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Iron in PDB 4yt0: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.

Enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide., PDB code: 4yt0 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 / 3.66
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 122.803, 123.392, 219.001, 90.00, 90.00, 90.00
R / Rfree (%) 19.3 / 26.2

Iron Binding Sites:

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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. (pdb code 4yt0). 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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide., PDB code: 4yt0:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 4yt0

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Iron binding site 1 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:22.2
occ:1.00
 FE1 B:FES301 0.0 22.2 1.0
SG B:CYS109 2.2 50.7 1.0
S1 B:FES301 2.2 22.6 1.0
S2 B:FES301 2.2 23.2 1.0
SG B:CYS97 2.5 36.1 1.0
FE2 B:FES301 2.8 23.2 1.0
CB B:CYS109 3.0 48.3 1.0
CB B:CYS97 3.4 37.8 1.0
N B:CYS109 3.9 44.7 1.0
SG B:CYS89 4.0 49.4 1.0
CA B:CYS109 4.1 46.9 1.0
CA B:GLY92 4.3 38.6 1.0
CB B:LEU107 4.3 47.3 1.0
O B:CYS89 4.3 45.3 1.0
N B:CYS97 4.3 38.4 1.0
CA B:CYS97 4.4 38.7 1.0
CD1 B:LEU69 4.5 41.6 1.0
N B:GLY92 4.5 39.0 1.0
SG B:CYS94 4.7 48.8 1.0
CD1 B:LEU107 4.8 45.3 1.0
N B:ALA108 4.8 44.5 1.0
CG B:LEU107 4.9 46.1 1.0
CD2 B:LEU107 4.9 46.0 1.0

Iron binding site 2 out of 20 in 4yt0

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Iron binding site 2 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:23.2
occ:1.00
 FE2 B:FES301 0.0 23.2 1.0
SG B:CYS89 2.0 49.4 1.0
S1 B:FES301 2.2 22.6 1.0
S2 B:FES301 2.2 23.2 1.0
SG B:CYS94 2.3 48.8 1.0
FE1 B:FES301 2.8 22.2 1.0
CB B:CYS89 3.3 47.8 1.0
CB B:CYS94 3.4 46.7 1.0
O B:CYS89 3.5 45.3 1.0
N B:CYS89 3.6 44.8 1.0
N B:CYS94 3.7 45.5 1.0
CA B:CYS89 3.7 46.3 1.0
N B:GLY95 3.8 45.2 1.0
C B:CYS89 3.8 46.2 1.0
CA B:CYS94 4.0 46.3 1.0
SG B:CYS109 4.2 50.7 1.0
N B:ILE93 4.3 39.1 1.0
N B:SER96 4.3 41.0 1.0
CA B:GLY92 4.4 38.6 1.0
N B:GLY92 4.4 39.0 1.0
C B:CYS94 4.5 46.1 1.0
OG B:SER96 4.5 37.5 1.0
N B:SER88 4.6 41.4 1.0
N B:CYS97 4.7 38.4 1.0
C B:SER88 4.7 43.6 1.0
CB B:SER96 4.7 38.7 1.0
C B:GLY92 4.7 38.3 1.0
SG B:CYS97 4.8 36.1 1.0
CA B:GLY95 4.8 43.8 1.0
N B:ARG90 4.8 46.6 1.0
C B:ILE93 4.9 43.6 1.0
C B:GLY95 5.0 42.5 1.0

Iron binding site 3 out of 20 in 4yt0

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Iron binding site 3 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:28.7
occ:1.00
 FE1 B:SF4302 0.0 28.7 1.0
S4 B:SF4302 2.1 27.9 1.0
S2 B:SF4302 2.1 27.2 1.0
S3 B:SF4302 2.1 27.1 1.0
SG B:CYS185 2.3 34.2 1.0
FE2 B:SF4302 3.1 27.4 1.0
FE3 B:SF4302 3.1 27.8 1.0
FE4 B:SF4302 3.1 26.7 1.0
CB B:CYS185 3.2 35.0 1.0
N B:CYS185 3.6 36.0 1.0
S1 B:SF4302 3.7 26.9 1.0
N B:ALA186 3.7 33.4 1.0
CA B:CYS185 3.9 35.3 1.0
N B:CYS187 4.0 33.7 1.0
C B:CYS185 4.3 34.7 1.0
CD B:PRO250 4.3 45.0 1.0
CG1 B:ILE183 4.4 44.8 1.0
CB B:CYS187 4.5 36.1 1.0
CG B:PRO250 4.5 44.7 1.0
CA B:ALA186 4.6 32.3 1.0
SG B:CYS249 4.7 41.5 1.0
N B:LEU184 4.7 39.8 1.0
C B:LEU184 4.7 37.2 1.0
SG B:CYS182 4.7 53.6 1.0
CA B:CYS187 4.8 35.7 1.0
C B:ALA186 4.9 32.3 1.0
N B:CYS188 4.9 37.6 1.0
N B:ILE183 4.9 44.1 1.0
CA B:LEU184 5.0 38.8 1.0
CD1 B:ILE183 5.0 45.4 1.0

Iron binding site 4 out of 20 in 4yt0

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Iron binding site 4 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:27.4
occ:1.00
 FE2 B:SF4302 0.0 27.4 1.0
S3 B:SF4302 2.1 27.1 1.0
S1 B:SF4302 2.1 26.9 1.0
S4 B:SF4302 2.1 27.9 1.0
SG B:CYS188 2.4 40.9 1.0
CB B:CYS188 3.0 39.0 1.0
FE1 B:SF4302 3.1 28.7 1.0
FE4 B:SF4302 3.1 26.7 1.0
FE3 B:SF4302 3.1 27.8 1.0
CB B:ALA206 3.6 34.0 1.0
S2 B:SF4302 3.7 27.2 1.0
N B:CYS188 3.8 37.6 1.0
CA B:CYS188 4.0 37.7 1.0
CA B:ALA206 4.2 33.9 1.0
SG B:CYS182 4.3 53.6 1.0
N B:CYS187 4.6 33.7 1.0
SG B:CYS185 4.6 34.2 1.0
N B:ALA206 4.6 35.1 1.0
N B:ALA186 4.7 33.4 1.0
SG B:CYS249 4.8 41.5 1.0
CA B:ALA186 4.8 32.3 1.0
N B:SER189 4.9 35.8 1.0
CG B:PRO255 4.9 48.5 1.0
C B:CYS187 4.9 37.0 1.0
C B:CYS188 4.9 36.2 1.0
C B:ALA186 5.0 32.3 1.0

Iron binding site 5 out of 20 in 4yt0

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Iron binding site 5 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:27.8
occ:1.00
 FE3 B:SF4302 0.0 27.8 1.0
SG B:CYS182 1.9 53.6 1.0
S2 B:SF4302 2.1 27.2 1.0
S4 B:SF4302 2.1 27.9 1.0
S1 B:SF4302 2.1 26.9 1.0
CB B:CYS182 2.9 50.4 1.0
FE1 B:SF4302 3.1 28.7 1.0
FE2 B:SF4302 3.1 27.4 1.0
FE4 B:SF4302 3.1 26.7 1.0
CA B:CYS182 3.2 48.1 1.0
S3 B:SF4302 3.7 27.1 1.0
N B:ILE183 3.7 44.1 1.0
C B:CYS182 3.8 45.5 1.0
N B:LEU184 4.1 39.8 1.0
CE B:MET209 4.4 40.8 1.0
N B:CYS182 4.5 48.0 1.0
CB B:ALA206 4.6 34.0 1.0
CA B:LEU184 4.7 38.8 1.0
CD1 B:LEU253 4.8 46.0 1.0
O B:CYS182 4.8 44.5 1.0
N B:CYS185 4.9 36.0 1.0
CA B:ILE183 4.9 43.5 1.0

Iron binding site 6 out of 20 in 4yt0

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Iron binding site 6 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:26.7
occ:1.00
 FE4 B:SF4302 0.0 26.7 1.0
SG B:CYS249 2.1 41.5 1.0
S1 B:SF4302 2.1 26.9 1.0
S3 B:SF4302 2.1 27.1 1.0
S2 B:SF4302 2.1 27.2 1.0
FE1 B:SF4302 3.1 28.7 1.0
FE2 B:SF4302 3.1 27.4 1.0
FE3 B:SF4302 3.1 27.8 1.0
CB B:CYS249 3.4 42.7 1.0
S4 B:SF4302 3.7 27.9 1.0
CA B:CYS249 4.2 44.6 1.0
CD B:PRO250 4.2 45.0 1.0
CD1 B:LEU253 4.5 46.0 1.0
CB B:LEU253 4.6 46.6 1.0
N B:LYS251 4.6 47.8 1.0
N B:PRO250 4.7 45.2 1.0
CB B:LYS251 4.7 51.2 1.0
C B:CYS249 4.7 45.2 1.0
CG B:LEU253 4.7 46.0 1.0
SG B:CYS182 4.8 53.6 1.0

Iron binding site 7 out of 20 in 4yt0

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Iron binding site 7 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:40.5
occ:1.00
 FE1 B:F3S303 0.0 40.5 1.0
SG B:CYS239 2.1 53.4 1.0
S3 B:F3S303 2.2 39.6 1.0
S2 B:F3S303 2.2 45.4 1.0
S1 B:F3S303 2.2 46.6 1.0
FE3 B:F3S303 3.0 41.5 1.0
FE4 B:F3S303 3.0 41.2 1.0
CB B:CYS239 3.3 54.8 1.0
OH B:TYR202 3.6 40.0 1.0
CA B:CYS239 3.6 55.4 1.0
N B:THR241 3.8 61.5 1.0
C B:CYS239 3.9 56.4 1.0
CD1 B:ILE259 4.0 47.9 1.0
N B:HIS240 4.1 58.9 1.0
CA B:THR241 4.2 61.2 1.0
N B:ILE242 4.2 61.7 1.0
S4 B:F3S303 4.2 42.9 1.0
O B:CYS239 4.6 54.8 1.0
C B:HIS240 4.7 60.8 1.0
C B:THR241 4.7 60.0 1.0
SG B:CYS192 4.7 36.5 1.0
CZ B:TYR202 4.8 41.5 1.0
N B:CYS239 5.0 54.0 1.0

Iron binding site 8 out of 20 in 4yt0

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Iron binding site 8 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:41.5
occ:1.00
 FE3 B:F3S303 0.0 41.5 1.0
S3 B:F3S303 2.2 39.6 1.0
S4 B:F3S303 2.2 42.9 1.0
S1 B:F3S303 2.2 46.6 1.0
SG B:CYS245 2.4 49.0 1.0
FE4 B:F3S303 2.9 41.2 1.0
FE1 B:F3S303 3.0 40.5 1.0
CB B:CYS245 3.4 50.0 1.0
N B:MET243 3.7 59.8 1.0
N B:CYS245 3.9 52.7 1.0
CA B:MET243 3.9 59.8 1.0
S2 B:F3S303 4.1 45.4 1.0
N B:ASN244 4.2 59.1 1.0
C B:MET243 4.2 59.6 1.0
CA B:CYS245 4.3 50.3 1.0
CB B:ALA256 4.6 48.9 1.0
N B:ILE242 4.6 61.7 1.0
CA B:ALA256 4.8 48.8 1.0
SG B:CYS239 4.8 53.4 1.0
CB B:PRO205 4.8 37.3 1.0
CG B:PRO205 4.8 37.7 1.0
N B:ALA256 4.8 48.5 1.0
C B:ILE242 4.8 60.9 1.0
CD1 B:ILE259 4.9 47.9 1.0
CE B:MET243 4.9 59.4 1.0
C B:ASN244 5.0 55.6 1.0
CB B:CYS192 5.0 38.0 1.0

Iron binding site 9 out of 20 in 4yt0

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Iron binding site 9 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:41.2
occ:1.00
 FE4 B:F3S303 0.0 41.2 1.0
S4 B:F3S303 2.2 42.9 1.0
S3 B:F3S303 2.2 39.6 1.0
S2 B:F3S303 2.2 45.4 1.0
SG B:CYS192 2.5 36.5 1.0
FE3 B:F3S303 2.9 41.5 1.0
FE1 B:F3S303 3.0 40.5 1.0
CB B:CYS192 3.1 38.0 1.0
CA B:CYS192 3.6 38.7 1.0
CD1 B:ILE242 3.9 60.7 1.0
CB B:ILE242 4.0 62.4 1.0
S1 B:F3S303 4.1 46.6 1.0
CG1 B:ILE242 4.3 61.2 1.0
OH B:TYR202 4.3 40.0 1.0
C B:CYS192 4.4 39.8 1.0
CD B:PRO193 4.5 40.5 1.0
N B:ILE242 4.5 61.7 1.0
N B:PRO193 4.6 40.5 1.0
N B:MET243 4.6 59.8 1.0
CA B:ILE242 4.8 62.2 1.0
N B:CYS192 4.8 39.5 1.0
CG2 B:ILE242 4.9 62.8 1.0
CB B:SER194 5.0 39.9 1.0
N B:SER194 5.0 39.2 1.0

Iron binding site 10 out of 20 in 4yt0

Go back to Iron Binding Sites List in 4yt0
Iron binding site 10 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide.


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 2-Methyl-N-[3-(1-Methylethoxy)Phenyl]Benzamide. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:69.7
occ:1.00
 FE C:HEM201 0.0 69.7 1.0
ND C:HEM201 1.9 69.6 1.0
NA C:HEM201 2.0 72.5 1.0
NC C:HEM201 2.1 68.8 1.0
NB C:HEM201 2.1 71.1 1.0
NE2 C:HIS131 2.5 54.0 1.0
NE2 D:HIS95 2.6 63.5 1.0
C4D C:HEM201 2.9 71.6 1.0
C1D C:HEM201 2.9 70.0 1.0
C1A C:HEM201 3.0 72.6 1.0
C4A C:HEM201 3.0 72.9 1.0
C1B C:HEM201 3.1 72.2 1.0
C1C C:HEM201 3.1 69.9 1.0
C4B C:HEM201 3.1 72.2 1.0
C4C C:HEM201 3.1 69.0 1.0
CD2 D:HIS95 3.3 64.0 1.0
CD2 C:HIS131 3.3 54.0 1.0
CHA C:HEM201 3.4 73.0 1.0
CHD C:HEM201 3.4 70.0 1.0
CHB C:HEM201 3.4 73.8 1.0
CHC C:HEM201 3.4 72.0 1.0
CE1 C:HIS131 3.5 54.0 1.0
CE1 D:HIS95 3.7 63.7 1.0
C2D C:HEM201 4.2 70.7 1.0
C3D C:HEM201 4.2 73.8 1.0
C2A C:HEM201 4.2 72.8 1.0
C3A C:HEM201 4.2 72.1 1.0
C2C C:HEM201 4.3 69.4 1.0
C3C C:HEM201 4.3 68.1 1.0
C2B C:HEM201 4.3 71.1 1.0
C3B C:HEM201 4.3 73.0 1.0
CG C:HIS131 4.5 54.4 1.0
ND1 C:HIS131 4.5 54.0 1.0
CG D:HIS95 4.5 64.3 1.0
NE2 C:HIS75 4.5 42.0 1.0
ND1 D:HIS95 4.7 64.5 1.0
CE1 C:HIS75 4.9 42.0 1.0

Reference:

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
Page generated: Mon Aug 5 16:42:47 2024

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