Iron in PDB 5c3j: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1:
1.3.5.1;

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1, PDB code: 5c3j 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 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	123.750, 126.827, 220.449, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 26

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 Ubiquinone-1 (pdb code 5c3j). 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 Ubiquinone-1, PDB code: 5c3j:
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 Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:30.1 occ:1.00 FE1 B:FES301 0.0 30.1 1.0 SG B:CYS97 2.1 35.3 1.0 S1 B:FES301 2.2 29.7 1.0 S2 B:FES301 2.2 33.6 1.0 SG B:CYS109 2.4 32.6 1.0 FE2 B:FES301 2.7 33.1 1.0 CB B:CYS109 3.0 34.4 1.0 CB B:CYS97 3.1 33.1 1.0 SG B:CYS89 3.8 33.7 1.0 N B:CYS109 3.9 34.9 1.0 N B:CYS97 4.0 31.8 1.0 CA B:CYS109 4.0 33.8 1.0 CA B:CYS97 4.1 32.7 1.0 CB B:LEU107 4.4 31.8 1.0 SG B:CYS94 4.8 27.7 1.0 N B:ALA108 4.8 35.8 1.0 CD2 B:LEU107 4.8 30.2 1.0 CA B:GLY92 4.8 31.2 1.0 CD1 B:LEU69 4.9 37.2 1.0 C B:CYS97 4.9 32.4 1.0

Iron binding site 2 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe301 b:33.1 occ:1.00 FE2 B:FES301 0.0 33.1 1.0 S2 B:FES301 2.2 33.6 1.0 S1 B:FES301 2.2 29.7 1.0 SG B:CYS94 2.3 27.7 1.0 SG B:CYS89 2.3 33.7 1.0 FE1 B:FES301 2.7 30.1 1.0 CB B:CYS89 3.5 29.9 1.0 CB B:CYS94 3.5 28.8 1.0 N B:GLY95 3.5 32.4 1.0 N B:CYS89 3.8 30.5 1.0 N B:CYS94 3.8 28.8 1.0 N B:SER96 3.9 31.5 1.0 CA B:CYS94 4.0 29.8 1.0 SG B:CYS109 4.0 32.6 1.0 CA B:CYS89 4.1 32.1 1.0 C B:CYS94 4.2 31.9 1.0 N B:SER88 4.4 27.3 1.0 N B:CYS97 4.4 31.8 1.0 CA B:GLY95 4.4 32.3 1.0 C B:CYS89 4.4 36.0 1.0 SG B:CYS97 4.5 35.3 1.0 CB B:SER96 4.5 30.3 1.0 O B:CYS89 4.5 37.3 1.0 C B:GLY95 4.6 32.4 1.0 N B:ILE93 4.6 31.0 1.0 CA B:SER96 4.7 31.1 1.0 C B:SER88 4.7 27.9 1.0 CB B:CYS97 4.8 33.1 1.0 CA B:GLY92 4.9 31.2 1.0 C B:ILE93 4.9 29.3 1.0 N B:GLY92 4.9 33.0 1.0 CB B:CYS109 4.9 34.4 1.0 OG B:SER96 5.0 32.7 1.0

Iron binding site 3 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:33.4 occ:1.00 FE1 B:SF4302 0.0 33.4 1.0 S2 B:SF4302 2.1 29.3 1.0 S3 B:SF4302 2.1 31.5 1.0 S4 B:SF4302 2.1 29.5 1.0 SG B:CYS185 2.3 30.3 1.0 FE2 B:SF4302 3.0 31.8 1.0 FE4 B:SF4302 3.1 31.9 1.0 FE3 B:SF4302 3.1 30.0 1.0 CB B:CYS185 3.5 28.9 1.0 N B:CYS185 3.6 28.6 1.0 N B:ALA186 3.7 31.2 1.0 S1 B:SF4302 3.7 27.1 1.0 CA B:CYS185 4.0 29.1 1.0 N B:CYS187 4.1 32.1 1.0 C B:CYS185 4.2 31.1 1.0 CD B:PRO250 4.2 37.5 1.0 CB B:CYS187 4.5 33.5 1.0 CG1 B:ILE183 4.6 34.5 1.0 CA B:ALA186 4.7 29.8 1.0 N B:LEU184 4.7 28.9 1.0 CG B:PRO250 4.7 38.0 1.0 C B:LEU184 4.7 27.1 1.0 N B:CYS188 4.8 34.2 1.0 C B:ALA186 4.8 30.2 1.0 CA B:CYS187 4.9 33.3 1.0 SG B:CYS182 4.9 29.5 1.0

Iron binding site 4 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:31.8 occ:1.00 FE2 B:SF4302 0.0 31.8 1.0 S3 B:SF4302 2.1 31.5 1.0 S1 B:SF4302 2.1 27.1 1.0 S4 B:SF4302 2.1 29.5 1.0 SG B:CYS188 2.4 39.1 1.0 FE4 B:SF4302 3.0 31.9 1.0 CB B:CYS188 3.0 35.5 1.0 FE1 B:SF4302 3.0 33.4 1.0 FE3 B:SF4302 3.0 30.0 1.0 S2 B:SF4302 3.6 29.3 1.0 N B:CYS188 3.8 34.2 1.0 CA B:CYS188 4.0 34.3 1.0 CB B:ALA206 4.0 32.1 1.0 CA B:ALA206 4.3 32.4 1.0 CG B:PRO255 4.7 41.7 1.0 N B:ALA206 4.7 32.4 1.0 SG B:CYS182 4.8 29.5 1.0 N B:CYS187 4.8 32.1 1.0 N B:SER189 4.8 33.1 1.0 N B:ALA186 4.8 31.2 1.0 C B:CYS188 5.0 33.3 1.0 SG B:CYS185 5.0 30.3 1.0

Iron binding site 5 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:30.0 occ:1.00 FE3 B:SF4302 0.0 30.0 1.0 S1 B:SF4302 2.1 27.1 1.0 S4 B:SF4302 2.1 29.5 1.0 S2 B:SF4302 2.1 29.3 1.0 SG B:CYS182 2.3 29.5 1.0 FE4 B:SF4302 3.0 31.9 1.0 CB B:CYS182 3.0 31.7 1.0 FE2 B:SF4302 3.0 31.8 1.0 FE1 B:SF4302 3.1 33.4 1.0 CA B:CYS182 3.5 32.7 1.0 S3 B:SF4302 3.7 31.5 1.0 N B:ILE183 3.9 30.7 1.0 C B:CYS182 4.1 32.3 1.0 N B:LEU184 4.1 28.9 1.0 CE B:MET209 4.5 41.9 1.0 CD1 B:LEU253 4.7 39.3 1.0 CA B:LEU184 4.8 27.3 1.0 N B:CYS182 4.8 32.4 1.0 N B:CYS185 4.9 28.6 1.0

Iron binding site 6 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe302 b:31.9 occ:1.00 FE4 B:SF4302 0.0 31.9 1.0 S1 B:SF4302 2.1 27.1 1.0 S2 B:SF4302 2.1 29.3 1.0 S3 B:SF4302 2.1 31.5 1.0 SG B:CYS249 2.4 32.2 1.0 FE2 B:SF4302 3.0 31.8 1.0 FE3 B:SF4302 3.0 30.0 1.0 FE1 B:SF4302 3.1 33.4 1.0 CB B:CYS249 3.2 32.6 1.0 S4 B:SF4302 3.6 29.5 1.0 CA B:CYS249 3.9 33.5 1.0 CD B:PRO250 3.9 37.5 1.0 C B:CYS249 4.4 34.1 1.0 N B:PRO250 4.5 36.4 1.0 CB B:LEU253 4.6 37.4 1.0 N B:LYS251 4.6 36.6 1.0 CD1 B:LEU253 4.6 39.3 1.0 CB B:LYS251 4.6 37.2 1.0 CG B:LEU253 4.7 37.5 1.0 CG B:LYS251 4.8 37.7 1.0

Iron binding site 7 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:46.2 occ:1.00 FE1 B:F3S303 0.0 46.2 1.0 S2 B:F3S303 2.2 46.5 1.0 S1 B:F3S303 2.2 46.7 1.0 S3 B:F3S303 2.2 36.3 1.0 SG B:CYS239 2.3 41.5 1.0 FE3 B:F3S303 2.8 39.6 1.0 FE4 B:F3S303 2.9 40.8 1.0 CB B:CYS239 3.6 43.4 1.0 N B:THR241 3.6 38.7 1.0 N B:ILE242 3.9 45.5 1.0 CA B:THR241 3.9 38.9 1.0 CA B:CYS239 4.0 42.1 1.0 S4 B:F3S303 4.0 40.9 1.0 N B:HIS240 4.0 41.0 1.0 OH B:TYR202 4.1 44.7 1.0 C B:CYS239 4.1 43.4 1.0 C B:THR241 4.4 42.7 1.0 C B:HIS240 4.5 39.9 1.0 N B:MET243 4.5 49.2 1.0 CD1 B:ILE259 4.7 41.6 1.0 SG B:CYS192 4.8 37.5 1.0 SG B:CYS245 4.8 35.4 1.0 CA B:HIS240 4.9 40.4 1.0 O B:CYS239 4.9 46.2 1.0 CA B:ILE242 4.9 47.0 1.0 CB B:ILE242 5.0 48.5 1.0

Iron binding site 8 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:39.6 occ:1.00 FE3 B:F3S303 0.0 39.6 1.0 S3 B:F3S303 2.2 36.3 1.0 S1 B:F3S303 2.2 46.7 1.0 S4 B:F3S303 2.2 40.9 1.0 SG B:CYS245 2.3 35.4 1.0 FE4 B:F3S303 2.8 40.8 1.0 FE1 B:F3S303 2.8 46.2 1.0 CB B:CYS245 3.4 35.7 1.0 N B:CYS245 3.7 35.3 1.0 N B:MET243 3.8 49.2 1.0 S2 B:F3S303 3.9 46.5 1.0 N B:ASN244 4.0 45.1 1.0 CA B:MET243 4.0 49.6 1.0 CA B:CYS245 4.2 36.8 1.0 C B:MET243 4.3 48.2 1.0 CB B:ALA256 4.6 40.2 1.0 SG B:CYS239 4.8 41.5 1.0 C B:ASN244 4.8 40.9 1.0 N B:ILE242 4.8 45.5 1.0 C B:ILE242 4.8 47.0 1.0 CB B:CYS192 4.9 38.0 1.0 CB B:PRO205 4.9 30.1 1.0 CG B:PRO205 4.9 30.1 1.0 CA B:ASN244 4.9 44.2 1.0 SG B:CYS192 4.9 37.5 1.0 CA B:ALA256 4.9 40.8 1.0

Iron binding site 9 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Fe303 b:40.8 occ:1.00 FE4 B:F3S303 0.0 40.8 1.0 S3 B:F3S303 2.2 36.3 1.0 S4 B:F3S303 2.2 40.9 1.0 S2 B:F3S303 2.2 46.5 1.0 SG B:CYS192 2.3 37.5 1.0 FE3 B:F3S303 2.8 39.6 1.0 FE1 B:F3S303 2.9 46.2 1.0 CB B:CYS192 2.9 38.0 1.0 CA B:CYS192 3.7 36.9 1.0 S1 B:F3S303 4.1 46.7 1.0 OH B:TYR202 4.3 44.7 1.0 C B:CYS192 4.4 36.6 1.0 CD1 B:ILE242 4.4 48.4 1.0 CB B:ILE242 4.5 48.5 1.0 N B:PRO193 4.8 37.1 1.0 CB B:SER194 4.8 37.7 1.0 CE2 B:TYR202 4.8 38.8 1.0 SG B:CYS245 4.8 35.4 1.0 CG1 B:ILE242 4.9 48.6 1.0 N B:CYS192 4.9 34.4 1.0 CD B:PRO193 4.9 38.5 1.0 N B:ILE242 4.9 45.5 1.0 CG B:PRO205 4.9 30.1 1.0 CD B:PRO205 4.9 29.4 1.0 SG B:CYS239 4.9 41.5 1.0 N B:MET243 5.0 49.2 1.0

Iron binding site 10 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with Ubiquinone-1


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 Ubiquinone-1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Fe201 b:57.8 occ:1.00 FE C:HEM201 0.0 57.8 1.0 ND C:HEM201 1.9 63.7 1.0 NA C:HEM201 2.0 65.9 1.0 NC C:HEM201 2.1 68.9 1.0 NB C:HEM201 2.1 66.4 1.0 NE2 C:HIS131 2.1 39.7 1.0 NE2 D:HIS95 2.3 50.7 1.0 C4D C:HEM201 2.9 66.1 1.0 C1D C:HEM201 2.9 66.5 1.0 CD2 C:HIS131 3.0 41.0 1.0 C1A C:HEM201 3.0 63.0 1.0 C4A C:HEM201 3.1 63.5 1.0 C4C C:HEM201 3.1 69.1 1.0 C1B C:HEM201 3.1 68.8 1.0 C1C C:HEM201 3.1 70.6 1.0 C4B C:HEM201 3.1 70.2 1.0 CE1 C:HIS131 3.1 41.6 1.0 CD2 D:HIS95 3.1 51.8 1.0 CHA C:HEM201 3.3 66.4 1.0 CE1 D:HIS95 3.4 53.9 1.0 CHD C:HEM201 3.4 70.4 1.0 CHC C:HEM201 3.5 72.0 1.0 CHB C:HEM201 3.5 65.7 1.0 C3D C:HEM201 4.1 64.9 1.0 CG C:HIS131 4.1 43.7 1.0 C2D C:HEM201 4.2 64.7 1.0 ND1 C:HIS131 4.2 42.8 1.0 C2A C:HEM201 4.2 58.5 1.0 C3A C:HEM201 4.2 60.9 1.0 C2C C:HEM201 4.3 68.6 1.0 C3C C:HEM201 4.3 68.3 1.0 C2B C:HEM201 4.3 74.5 1.0 CG D:HIS95 4.4 51.4 1.0 C3B C:HEM201 4.4 75.9 1.0 ND1 D:HIS95 4.4 53.6 1.0 NE2 C:HIS75 4.8 43.0 1.0 CE1 C:HIS75 5.0 44.0 1.0

S.Harada, T.Shiba, D.Sato, A.Yamamoto, M.Nagahama, A.Yone, D.K.Inaoka, K.Sakamoto, M.Inoue, T.Honma, K.Kita. Structural Insights Into the Molecular Design of Flutolanil Derivatives Targeted For Fumarate Respiration of Parasite Mitochondria To Be Published.