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Iodine in PDB 4ysz: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide

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

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-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-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide, PDB code: 4ysz 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) 29.82 / 3.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 123.934, 126.968, 219.335, 90.00, 90.00, 90.00
R / Rfree (%) 17.9 / 25

Other elements in 4ysz:

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide also contains other interesting chemical elements:

Iron (Fe) 20 atoms

Iodine Binding Sites:

The binding sites of Iodine atom in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide (pdb code 4ysz). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide, PDB code: 4ysz:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in 4ysz

Go back to Iodine Binding Sites List in 4ysz
Iodine binding site 1 out of 2 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I202

b:70.8
occ:1.00
 I C:12J202 0.0 70.8 1.0
C1 C:12J202 2.1 72.1 1.0
O1 C:12J202 2.9 66.3 1.0
C6 C:12J202 3.0 75.2 1.0
C2 C:12J202 3.1 70.1 1.0
C7 C:12J202 3.3 68.8 1.0
CD1 B:TRP197 3.6 43.0 1.0
NE1 B:TRP197 3.8 42.6 1.0
OD1 D:ASP106 3.8 58.2 1.0
NH1 C:ARG76 4.0 49.4 1.0
CA B:SER194 4.0 45.2 1.0
CG D:ASP106 4.1 59.7 1.0
N B:SER194 4.1 42.2 1.0
OH D:TYR107 4.2 54.9 1.0
CB B:SER194 4.2 44.7 1.0
C B:PRO193 4.3 43.0 1.0
OG B:SER194 4.4 47.6 1.0
C5 C:12J202 4.4 75.9 1.0
C3 C:12J202 4.4 71.3 1.0
CB D:ASP106 4.4 60.3 1.0
O B:PRO193 4.4 40.9 1.0
CE2 D:TYR107 4.5 58.8 1.0
N C:12J202 4.5 68.3 1.0
CD1 B:ILE242 4.5 54.8 1.0
OD2 D:ASP106 4.6 57.0 1.0
CD2 B:HIS240 4.7 65.4 1.0
CZ D:TYR107 4.7 57.2 1.0
CZ C:ARG76 4.7 49.1 1.0
CB B:PRO193 4.7 44.5 1.0
CG B:TRP197 4.8 43.2 1.0
NH2 C:ARG76 4.9 48.2 1.0
C4 C:12J202 4.9 74.5 1.0

Iodine binding site 2 out of 2 in 4ysz

Go back to Iodine Binding Sites List in 4ysz
Iodine binding site 2 out of 2 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with 2-Iodo-N-[3-(1-Methylethoxy)Phenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
G:I202

b:70.1
occ:1.00
 I G:12J202 0.0 70.1 1.0
C1 G:12J202 2.1 59.9 1.0
O1 G:12J202 3.0 56.0 1.0
C6 G:12J202 3.1 60.1 1.0
C2 G:12J202 3.1 59.3 1.0
C7 G:12J202 3.3 60.4 1.0
OD2 H:ASP106 3.4 61.3 1.0
CD1 F:TRP197 3.6 47.5 1.0
CG H:ASP106 3.9 62.3 1.0
CA F:SER194 4.0 51.6 1.0
NE1 F:TRP197 4.0 47.3 1.0
CB F:SER194 4.1 52.6 1.0
N F:SER194 4.2 48.5 1.0
OG F:SER194 4.3 55.6 1.0
C5 G:12J202 4.4 57.9 1.0
CB H:ASP106 4.4 60.2 1.0
C3 G:12J202 4.4 56.9 1.0
NH1 G:ARG76 4.5 49.0 1.0
N G:12J202 4.5 60.2 1.0
C F:PRO193 4.5 48.1 1.0
CE2 H:TYR107 4.5 55.0 1.0
OD1 H:ASP106 4.5 64.1 1.0
CD2 F:HIS240 4.5 61.7 1.0
OH H:TYR107 4.5 50.7 1.0
O F:PRO193 4.7 45.6 1.0
CB F:PRO193 4.7 51.0 1.0
CG F:TRP197 4.9 46.6 1.0
CZ G:ARG76 4.9 51.3 1.0
CZ H:TYR107 4.9 53.2 1.0
C4 G:12J202 5.0 57.2 1.0
CD1 F:ILE242 5.0 66.2 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: Sun Aug 11 20:26:20 2024

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