.2 1.0
HA2 C:GLY130 4.5 96.6 1.0
HD12 C:LEU133 4.7 89.9 1.0
CA C:GLY130 4.8 80.3 1.0
CA C:GLY48 5.0 70.0 1.0

Iron binding site 2 out of 5 in 5klv

Go back to Iron Binding Sites List in 5klv
Iron binding site 2 out of 5 in the Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe1002

b:57.2
occ:1.00
FE C:HEM1002 0.0 57.2 1.0
NA C:HEM1002 2.0 60.9 1.0
NE2 C:HIS196 2.0 46.1 1.0
ND C:HEM1002 2.0 56.4 1.0
NE2 C:HIS97 2.0 47.8 1.0
NB C:HEM1002 2.1 61.1 1.0
NC C:HEM1002 2.2 61.3 1.0
CD2 C:HIS196 2.8 45.9 1.0
HD2 C:HIS196 2.8 55.2 1.0
CD2 C:HIS97 2.9 49.4 1.0
C1A C:HEM1002 3.0 60.8 1.0
C4A C:HEM1002 3.0 61.8 1.0
C4D C:HEM1002 3.0 56.8 1.0
HD2 C:HIS97 3.0 59.5 1.0
C1B C:HEM1002 3.0 61.9 1.0
C4B C:HEM1002 3.1 60.9 1.0
C1D C:HEM1002 3.1 57.1 1.0
CE1 C:HIS97 3.1 49.5 1.0
C1C C:HEM1002 3.1 61.1 1.0
CE1 C:HIS196 3.1 48.3 1.0
C4C C:HEM1002 3.1 59.5 1.0
CHA C:HEM1002 3.4 58.8 1.0
HE1 C:HIS97 3.4 59.6 1.0
CHB C:HEM1002 3.4 62.8 1.0
HE1 C:HIS196 3.4 58.2 1.0
CHC C:HEM1002 3.5 61.2 1.0
CHD C:HEM1002 3.5 58.6 1.0
CG C:HIS196 4.0 49.2 1.0
CG C:HIS97 4.1 51.7 1.0
ND1 C:HIS196 4.1 46.2 1.0
ND1 C:HIS97 4.2 49.8 1.0
C2A C:HEM1002 4.2 61.5 1.0
C3A C:HEM1002 4.2 62.4 1.0
C3D C:HEM1002 4.3 56.1 1.0
C2B C:HEM1002 4.3 62.0 1.0
C3B C:HEM1002 4.3 61.9 1.0
C2D C:HEM1002 4.3 55.8 1.0
C2C C:HEM1002 4.3 60.6 1.0
C3C C:HEM1002 4.3 59.8 1.0
HHA C:HEM1002 4.3 70.8 1.0
HHB C:HEM1002 4.4 75.5 1.0
HHC C:HEM1002 4.4 73.7 1.0
HHD C:HEM1002 4.5 70.5 1.0
HH22 C:ARG100 4.5 59.5 1.0
HD12 C:LEU37 4.6 62.6 1.0
HH21 C:ARG100 4.7 59.5 1.0
HD13 C:LEU37 4.7 62.6 1.0
HA2 C:GLY34 4.9 67.7 1.0
HD13 C:LEU119 4.9 73.3 1.0
NH2 C:ARG100 5.0 49.4 1.0
HG22 C:THR112 5.0 74.4 1.0

Iron binding site 3 out of 5 in 5klv

Go back to Iron Binding Sites List in 5klv
Iron binding site 3 out of 5 in the Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Fe1001

b:0.5
occ:1.00
FE D:HEC1001 0.0 0.5 1.0
NE2 D:HIS41 2.0 0.2 1.0
NC D:HEC1001 2.0 0.2 1.0
NB D:HEC1001 2.1 0.9 1.0
ND D:HEC1001 2.1 0.7 1.0
NA D:HEC1001 2.1 0.7 1.0
SD D:MET160 2.2 0.2 1.0
CE1 D:HIS41 2.9 0.1 1.0
C4C D:HEC1001 3.0 0.2 1.0
CD2 D:HIS41 3.0 1.0 1.0
C1C D:HEC1001 3.0 0.2 1.0
C1B D:HEC1001 3.1 0.1 1.0
C1D D:HEC1001 3.1 0.9 1.0
HE1 D:HIS41 3.1 0.8 1.0
C4A D:HEC1001 3.1 0.7 1.0
C4B D:HEC1001 3.1 0.1 1.0
C4D D:HEC1001 3.1 0.1 1.0
C1A D:HEC1001 3.1 0.6 1.0
HD2 D:HIS41 3.3 0.0 1.0
CHD D:HEC1001 3.4 0.2 1.0
CE D:MET160 3.4 0.2 1.0
HG3 D:MET160 3.4 0.6 1.0
CHB D:HEC1001 3.4 0.9 1.0
CHC D:HEC1001 3.4 0.1 1.0
HE1 D:MET160 3.5 0.1 1.0
CG D:MET160 3.5 1.0 1.0
CHA D:HEC1001 3.5 0.3 1.0
HE2 D:MET160 3.6 0.1 1.0
HB2 D:MET160 4.0 0.3 1.0
ND1 D:HIS41 4.1 0.5 1.0
HB3 D:PRO110 4.1 0.1 1.0
CG D:HIS41 4.2 0.3 1.0
HG2 D:MET160 4.2 0.6 1.0
HE3 D:MET160 4.2 0.1 1.0
C3C D:HEC1001 4.2 0.7 1.0
C2C D:HEC1001 4.3 0.5 1.0
C2B D:HEC1001 4.3 0.4 1.0
CB D:MET160 4.3 0.4 1.0
HG3 D:PRO163 4.3 0.0 1.0
C3B D:HEC1001 4.3 0.7 1.0
C2D D:HEC1001 4.3 0.9 1.0
C3A D:HEC1001 4.3 0.6 1.0
C3D D:HEC1001 4.3 0.1 1.0
C2A D:HEC1001 4.4 0.3 1.0
HHD D:HEC1001 4.4 0.1 1.0
HHB D:HEC1001 4.4 0.1 1.0
HHC D:HEC1001 4.4 0.7 1.0
HHA D:HEC1001 4.5 0.7 1.0
HB3 D:MET160 4.6 0.3 1.0
HB3 D:PRO163 4.9 0.3 1.0
HB2 D:CYS40 4.9 0.2 1.0
HD2 D:PRO111 5.0 0.4 1.0
HA D:PRO110 5.0 0.2 1.0
HD21 D:LEU113 5.0 0.9 1.0

Iron binding site 4 out of 5 in 5klv

Go back to Iron Binding Sites List in 5klv
Iron binding site 4 out of 5 in the Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1001

b:0.5
occ:1.00
FE1 E:FES1001 0.0 0.5 1.0
S1 E:FES1001 2.2 0.8 1.0
S2 E:FES1001 2.2 0.9 1.0
SG E:CYS158 2.3 0.6 1.0
SG E:CYS139 2.3 0.1 1.0
HB3 E:CYS139 2.7 0.5 1.0
HB2 E:CYS139 2.8 0.5 1.0
CB E:CYS139 2.8 0.6 1.0
FE2 E:FES1001 3.1 0.0 1.0
HB3 E:CYS158 3.2 0.7 1.0
HB3 E:HIS141 3.3 0.9 1.0
HB2 E:CYS144 3.3 0.9 1.0
CB E:CYS158 3.3 0.2 1.0
HB2 E:CYS160 3.4 0.8 1.0
HB2 E:CYS158 3.6 0.7 1.0
H E:LEU142 3.9 0.6 1.0
HB2 E:SER163 3.9 0.8 1.0
H E:CYS144 4.0 0.1 1.0
HG E:SER163 4.1 0.4 1.0
CB E:HIS141 4.1 0.6 1.0
H E:HIS161 4.2 0.1 1.0
HB2 E:HIS141 4.2 0.9 1.0
CB E:CYS144 4.2 0.0 1.0
H E:HIS141 4.3 0.9 1.0
CA E:CYS139 4.3 0.6 1.0
CB E:CYS160 4.4 0.7 1.0
OG E:SER163 4.4 0.7 1.0
HH E:TYR165 4.5 0.5 1.0
H E:CYS160 4.5 0.7 1.0
HB3 E:CYS160 4.6 0.8 1.0
O E:CYS144 4.6 0.8 1.0
HA E:CYS139 4.7 0.5 1.0
CB E:SER163 4.7 0.1 1.0
N E:CYS144 4.7 0.2 1.0
N E:LEU142 4.7 0.9 1.0
H E:GLY143 4.7 0.7 1.0
CA E:CYS158 4.7 0.8 1.0
HB2 E:HIS161 4.7 0.2 1.0
ND1 E:HIS141 4.8 0.5 1.0
HB3 E:CYS144 4.8 0.9 1.0
H E:CYS139 4.8 0.4 1.0
ND1 E:HIS161 4.8 0.4 1.0
N E:HIS161 4.9 0.1 1.0
CA E:CYS144 4.9 0.6 1.0
SG E:CYS144 4.9 0.6 1.0
H E:SER163 4.9 0.9 1.0
C E:CYS139 4.9 0.1 1.0
N E:HIS141 5.0 0.4 1.0
CG E:HIS141 5.0 0.3 1.0
HB2 E:ALA176 5.0 0.6 1.0

Iron binding site 5 out of 5 in 5klv

Go back to Iron Binding Sites List in 5klv
Iron binding site 5 out of 5 in the Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Structure of Bos Taurus Cytochrome BC1 with Fenamidone Inhibited within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Fe1001

b:0.0
occ:1.00
FE2 E:FES1001 0.0 0.0 1.0
ND1 E:HIS161 2.1 0.4 1.0
ND1 E:HIS141 2.1 0.5 1.0
S2 E:FES1001 2.2 0.9 1.0
S1 E:FES1001 2.2 0.8 1.0
HB3 E:HIS141 2.6 0.9 1.0
HB2 E:HIS161 2.6 0.2 1.0
CG E:HIS141 3.0 0.3 1.0
CG E:HIS161 3.1 0.2 1.0
FE1 E:FES1001 3.1 0.5 1.0
CE1 E:HIS161 3.1 0.3 1.0
CE1 E:HIS141 3.2 0.5 1.0
CB E:HIS141 3.2 0.6 1.0
CB E:HIS161 3.3 0.5 1.0
HE1 E:HIS161 3.4 0.7 1.0
HE1 E:HIS141 3.4 0.9 1.0
HB2 E:LEU142 3.6 0.0 1.0
HB2 E:HIS141 3.6 0.9 1.0
H E:LEU142 3.6 0.6 1.0
H E:HIS161 3.8 0.1 1.0
HB2 E:CYS160 3.9 0.8 1.0
HB3 E:CYS160 3.9 0.8 1.0
HD12 E:LEU142 4.0 0.3 1.0
HB3 E:HIS161 4.0 0.2 1.0
N E:HIS161 4.0 0.1 1.0
HG2 E:PRO175 4.1 0.1 1.0
N E:LEU142 4.1 0.9 1.0
CD2 E:HIS141 4.2 0.5 1.0
CD2 E:HIS161 4.2 0.0 1.0
HG E:SER163 4.2 0.4 1.0
HG E:LEU142 4.2 0.1 1.0
NE2 E:HIS141 4.2 0.6 1.0
NE2 E:HIS161 4.2 0.4 1.0
CA E:HIS161 4.3 0.1 1.0
CB E:CYS160 4.4 0.7 1.0
CB E:LEU142 4.4 0.2 1.0
CA E:HIS141 4.5 0.5 1.0
SG E:CYS139 4.5 0.1 1.0
CG E:LEU142 4.7 0.1 1.0
C E:HIS141 4.7 0.9 1.0
OG E:SER163 4.7 0.7 1.0
C E:CYS160 4.7 0.7 1.0
CD1 E:LEU142 4.8 0.1 1.0
HG3 E:PRO175 4.8 0.1 1.0
CA E:LEU142 4.8 0.1 1.0
HB3 E:CYS139 4.8 0.5 1.0
CG E:PRO175 4.9 0.0 1.0
H E:HIS141 5.0 0.9 1.0
SG E:CYS158 5.0 0.6 1.0
C E:HIS161 5.0 0.8 1.0
HD2 E:HIS141 5.0 0.2 1.0

Reference:

L.Esser, F.Zhou, Y.Zhou, Y.Xiao, W.K.Tang, C.A.Yu, Z.Qin, D.Xia. Hydrogen Bonding to the Substrate Is Not Required For Rieske Iron-Sulfur Protein Docking to the Quinol Oxidation Site of Complex III. J.Biol.Chem. V. 291 25019 2016.
ISSN: ESSN 1083-351X
PubMed: 27758861
DOI: 10.1074/JBC.M116.744391
Page generated: Sun Dec 13 16:05:44 2020

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