Iron in PDB 5c2t: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2:
1.3.5.1;

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2, PDB code: 5c2t was solved by S.Harada, T.Shiba, D.Sato, A.Yamamoto, M.Nagahama, A.Yone, D.K.Inaoka, K.Sakamoto, M.Inoue, T.Honma, K.Kita, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	122.813, 123.632, 219.812, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 25.2

Pages:

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

Binding sites:

The binding sites of Iron atom in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 (pdb code 5c2t). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2, PDB code: 5c2t:
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 Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:24.8 occ:1.00 FE1 B:FES301 0.0 24.8 1.0 SG B:CYS97 2.1 32.9 1.0 S2 B:FES301 2.2 26.8 1.0 S1 B:FES301 2.2 22.8 1.0 SG B:CYS109 2.3 26.1 1.0 FE2 B:FES301 2.6 31.4 1.0 CB B:CYS109 3.0 29.3 1.0 CB B:CYS97 3.3 31.9 1.0 SG B:CYS89 3.8 37.1 1.0 N B:CYS109 4.0 31.4 1.0 N B:CYS97 4.1 32.2 1.0 CA B:CYS109 4.2 30.8 1.0 CA B:CYS97 4.3 31.7 1.0 CB B:LEU107 4.3 31.2 1.0 SG B:CYS94 4.5 29.8 1.0 CA B:GLY92 4.5 30.2 1.0 N B:GLY92 4.7 32.0 1.0 N B:ALA108 4.9 33.5 1.0 CD2 B:LEU107 4.9 30.1 1.0 CG B:LEU107 5.0 30.2 1.0 CD1 B:LEU107 5.0 30.0 1.0

Iron binding site 2 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:31.4 occ:1.00 FE2 B:FES301 0.0 31.4 1.0 SG B:CYS89 2.1 37.1 1.0 S2 B:FES301 2.2 26.8 1.0 SG B:CYS94 2.2 29.8 1.0 S1 B:FES301 2.2 22.8 1.0 FE1 B:FES301 2.6 24.8 1.0 CB B:CYS94 3.4 28.4 1.0 CB B:CYS89 3.5 32.9 1.0 N B:GLY95 3.6 29.3 1.0 N B:CYS94 3.7 26.9 1.0 N B:CYS89 3.8 32.6 1.0 CA B:CYS94 3.9 27.6 1.0 N B:SER96 4.0 31.2 1.0 SG B:CYS109 4.1 26.1 1.0 CA B:CYS89 4.1 34.0 1.0 C B:CYS94 4.2 27.2 1.0 N B:ILE93 4.3 27.7 1.0 SG B:CYS97 4.3 32.9 1.0 CA B:GLY92 4.4 30.2 1.0 C B:CYS89 4.5 36.4 1.0 N B:GLY92 4.5 32.0 1.0 CA B:GLY95 4.5 29.6 1.0 O B:CYS89 4.6 38.4 1.0 OG B:SER96 4.6 39.1 1.0 N B:SER88 4.6 28.8 1.0 N B:CYS97 4.6 32.2 1.0 C B:GLY92 4.7 28.9 1.0 CB B:SER96 4.7 34.5 1.0 C B:GLY95 4.7 30.5 1.0 C B:ILE93 4.7 26.7 1.0 C B:SER88 4.8 31.0 1.0 CA B:SER96 4.9 32.4 1.0 CB B:CYS97 5.0 31.9 1.0

Iron binding site 3 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:30.1 occ:1.00 FE1 B:SF4302 0.0 30.1 1.0 S4 B:SF4302 2.1 26.2 1.0 S3 B:SF4302 2.1 27.1 1.0 S2 B:SF4302 2.1 26.2 1.0 SG B:CYS185 2.1 29.2 1.0 FE2 B:SF4302 3.0 28.3 1.0 FE3 B:SF4302 3.0 28.3 1.0 FE4 B:SF4302 3.1 28.5 1.0 CB B:CYS185 3.4 28.2 1.0 N B:CYS185 3.6 28.3 1.0 N B:ALA186 3.7 29.3 1.0 S1 B:SF4302 3.8 24.4 1.0 CA B:CYS185 3.9 28.2 1.0 N B:CYS187 4.0 29.6 1.0 C B:CYS185 4.2 28.4 1.0 CG1 B:ILE183 4.3 30.3 1.0 CB B:CYS187 4.5 30.6 1.0 CD B:PRO250 4.5 33.1 1.0 CA B:ALA186 4.6 29.3 1.0 SG B:CYS182 4.7 25.6 1.0 C B:LEU184 4.7 28.0 1.0 N B:LEU184 4.7 29.1 1.0 C B:ALA186 4.8 29.5 1.0 CG B:PRO250 4.8 33.7 1.0 CA B:CYS187 4.8 30.1 1.0 N B:CYS188 4.9 30.2 1.0 SG B:CYS249 4.9 25.9 1.0 CA B:LEU184 5.0 28.4 1.0 SG B:CYS188 5.0 31.1 1.0 CD1 B:ILE183 5.0 30.1 1.0

Iron binding site 4 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:28.3 occ:1.00 FE2 B:SF4302 0.0 28.3 1.0 S3 B:SF4302 2.1 27.1 1.0 S4 B:SF4302 2.1 26.2 1.0 S1 B:SF4302 2.1 24.4 1.0 SG B:CYS188 2.3 31.1 1.0 FE3 B:SF4302 2.9 28.3 1.0 FE1 B:SF4302 3.0 30.1 1.0 FE4 B:SF4302 3.0 28.5 1.0 CB B:CYS188 3.1 30.2 1.0 S2 B:SF4302 3.6 26.2 1.0 N B:CYS188 3.8 30.2 1.0 CB B:ALA206 4.0 29.8 1.0 CA B:CYS188 4.1 30.1 1.0 N B:CYS187 4.5 29.6 1.0 CA B:ALA206 4.5 29.6 1.0 SG B:CYS185 4.7 29.2 1.0 SG B:CYS182 4.7 25.6 1.0 N B:ALA186 4.7 29.3 1.0 CA B:ALA186 4.8 29.3 1.0 N B:ALA206 4.9 29.4 1.0 CG B:PRO255 4.9 32.4 1.0 C B:ALA186 4.9 29.5 1.0 C B:CYS187 4.9 29.9 1.0 SG B:CYS249 4.9 25.9 1.0 N B:SER189 5.0 30.2 1.0

Iron binding site 5 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


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 Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:28.3 occ:1.00 FE3 B:SF4302 0.0 28.3 1.0 S1 B:SF4302 2.1 24.4 1.0 S2 B:SF4302 2.1 26.2 1.0 S4 B:SF4302 2.1 26.2 1.0 SG B:CYS182 2.2 25.6 1.0 FE2 B:SF4302 2.9 28.3 1.0 FE4 B:SF4302 2.9 28.5 1.0 FE1 B:SF4302 3.0 30.1 1.0 CB B:CYS182 3.2 28.5 1.0 S3 B:SF4302 3.6 27.1 1.0 CA B:CYS182 3.7 29.7 1.0 N B:ILE183 4.1 29.4 1.0 C B:CYS182 4.3 29.5 1.0 N B:LEU184 4.4 29.1 1.0 CD1 B:LEU253 4.5 28.7 1.0 CE B:MET209 4.7 40.1 1.0 CB B:ALA206 4.9 29.8 1.0 SG B:CYS188 4.9 31.1 1.0 CA B:LEU184 4.9 28.4 1.0 N B:CYS182 4.9 30.8 1.0

Iron binding site 6 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:28.5 occ:1.00 FE4 B:SF4302 0.0 28.5 1.0 S1 B:SF4302 2.1 24.4 1.0 S3 B:SF4302 2.1 27.1 1.0 S2 B:SF4302 2.1 26.2 1.0 SG B:CYS249 2.2 25.9 1.0 FE3 B:SF4302 2.9 28.3 1.0 FE2 B:SF4302 3.0 28.3 1.0 FE1 B:SF4302 3.1 30.1 1.0 CB B:CYS249 3.2 29.2 1.0 S4 B:SF4302 3.7 26.2 1.0 CA B:CYS249 3.9 29.6 1.0 CD1 B:LEU253 4.2 28.7 1.0 CD B:PRO250 4.3 33.1 1.0 CB B:LEU253 4.5 27.9 1.0 C B:CYS249 4.5 30.5 1.0 CG B:LEU253 4.5 28.0 1.0 N B:PRO250 4.6 32.1 1.0 N B:LYS251 4.7 32.7 1.0 CB B:LYS251 4.8 33.3 1.0 SG B:CYS185 4.9 29.2 1.0

Iron binding site 7 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:37.0 occ:1.00 FE1 B:F3S303 0.0 37.0 1.0 SG B:CYS239 2.1 35.2 1.0 S2 B:F3S303 2.2 36.2 1.0 S3 B:F3S303 2.2 31.7 1.0 S1 B:F3S303 2.2 37.3 1.0 FE3 B:F3S303 2.9 36.1 1.0 FE4 B:F3S303 2.9 35.9 1.0 CB B:CYS239 3.5 35.4 1.0 N B:THR241 3.7 35.9 1.0 CA B:CYS239 3.8 35.9 1.0 OH B:TYR202 3.9 35.2 1.0 N B:HIS240 4.0 36.9 1.0 CA B:THR241 4.0 34.1 1.0 C B:CYS239 4.1 35.9 1.0 S4 B:F3S303 4.1 33.8 1.0 N B:ILE242 4.1 35.8 1.0 CD1 B:ILE259 4.5 34.0 1.0 C B:HIS240 4.6 39.2 1.0 C B:THR241 4.6 35.8 1.0 SG B:CYS245 4.8 27.6 1.0 SG B:CYS192 4.9 29.8 1.0 O B:CYS239 4.9 33.9 1.0 CA B:HIS240 4.9 38.1 1.0 N B:MET243 5.0 36.6 1.0

Iron binding site 8 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:36.1 occ:1.00 FE3 B:F3S303 0.0 36.1 1.0 S3 B:F3S303 2.2 31.7 1.0 S4 B:F3S303 2.2 33.8 1.0 S1 B:F3S303 2.2 37.3 1.0 SG B:CYS245 2.2 27.6 1.0 FE4 B:F3S303 2.8 35.9 1.0 FE1 B:F3S303 2.9 37.0 1.0 CB B:CYS245 3.4 29.9 1.0 N B:CYS245 3.8 32.4 1.0 N B:MET243 3.9 36.6 1.0 S2 B:F3S303 3.9 36.2 1.0 CA B:MET243 4.2 38.4 1.0 CA B:CYS245 4.2 30.9 1.0 N B:ASN244 4.3 37.5 1.0 C B:MET243 4.5 38.0 1.0 SG B:CYS239 4.7 35.2 1.0 N B:ILE242 4.7 35.8 1.0 CB B:ALA256 4.8 33.9 1.0 CB B:PRO205 4.9 29.5 1.0 CG B:PRO205 4.9 29.2 1.0 C B:ILE242 4.9 35.4 1.0 SG B:CYS192 4.9 29.8 1.0 C B:ASN244 4.9 33.9 1.0 CB B:CYS192 5.0 31.2 1.0

Iron binding site 9 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:35.9 occ:1.00 FE4 B:F3S303 0.0 35.9 1.0 S4 B:F3S303 2.2 33.8 1.0 S3 B:F3S303 2.2 31.7 1.0 S2 B:F3S303 2.2 36.2 1.0 SG B:CYS192 2.4 29.8 1.0 FE3 B:F3S303 2.8 36.1 1.0 FE1 B:F3S303 2.9 37.0 1.0 CB B:CYS192 3.1 31.2 1.0 CA B:CYS192 3.8 32.0 1.0 S1 B:F3S303 4.0 37.3 1.0 CB B:ILE242 4.4 32.6 1.0 OH B:TYR202 4.6 35.2 1.0 C B:CYS192 4.6 34.1 1.0 CD1 B:ILE242 4.6 32.4 1.0 CB B:SER194 4.7 34.5 1.0 SG B:CYS245 4.7 27.6 1.0 N B:ILE242 4.8 35.8 1.0 CG1 B:ILE242 4.8 33.2 1.0 SG B:CYS239 4.9 35.2 1.0 CD B:PRO205 4.9 29.5 1.0 CE2 B:TYR202 4.9 33.3 1.0 N B:PRO193 5.0 35.3 1.0

Iron binding site 10 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Rhodoquinone-2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:49.2 occ:1.00 FE C:HEM201 0.0 49.2 1.0 ND C:HEM201 1.9 52.4 1.0 NA C:HEM201 2.0 54.6 1.0 NC C:HEM201 2.1 53.2 1.0 NB C:HEM201 2.1 55.5 1.0 NE2 D:HIS95 2.1 38.8 1.0 NE2 C:HIS131 2.2 39.0 1.0 C4D C:HEM201 2.9 53.4 1.0 C1D C:HEM201 2.9 51.8 1.0 C1A C:HEM201 3.0 52.6 1.0 C4A C:HEM201 3.0 55.6 1.0 C1C C:HEM201 3.1 53.8 1.0 C1B C:HEM201 3.1 57.0 1.0 C4B C:HEM201 3.1 55.4 1.0 C4C C:HEM201 3.1 53.6 1.0 CD2 C:HIS131 3.1 39.7 1.0 CE1 D:HIS95 3.1 40.6 1.0 CD2 D:HIS95 3.1 41.7 1.0 CE1 C:HIS131 3.2 40.4 1.0 CHA C:HEM201 3.4 53.6 1.0 CHD C:HEM201 3.4 53.9 1.0 CHB C:HEM201 3.4 56.7 1.0 CHC C:HEM201 3.4 53.7 1.0 C3D C:HEM201 4.2 50.5 1.0 C2D C:HEM201 4.2 51.0 1.0 ND1 D:HIS95 4.2 41.2 1.0 C3A C:HEM201 4.2 54.3 1.0 C2A C:HEM201 4.2 51.3 1.0 CG D:HIS95 4.2 42.8 1.0 C2C C:HEM201 4.2 53.3 1.0 ND1 C:HIS131 4.3 40.0 1.0 CG C:HIS131 4.3 41.4 1.0 C3C C:HEM201 4.3 53.7 1.0 C2B C:HEM201 4.3 59.4 1.0 C3B C:HEM201 4.3 61.6 1.0 NE2 C:HIS75 4.7 46.3 1.0 CE1 C:HIS75 4.9 45.3 1.0

D.K.Inaoka, T.Shiba, D.Sato, E.O.Balogun, T.Sasaki, M.Nagahama, M.Oda, S.Matsuoka, J.Ohmori, T.Honma, M.Inoue, K.Kita, S.Harada. Structural Insights Into the Molecular Design of Flutolanil Derivatives Targeted For Fumarate Respiration of Parasite Mitochondria Int J Mol Sci V. 16 15287 2015.
ISSN: ESSN 1422-0067
PubMed: 26198225
DOI: 10.3390/IJMS160715287