Iron in PDB 3vra: Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5

The structure of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5, PDB code: 3vra 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)	49.72 / 3.44
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.823, 132.250, 220.577, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 28.1

The structure of Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

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 Atpenin A5 (pdb code 3vra). 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 Atpenin A5, PDB code: 3vra:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:78.3 occ:1.00 FE1 B:FES301 0.0 78.3 1.0 S2 B:FES301 2.2 82.2 1.0 S1 B:FES301 2.2 78.8 1.0 SG B:CYS97 2.2 83.4 1.0 SG B:CYS109 2.3 91.2 1.0 CB B:CYS109 2.6 92.9 1.0 FE2 B:FES301 3.0 80.4 1.0 CB B:CYS97 3.1 85.4 1.0 CA B:CYS109 3.8 92.8 1.0 N B:CYS109 3.8 92.6 1.0 N B:CYS97 3.9 86.3 1.0 SG B:CYS89 4.1 91.6 1.0 CA B:CYS97 4.1 86.0 1.0 CD1 B:LEU69 4.5 94.4 1.0 N B:ARG90 4.6 94.0 1.0 SG B:CYS94 4.7 83.9 1.0 CD2 B:LEU107 4.7 93.3 1.0 N B:SER96 4.8 86.5 1.0 CA B:ARG90 4.8 95.1 1.0 CB B:LEU107 4.8 94.2 1.0 C B:CYS109 4.9 93.5 1.0 N B:GLY92 4.9 91.9 1.0 C B:CYS97 5.0 86.7 1.0 N B:GLY95 5.0 85.8 1.0

Iron binding site 2 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:80.4 occ:1.00 FE2 B:FES301 0.0 80.4 1.0 SG B:CYS94 2.1 83.9 1.0 SG B:CYS89 2.1 91.6 1.0 S2 B:FES301 2.2 82.2 1.0 S1 B:FES301 2.2 78.8 1.0 FE1 B:FES301 3.0 78.3 1.0 CB B:CYS89 3.2 93.6 1.0 N B:CYS94 3.2 85.4 1.0 CB B:CYS94 3.2 85.1 1.0 N B:GLY95 3.6 85.8 1.0 CA B:CYS94 3.6 85.1 1.0 N B:CYS89 3.8 93.6 1.0 N B:ARG90 3.8 94.0 1.0 CA B:CYS89 3.9 93.3 1.0 C B:SER88 4.0 93.7 1.0 SG B:CYS109 4.1 91.2 1.0 C B:CYS94 4.1 85.1 1.0 N B:SER96 4.1 86.5 1.0 N B:ILE93 4.2 88.2 1.0 C B:CYS89 4.4 93.5 1.0 O B:SER88 4.4 94.0 1.0 C B:ILE93 4.4 86.0 1.0 N B:SER88 4.4 92.9 1.0 CA B:SER88 4.6 93.5 1.0 CA B:GLY95 4.6 86.3 1.0 OG B:SER96 4.6 87.2 1.0 CA B:ARG90 4.8 95.1 1.0 CB B:SER88 4.8 93.4 1.0 CA B:ILE93 4.8 87.0 1.0 N B:GLY92 4.9 91.9 1.0 CB B:SER96 4.9 86.8 1.0 N B:CYS97 4.9 86.3 1.0 C B:GLY95 4.9 86.5 1.0 SG B:CYS97 4.9 83.4 1.0

Iron binding site 3 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:73.4 occ:1.00 FE1 B:SF4302 0.0 73.4 1.0 SG B:CYS185 1.9 77.0 1.0 S2 B:SF4302 2.3 75.3 1.0 S4 B:SF4302 2.3 72.7 1.0 S3 B:SF4302 2.3 70.9 1.0 FE4 B:SF4302 2.5 76.0 1.0 FE3 B:SF4302 2.8 71.0 1.0 FE2 B:SF4302 2.8 67.2 1.0 CB B:CYS185 3.4 77.8 1.0 N B:CYS185 3.4 78.7 1.0 S1 B:SF4302 3.9 72.5 1.0 CA B:CYS185 3.9 78.3 1.0 N B:ALA186 3.9 79.1 1.0 CG1 B:ILE183 4.1 78.8 1.0 C B:CYS185 4.3 78.7 1.0 N B:LEU184 4.3 80.7 1.0 N B:CYS187 4.4 79.9 1.0 C B:LEU184 4.4 79.3 1.0 SG B:CYS188 4.6 82.2 1.0 CA B:LEU184 4.6 79.8 1.0 CD B:PRO250 4.6 90.2 1.0 CD1 B:ILE183 4.6 77.0 1.0 CB B:CYS187 4.7 80.3 1.0 N B:ILE183 4.8 82.2 1.0 SG B:CYS182 4.8 81.6 1.0 SG B:CYS187 4.8 82.9 1.0 CA B:ALA186 4.9 79.2 1.0 CG B:PRO250 4.9 90.7 1.0 SG B:CYS249 5.0 88.1 1.0

Iron binding site 4 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:67.2 occ:1.00 FE2 B:SF4302 0.0 67.2 1.0 S1 B:SF4302 2.3 72.5 1.0 S4 B:SF4302 2.3 72.7 1.0 S3 B:SF4302 2.3 70.9 1.0 SG B:CYS249 2.5 88.1 1.0 FE4 B:SF4302 2.7 76.0 1.0 FE3 B:SF4302 2.7 71.0 1.0 FE1 B:SF4302 2.8 73.4 1.0 CB B:CYS249 3.3 89.9 1.0 CD1 B:LEU253 3.6 92.3 1.0 CA B:CYS249 3.9 90.1 1.0 S2 B:SF4302 4.0 75.3 1.0 CD B:PRO250 4.4 90.2 1.0 SG B:CYS185 4.4 77.0 1.0 SG B:CYS188 4.5 82.2 1.0 CB B:LYS251 4.6 89.6 1.0 CG B:LEU253 4.7 91.5 1.0 C B:CYS249 4.7 90.5 1.0 N B:PRO250 4.8 90.4 1.0 N B:LYS251 4.8 89.8 1.0 CB B:LEU253 4.9 91.9 1.0 CG B:LYS251 5.0 89.0 1.0

Iron binding site 5 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:71.0 occ:1.00 FE3 B:SF4302 0.0 71.0 1.0 S4 B:SF4302 2.3 72.7 1.0 S1 B:SF4302 2.3 72.5 1.0 S2 B:SF4302 2.3 75.3 1.0 SG B:CYS182 2.4 81.6 1.0 FE4 B:SF4302 2.7 76.0 1.0 FE2 B:SF4302 2.7 67.2 1.0 FE1 B:SF4302 2.8 73.4 1.0 CB B:CYS182 3.2 84.3 1.0 CA B:CYS182 3.6 84.0 1.0 S3 B:SF4302 4.0 70.9 1.0 N B:LEU184 4.0 80.7 1.0 N B:ILE183 4.1 82.2 1.0 C B:CYS182 4.1 83.2 1.0 CD1 B:LEU253 4.3 92.3 1.0 CA B:LEU184 4.5 79.8 1.0 CB B:ALA206 4.5 93.0 1.0 SG B:CYS188 4.6 82.2 1.0 SG B:CYS185 4.6 77.0 1.0 N B:CYS185 4.7 78.7 1.0 CA B:ALA206 4.8 93.5 1.0 N B:CYS182 4.9 86.0 1.0

Iron binding site 6 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:76.0 occ:1.00 FE4 B:SF4302 0.0 76.0 1.0 SG B:CYS188 2.2 82.2 1.0 S3 B:SF4302 2.3 70.9 1.0 S2 B:SF4302 2.3 75.3 1.0 S1 B:SF4302 2.4 72.5 1.0 FE1 B:SF4302 2.5 73.4 1.0 FE2 B:SF4302 2.7 67.2 1.0 FE3 B:SF4302 2.7 71.0 1.0 CB B:CYS188 3.5 80.5 1.0 S4 B:SF4302 3.7 72.7 1.0 N B:CYS188 3.8 80.2 1.0 SG B:CYS185 3.9 77.0 1.0 CB B:ALA206 3.9 93.0 1.0 CA B:CYS188 4.3 80.2 1.0 CA B:ALA206 4.3 93.5 1.0 N B:CYS187 4.3 79.9 1.0 N B:ALA186 4.4 79.1 1.0 CA B:ALA186 4.7 79.2 1.0 SG B:CYS182 4.7 81.6 1.0 N B:ALA206 4.8 93.6 1.0 C B:ALA186 4.8 79.5 1.0 C B:CYS187 4.9 80.3 1.0 CB B:CYS187 4.9 80.3 1.0 SG B:CYS249 4.9 88.1 1.0 N B:CYS185 5.0 78.7 1.0 CB B:CYS249 5.0 89.9 1.0 CA B:CYS187 5.0 80.3 1.0

Iron binding site 7 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:90.0 occ:1.00 FE1 B:F3S303 0.0 90.0 1.0 S3 B:F3S303 2.1 93.6 1.0 S1 B:F3S303 2.2 91.2 1.0 S2 B:F3S303 2.2 90.5 1.0 SG B:CYS239 2.4 98.9 1.0 FE3 B:F3S303 2.5 89.4 1.0 FE4 B:F3S303 2.5 92.4 1.0 CB B:CYS239 3.6 98.5 1.0 S4 B:F3S303 3.7 91.3 1.0 OH B:TYR202 4.0 95.2 1.0 CA B:CYS239 4.1 98.5 1.0 CD1 B:ILE259 4.2 89.2 1.0 CA B:THR241 4.2 97.7 1.0 N B:THR241 4.2 98.6 1.0 N B:ILE242 4.2 96.0 1.0 SG B:CYS192 4.4 84.9 1.0 C B:THR241 4.6 96.9 1.0 C B:CYS239 4.7 98.6 1.0 N B:MET243 4.7 94.3 1.0 SG B:CYS245 4.7 92.8 1.0 N B:HIS240 4.9 99.1 1.0

Iron binding site 8 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:89.4 occ:1.00 FE3 B:F3S303 0.0 89.4 1.0 S3 B:F3S303 2.1 93.6 1.0 S1 B:F3S303 2.2 91.2 1.0 S4 B:F3S303 2.2 91.3 1.0 SG B:CYS245 2.4 92.8 1.0 FE4 B:F3S303 2.5 92.4 1.0 FE1 B:F3S303 2.5 90.0 1.0 CB B:CYS245 3.1 92.2 1.0 S2 B:F3S303 3.6 90.5 1.0 N B:CYS245 3.9 92.8 1.0 CA B:CYS245 4.1 92.3 1.0 SG B:CYS192 4.1 84.9 1.0 N B:MET243 4.2 94.3 1.0 CA B:MET243 4.4 94.3 1.0 CB B:PRO205 4.5 93.0 1.0 C B:MET243 4.6 94.1 1.0 N B:ASN244 4.6 93.6 1.0 CB B:CYS192 4.7 86.0 1.0 CG B:PRO205 4.8 93.0 1.0 SG B:CYS239 4.9 98.9 1.0 CD B:PRO205 5.0 92.9 1.0 CD1 B:ILE259 5.0 89.2 1.0

Iron binding site 9 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:92.4 occ:1.00 FE4 B:F3S303 0.0 92.4 1.0 SG B:CYS192 1.9 84.9 1.0 S3 B:F3S303 2.1 93.6 1.0 S4 B:F3S303 2.2 91.3 1.0 S2 B:F3S303 2.2 90.5 1.0 FE3 B:F3S303 2.5 89.4 1.0 FE1 B:F3S303 2.5 90.0 1.0 CB B:CYS192 3.3 86.0 1.0 S1 B:F3S303 3.6 91.2 1.0 OH B:TYR202 4.2 95.2 1.0 CA B:CYS192 4.3 86.2 1.0 CE2 B:TYR202 4.5 96.4 1.0 CD B:PRO205 4.6 92.9 1.0 SG B:CYS239 4.6 98.9 1.0 CB B:SER194 4.7 90.3 1.0 SG B:CYS245 4.8 92.8 1.0 CB B:ILE242 4.8 94.8 1.0 CZ B:TYR202 4.8 96.4 1.0 CB B:CYS245 4.9 92.2 1.0 N B:ILE242 4.9 96.0 1.0 CG B:PRO205 4.9 93.0 1.0

Iron binding site 10 out of 20 in the Mitochondrial Rhodoquinol-Fumarate Reductase From the Parasitic Nematode Ascaris Suum with the Specific Inhibitor Atpenin A5


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 Atpenin A5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:0.7 occ:1.00 FE C:HEM201 0.0 0.7 1.0 NA C:HEM201 2.0 0.4 1.0 NB C:HEM201 2.0 0.8 1.0 NE2 C:HIS131 2.0 0.1 1.0 NE2 D:HIS95 2.1 93.9 1.0 ND C:HEM201 2.1 0.6 1.0 NC C:HEM201 2.1 0.6 1.0 CD2 C:HIS131 2.9 0.5 1.0 C1A C:HEM201 3.0 0.4 1.0 CD2 D:HIS95 3.0 93.5 1.0 C4D C:HEM201 3.0 0.2 1.0 C1B C:HEM201 3.0 0.5 1.0 C4A C:HEM201 3.1 0.8 1.0 C4B C:HEM201 3.1 0.3 1.0 C1C C:HEM201 3.1 0.2 1.0 CE1 D:HIS95 3.1 93.1 1.0 C4C C:HEM201 3.1 0.6 1.0 CE1 C:HIS131 3.1 0.2 1.0 C1D C:HEM201 3.1 0.3 1.0 CHA C:HEM201 3.3 0.1 1.0 CHC C:HEM201 3.4 0.2 1.0 CHB C:HEM201 3.4 0.8 1.0 CHD C:HEM201 3.5 0.4 1.0 CG C:HIS131 4.1 0.1 1.0 CG D:HIS95 4.2 93.5 1.0 ND1 C:HIS131 4.2 0.6 1.0 ND1 D:HIS95 4.2 93.8 1.0 C2A C:HEM201 4.2 0.1 1.0 C3A C:HEM201 4.2 0.7 1.0 C2B C:HEM201 4.3 0.5 1.0 C3B C:HEM201 4.3 0.8 1.0 C2C C:HEM201 4.3 0.8 1.0 C3C C:HEM201 4.3 0.3 1.0 C3D C:HEM201 4.3 0.2 1.0 NE2 C:HIS75 4.3 94.2 1.0 C2D C:HEM201 4.4 0.2 1.0 CE1 C:HIS75 4.6 94.2 1.0

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.