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Iron in PDB 3vr9: Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil

Protein crystallography data

The structure of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil, PDB code: 3vr9 was solved by H.Shimizu, T.Shiba, D.K.Inaoka, A.Osanai, K.Kita, K.Sakamoto, S.Harada, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.39 / 3.01
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.011, 135.333, 220.498, 90.00, 90.00, 90.00
R / Rfree (%) 21.6 / 27.7

Other elements in 3vr9:

The structure of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil (pdb code 3vr9). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil, PDB code: 3vr9:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 3vr9

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Iron binding site 1 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:54.7
occ:1.00
FE1 B:FES301 0.0 54.7 1.0
SG B:CYS97 2.1 60.2 1.0
S1 B:FES301 2.2 54.7 1.0
S2 B:FES301 2.2 52.3 1.0
SG B:CYS109 2.3 63.3 1.0
FE2 B:FES301 3.0 55.9 1.0
CB B:CYS109 3.2 66.6 1.0
CB B:CYS97 3.3 59.4 1.0
N B:CYS97 3.8 59.2 1.0
N B:CYS109 4.0 67.0 1.0
CA B:CYS97 4.1 59.5 1.0
CB B:LEU107 4.1 69.5 1.0
CA B:GLY92 4.1 63.4 1.0
CA B:CYS109 4.2 66.7 1.0
SG B:CYS94 4.4 57.9 1.0
CD1 B:LEU107 4.4 70.7 1.0
N B:GLY92 4.6 65.6 1.0
N B:SER96 4.6 58.6 1.0
C B:CYS97 4.7 59.8 1.0
CG B:LEU107 4.8 70.4 1.0
CA B:LEU107 4.8 69.3 1.0
C B:LEU107 4.9 69.3 1.0
N B:ALA108 4.9 68.7 1.0
C B:SER96 5.0 59.4 1.0
SG B:CYS89 5.0 67.3 1.0

Iron binding site 2 out of 20 in 3vr9

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Iron binding site 2 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:55.9
occ:1.00
FE2 B:FES301 0.0 55.9 1.0
SG B:CYS94 2.1 57.9 1.0
S2 B:FES301 2.2 52.3 1.0
S1 B:FES301 2.2 54.7 1.0
SG B:CYS89 2.4 67.3 1.0
FE1 B:FES301 3.0 54.7 1.0
CB B:CYS89 3.1 68.7 1.0
N B:CYS89 3.3 67.6 1.0
CA B:CYS89 3.5 68.5 1.0
CB B:CYS94 3.5 58.6 1.0
N B:CYS94 3.6 58.7 1.0
N B:ARG90 3.7 69.8 1.0
SG B:CYS109 3.8 63.3 1.0
N B:ILE93 3.8 61.0 1.0
C B:CYS89 3.9 69.1 1.0
N B:GLY92 4.0 65.6 1.0
CA B:GLY92 4.0 63.4 1.0
CA B:CYS94 4.0 58.8 1.0
N B:GLY95 4.1 58.2 1.0
C B:GLY92 4.3 62.3 1.0
N B:SER88 4.5 66.1 1.0
C B:SER88 4.5 66.6 1.0
N B:SER96 4.6 58.6 1.0
C B:CYS94 4.6 58.5 1.0
OG B:SER96 4.6 58.8 1.0
N B:GLU91 4.6 69.3 1.0
C B:ILE93 4.7 59.0 1.0
CB B:SER96 4.8 58.8 1.0
CA B:ARG90 4.8 71.0 1.0
CA B:ILE93 4.8 59.2 1.0
CB B:CYS109 4.8 66.6 1.0
CA B:SER88 4.9 65.9 1.0
O B:CYS89 4.9 69.8 1.0
SG B:CYS97 5.0 60.2 1.0

Iron binding site 3 out of 20 in 3vr9

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Iron binding site 3 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:55.4
occ:1.00
FE1 B:SF4302 0.0 55.4 1.0
S4 B:SF4302 2.3 48.8 1.0
S2 B:SF4302 2.3 49.7 1.0
S3 B:SF4302 2.3 51.2 1.0
SG B:CYS185 2.4 53.2 1.0
FE4 B:SF4302 2.6 49.2 1.0
FE2 B:SF4302 2.6 49.1 1.0
FE3 B:SF4302 2.7 49.9 1.0
CB B:CYS185 3.6 54.6 1.0
N B:CYS185 3.7 55.6 1.0
N B:ALA186 3.8 54.1 1.0
S1 B:SF4302 3.9 50.6 1.0
N B:CYS187 3.9 54.8 1.0
CA B:CYS185 4.0 54.9 1.0
SG B:CYS188 4.2 59.0 1.0
C B:CYS185 4.2 54.7 1.0
CB B:CYS187 4.3 55.3 1.0
N B:CYS188 4.5 55.4 1.0
CD B:PRO250 4.6 66.9 1.0
CA B:ALA186 4.6 54.0 1.0
SG B:CYS182 4.6 61.6 1.0
CA B:CYS187 4.7 55.4 1.0
C B:ALA186 4.8 54.5 1.0
SG B:CYS249 4.8 67.6 1.0
N B:LEU184 4.8 58.2 1.0
C B:LEU184 4.9 56.9 1.0
CG1 B:ILE183 4.9 57.0 1.0

Iron binding site 4 out of 20 in 3vr9

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Iron binding site 4 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:49.1
occ:1.00
FE2 B:SF4302 0.0 49.1 1.0
S1 B:SF4302 2.3 50.6 1.0
S3 B:SF4302 2.3 51.2 1.0
S4 B:SF4302 2.3 48.8 1.0
SG B:CYS249 2.3 67.6 1.0
FE4 B:SF4302 2.6 49.2 1.0
FE1 B:SF4302 2.6 55.4 1.0
FE3 B:SF4302 2.7 49.9 1.0
CB B:CYS249 3.6 67.5 1.0
S2 B:SF4302 3.8 49.7 1.0
CD1 B:LEU253 4.0 71.2 1.0
CA B:CYS249 4.0 67.6 1.0
CD B:PRO250 4.3 66.9 1.0
SG B:CYS185 4.6 53.2 1.0
CB B:LEU253 4.6 71.7 1.0
CG B:LYS251 4.7 69.7 1.0
CB B:LYS251 4.7 68.8 1.0
CG B:LEU253 4.7 72.3 1.0
C B:CYS249 4.8 67.5 1.0
N B:PRO250 4.8 67.2 1.0
SG B:CYS182 4.8 61.6 1.0
SG B:CYS188 4.8 59.0 1.0
N B:LYS251 4.8 68.0 1.0

Iron binding site 5 out of 20 in 3vr9

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Iron binding site 5 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:49.9
occ:1.00
FE3 B:SF4302 0.0 49.9 1.0
SG B:CYS182 2.2 61.6 1.0
S1 B:SF4302 2.3 50.6 1.0
S4 B:SF4302 2.3 48.8 1.0
S2 B:SF4302 2.3 49.7 1.0
FE2 B:SF4302 2.7 49.1 1.0
FE4 B:SF4302 2.7 49.2 1.0
FE1 B:SF4302 2.7 55.4 1.0
CB B:CYS182 3.3 61.7 1.0
CA B:CYS182 3.6 61.5 1.0
N B:ILE183 3.9 59.8 1.0
S3 B:SF4302 4.0 51.2 1.0
N B:LEU184 4.0 58.2 1.0
C B:CYS182 4.1 60.5 1.0
CD1 B:LEU253 4.2 71.2 1.0
N B:CYS185 4.5 55.6 1.0
CA B:LEU184 4.6 57.4 1.0
SG B:CYS188 4.7 59.0 1.0
SG B:CYS249 4.8 67.6 1.0
SG B:CYS185 4.9 53.2 1.0
C B:ILE183 4.9 59.0 1.0
N B:CYS182 4.9 62.6 1.0
CA B:ILE183 5.0 59.1 1.0

Iron binding site 6 out of 20 in 3vr9

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Iron binding site 6 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:49.2
occ:1.00
FE4 B:SF4302 0.0 49.2 1.0
S1 B:SF4302 2.3 50.6 1.0
SG B:CYS188 2.3 59.0 1.0
S3 B:SF4302 2.3 51.2 1.0
S2 B:SF4302 2.3 49.7 1.0
FE2 B:SF4302 2.6 49.1 1.0
FE1 B:SF4302 2.6 55.4 1.0
FE3 B:SF4302 2.7 49.9 1.0
CB B:CYS188 3.3 55.7 1.0
S4 B:SF4302 3.8 48.8 1.0
N B:CYS188 4.0 55.4 1.0
CA B:CYS188 4.3 55.8 1.0
CB B:ALA206 4.3 64.0 1.0
SG B:CYS249 4.4 67.6 1.0
CA B:ALA206 4.6 63.9 1.0
SG B:CYS182 4.6 61.6 1.0
SG B:CYS185 4.9 53.2 1.0

Iron binding site 7 out of 20 in 3vr9

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Iron binding site 7 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:59.8
occ:1.00
FE1 B:F3S303 0.0 59.8 1.0
S3 B:F3S303 2.1 62.0 1.0
S2 B:F3S303 2.2 56.1 1.0
S1 B:F3S303 2.3 55.6 1.0
SG B:CYS239 2.4 72.5 1.0
FE3 B:F3S303 2.5 60.8 1.0
FE4 B:F3S303 2.5 59.0 1.0
CB B:CYS239 3.6 71.8 1.0
OH B:TYR202 3.7 65.7 1.0
S4 B:F3S303 3.8 56.7 1.0
N B:THR241 4.1 70.2 1.0
CD1 B:ILE259 4.1 62.9 1.0
CA B:CYS239 4.1 71.8 1.0
SG B:CYS245 4.2 70.6 1.0
CA B:THR241 4.4 69.9 1.0
N B:ILE242 4.4 69.0 1.0
SG B:CYS192 4.4 60.8 1.0
N B:HIS240 4.5 71.0 1.0
C B:CYS239 4.6 71.4 1.0
CZ B:TYR202 4.8 63.8 1.0
C B:THR241 5.0 69.4 1.0
CG2 B:ILE259 5.0 63.3 1.0

Iron binding site 8 out of 20 in 3vr9

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Iron binding site 8 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:60.8
occ:1.00
FE3 B:F3S303 0.0 60.8 1.0
S3 B:F3S303 2.1 62.0 1.0
SG B:CYS245 2.1 70.6 1.0
S4 B:F3S303 2.2 56.7 1.0
S1 B:F3S303 2.2 55.6 1.0
FE1 B:F3S303 2.5 59.8 1.0
FE4 B:F3S303 2.6 59.0 1.0
CB B:CYS245 3.1 68.7 1.0
S2 B:F3S303 3.6 56.1 1.0
N B:CYS245 3.8 68.4 1.0
CA B:CYS245 4.1 68.7 1.0
N B:MET243 4.2 67.4 1.0
SG B:CYS192 4.3 60.8 1.0
N B:ASN244 4.4 68.0 1.0
CB B:PRO205 4.5 64.0 1.0
CA B:MET243 4.5 67.6 1.0
CB B:CYS192 4.6 61.1 1.0
CG B:PRO205 4.7 64.2 1.0
CD1 B:ILE259 4.8 62.9 1.0
SG B:CYS239 4.8 72.5 1.0
N B:ILE242 4.8 69.0 1.0
C B:MET243 4.8 67.9 1.0
C B:ASN244 5.0 68.3 1.0

Iron binding site 9 out of 20 in 3vr9

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Iron binding site 9 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:59.0
occ:1.00
FE4 B:F3S303 0.0 59.0 1.0
S3 B:F3S303 2.1 62.0 1.0
S4 B:F3S303 2.2 56.7 1.0
S2 B:F3S303 2.2 56.1 1.0
SG B:CYS192 2.2 60.8 1.0
FE1 B:F3S303 2.5 59.8 1.0
FE3 B:F3S303 2.6 60.8 1.0
CB B:CYS192 3.3 61.1 1.0
S1 B:F3S303 3.6 55.6 1.0
CA B:CYS192 4.1 61.4 1.0
CB B:ILE242 4.4 67.6 1.0
OH B:TYR202 4.5 65.7 1.0
SG B:CYS239 4.6 72.5 1.0
CD1 B:ILE242 4.6 68.7 1.0
SG B:CYS245 4.7 70.6 1.0
CE2 B:TYR202 4.7 64.8 1.0
CD B:PRO193 4.7 63.1 1.0
N B:ILE242 4.7 69.0 1.0
C B:CYS192 4.8 62.0 1.0
CG1 B:ILE242 4.8 66.7 1.0
CB B:SER194 4.9 65.5 1.0
N B:MET243 5.0 67.4 1.0

Iron binding site 10 out of 20 in 3vr9

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Iron binding site 10 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Flutolanil within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:80.8
occ:1.00
FE C:HEM201 0.0 80.8 1.0
NC C:HEM201 2.0 82.3 1.0
NE2 C:HIS131 2.0 78.6 1.0
NA C:HEM201 2.1 82.3 1.0
ND C:HEM201 2.1 79.9 1.0
NE2 D:HIS95 2.1 71.4 1.0
NB C:HEM201 2.1 84.6 1.0
CE1 C:HIS131 2.9 80.2 1.0
CD2 D:HIS95 2.9 72.1 1.0
C4C C:HEM201 3.0 82.4 1.0
C1C C:HEM201 3.0 83.6 1.0
C1A C:HEM201 3.0 82.0 1.0
CD2 C:HIS131 3.1 79.8 1.0
C1D C:HEM201 3.1 78.7 1.0
C4D C:HEM201 3.1 79.3 1.0
C4A C:HEM201 3.1 82.2 1.0
C4B C:HEM201 3.1 85.6 1.0
C1B C:HEM201 3.2 85.1 1.0
CE1 D:HIS95 3.2 72.9 1.0
CHD C:HEM201 3.4 80.1 1.0
CHA C:HEM201 3.4 80.7 1.0
CHC C:HEM201 3.4 84.9 1.0
CHB C:HEM201 3.5 83.4 1.0
ND1 C:HIS131 4.0 80.8 1.0
CG D:HIS95 4.1 72.0 1.0
CG C:HIS131 4.1 80.8 1.0
C3C C:HEM201 4.1 84.0 1.0
C2C C:HEM201 4.2 83.4 1.0
ND1 D:HIS95 4.2 72.3 1.0
C2A C:HEM201 4.3 82.6 1.0
C2D C:HEM201 4.3 78.0 1.0
C3A C:HEM201 4.3 82.4 1.0
C3D C:HEM201 4.3 77.5 1.0
C3B C:HEM201 4.4 87.1 1.0
C2B C:HEM201 4.4 86.0 1.0
CE1 C:HIS75 4.8 62.2 1.0
NE2 C:HIS75 4.9 63.6 1.0

Reference:

H.Shimizu, T.Shiba, D.K.Inaoka, A.Osanai, K.Kita, K.Sakamoto, S.Harada. Crystal Structure of Mitochondrial Quinol-Fumarate Reductase From Parasitic Nematode Ascaris Suum To Be Published.
Page generated: Sun Dec 13 15:25:04 2020

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