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Iron in PDB 4ysx: Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23

Enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23

All present enzymatic activity of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23, PDB code: 4ysx 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 / 2.25
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 124.200, 127.909, 220.546, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 22.1

Other elements in 4ysx:

The structure of Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23 also contains other interesting chemical elements:

Fluorine (F) 6 atoms

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 the Specific Inhibitor NN23 (pdb code 4ysx). 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 the Specific Inhibitor NN23, PDB code: 4ysx:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 4ysx

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Iron binding site 1 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:33.1
occ:1.00
 FE1 B:FES301 0.0 33.1 1.0
SG B:CYS97 2.2 34.3 1.0
S1 B:FES301 2.2 33.8 1.0
S2 B:FES301 2.2 34.8 1.0
SG B:CYS109 2.4 37.3 1.0
FE2 B:FES301 2.6 34.1 1.0
CB B:CYS109 3.2 37.2 1.0
CB B:CYS97 3.2 32.0 1.0
N B:CYS97 4.0 34.0 1.0
N B:CYS109 4.1 37.3 1.0
CA B:CYS97 4.1 34.4 1.0
SG B:CYS89 4.1 37.0 1.0
CA B:CYS109 4.2 37.0 1.0
O B:CYS89 4.4 45.8 1.0
CB B:LEU107 4.4 32.4 1.0
SG B:CYS94 4.6 34.9 1.0
CA B:GLY92 4.6 35.2 1.0
N B:GLY92 4.7 35.2 1.0
CD2 B:LEU107 4.8 32.1 1.0
C B:CYS97 4.9 33.5 1.0
N B:SER96 4.9 32.8 1.0

Iron binding site 2 out of 20 in 4ysx

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Iron binding site 2 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:34.1
occ:1.00
 FE2 B:FES301 0.0 34.1 1.0
S2 B:FES301 2.2 34.8 1.0
S1 B:FES301 2.2 33.8 1.0
SG B:CYS89 2.2 37.0 1.0
SG B:CYS94 2.3 34.9 1.0
FE1 B:FES301 2.6 33.1 1.0
CB B:CYS94 3.2 34.3 1.0
CB B:CYS89 3.5 39.1 1.0
N B:CYS94 3.6 29.9 1.0
N B:GLY95 3.6 31.7 1.0
N B:CYS89 3.6 37.0 1.0
O B:CYS89 3.7 45.8 1.0
CA B:CYS94 3.7 33.1 1.0
CA B:CYS89 3.9 41.6 1.0
N B:SER96 4.0 32.8 1.0
C B:CYS89 4.1 43.1 1.0
SG B:CYS109 4.1 37.3 1.0
C B:CYS94 4.1 31.3 1.0
N B:ILE93 4.5 33.7 1.0
CA B:GLY95 4.6 33.4 1.0
SG B:CYS97 4.6 34.3 1.0
CB B:SER96 4.6 36.9 1.0
N B:SER88 4.6 32.2 1.0
N B:CYS97 4.6 34.0 1.0
CA B:GLY92 4.6 35.2 1.0
N B:GLY92 4.6 35.2 1.0
C B:SER88 4.7 35.1 1.0
C B:GLY95 4.7 35.3 1.0
C B:ILE93 4.7 34.1 1.0
CA B:SER96 4.8 35.4 1.0
C B:GLY92 4.9 34.6 1.0
CB B:CYS97 5.0 32.0 1.0

Iron binding site 3 out of 20 in 4ysx

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Iron binding site 3 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:34.9
occ:1.00
 FE1 B:SF4302 0.0 34.9 1.0
S3 B:SF4302 2.1 37.0 1.0
S4 B:SF4302 2.1 35.8 1.0
S2 B:SF4302 2.1 36.9 1.0
SG B:CYS185 2.2 35.2 1.0
FE2 B:SF4302 2.9 36.2 1.0
FE4 B:SF4302 3.0 36.3 1.0
FE3 B:SF4302 3.0 35.3 1.0
CB B:CYS185 3.5 32.4 1.0
S1 B:SF4302 3.7 35.4 1.0
N B:CYS185 3.7 33.6 1.0
N B:ALA186 3.8 31.7 1.0
CA B:CYS185 4.0 33.9 1.0
N B:CYS187 4.2 33.6 1.0
C B:CYS185 4.3 35.3 1.0
CG1 B:ILE183 4.5 31.1 1.0
CD B:PRO250 4.5 39.6 1.0
CB B:CYS187 4.7 32.7 1.0
N B:LEU184 4.7 30.2 1.0
CG B:PRO250 4.7 37.5 1.0
CA B:ALA186 4.8 32.6 1.0
SG B:CYS182 4.8 35.8 1.0
C B:LEU184 4.8 32.8 1.0
N B:CYS188 4.8 34.3 1.0
SG B:CYS249 4.9 36.3 1.0
SG B:CYS188 4.9 33.1 1.0
C B:ALA186 5.0 32.4 1.0
CA B:CYS187 5.0 32.4 1.0

Iron binding site 4 out of 20 in 4ysx

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Iron binding site 4 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:36.2
occ:1.00
 FE2 B:SF4302 0.0 36.2 1.0
S4 B:SF4302 2.1 35.8 1.0
S1 B:SF4302 2.1 35.4 1.0
S3 B:SF4302 2.1 37.0 1.0
SG B:CYS188 2.3 33.1 1.0
FE1 B:SF4302 2.9 34.9 1.0
FE3 B:SF4302 2.9 35.3 1.0
FE4 B:SF4302 3.0 36.3 1.0
CB B:CYS188 3.1 32.8 1.0
S2 B:SF4302 3.6 36.9 1.0
N B:CYS188 3.8 34.3 1.0
CA B:CYS188 4.1 33.5 1.0
CB B:ALA206 4.1 33.8 1.0
CA B:ALA206 4.4 34.8 1.0
N B:CYS187 4.7 33.6 1.0
CG B:PRO255 4.7 40.2 1.0
SG B:CYS182 4.7 35.8 1.0
N B:ALA186 4.8 31.7 1.0
SG B:CYS185 4.8 35.2 1.0
N B:ALA206 4.8 34.5 1.0
SG B:CYS249 4.9 36.3 1.0
N B:SER189 5.0 34.8 1.0
C B:CYS187 5.0 33.1 1.0
CA B:ALA186 5.0 32.6 1.0

Iron binding site 5 out of 20 in 4ysx

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Iron binding site 5 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:35.3
occ:1.00
 FE3 B:SF4302 0.0 35.3 1.0
S1 B:SF4302 2.1 35.4 1.0
S4 B:SF4302 2.1 35.8 1.0
S2 B:SF4302 2.2 36.9 1.0
SG B:CYS182 2.2 35.8 1.0
FE2 B:SF4302 2.9 36.2 1.0
FE4 B:SF4302 3.0 36.3 1.0
FE1 B:SF4302 3.0 34.9 1.0
CB B:CYS182 3.1 34.9 1.0
CA B:CYS182 3.6 35.0 1.0
S3 B:SF4302 3.7 37.0 1.0
N B:ILE183 3.9 30.8 1.0
O B:HOH450 4.0 35.4 1.0
N B:LEU184 4.1 30.2 1.0
C B:CYS182 4.2 31.9 1.0
CD1 B:LEU253 4.5 39.8 1.0
CE B:MET209 4.8 36.7 1.0
CA B:LEU184 4.8 31.8 1.0
N B:CYS182 4.9 37.3 1.0
N B:CYS185 4.9 33.6 1.0
SG B:CYS188 5.0 33.1 1.0

Iron binding site 6 out of 20 in 4ysx

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Iron binding site 6 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:36.3
occ:1.00
 FE4 B:SF4302 0.0 36.3 1.0
S2 B:SF4302 2.1 36.9 1.0
S1 B:SF4302 2.1 35.4 1.0
S3 B:SF4302 2.2 37.0 1.0
SG B:CYS249 2.2 36.3 1.0
FE3 B:SF4302 3.0 35.3 1.0
FE1 B:SF4302 3.0 34.9 1.0
FE2 B:SF4302 3.0 36.2 1.0
CB B:CYS249 3.3 37.1 1.0
S4 B:SF4302 3.7 35.8 1.0
CA B:CYS249 4.0 37.4 1.0
CD1 B:LEU253 4.3 39.8 1.0
CD B:PRO250 4.3 39.6 1.0
CB B:LEU253 4.4 39.7 1.0
C B:CYS249 4.5 39.2 1.0
CG B:LEU253 4.5 40.6 1.0
CB B:LYS251 4.6 39.6 1.0
N B:PRO250 4.6 38.4 1.0
N B:LYS251 4.6 38.0 1.0
CG B:LYS251 4.8 42.4 1.0
SG B:CYS185 4.9 35.2 1.0

Iron binding site 7 out of 20 in 4ysx

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Iron binding site 7 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:37.2
occ:1.00
 FE1 B:F3S303 0.0 37.2 1.0
S3 B:F3S303 2.1 38.7 1.0
S2 B:F3S303 2.2 36.4 1.0
S1 B:F3S303 2.2 38.5 1.0
SG B:CYS239 2.3 41.7 1.0
FE4 B:F3S303 2.8 35.6 1.0
FE3 B:F3S303 2.9 36.0 1.0
CB B:CYS239 3.4 40.2 1.0
CA B:CYS239 3.7 38.7 1.0
N B:THR241 3.8 34.1 1.0
OH B:TYR202 3.8 33.1 1.0
S4 B:F3S303 4.0 36.6 1.0
N B:HIS240 4.0 38.9 1.0
N B:ILE242 4.1 36.7 1.0
C B:CYS239 4.1 40.0 1.0
CA B:THR241 4.2 35.5 1.0
CD1 B:ILE259 4.4 37.7 1.0
C B:THR241 4.7 34.7 1.0
C B:HIS240 4.7 35.5 1.0
SG B:CYS192 4.8 38.7 1.0
N B:MET243 4.8 35.4 1.0
SG B:CYS245 4.8 35.2 1.0
CA B:HIS240 5.0 38.3 1.0
CZ B:TYR202 5.0 34.8 1.0

Iron binding site 8 out of 20 in 4ysx

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Iron binding site 8 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:36.0
occ:1.00
 FE3 B:F3S303 0.0 36.0 1.0
S3 B:F3S303 2.2 38.7 1.0
S4 B:F3S303 2.2 36.6 1.0
S1 B:F3S303 2.2 38.5 1.0
SG B:CYS245 2.2 35.2 1.0
FE4 B:F3S303 2.8 35.6 1.0
FE1 B:F3S303 2.9 37.2 1.0
CB B:CYS245 3.2 40.5 1.0
N B:CYS245 3.7 37.1 1.0
N B:MET243 3.9 35.4 1.0
S2 B:F3S303 4.0 36.4 1.0
CA B:CYS245 4.1 37.7 1.0
CA B:MET243 4.2 38.8 1.0
N B:ASN244 4.3 36.8 1.0
C B:MET243 4.4 38.0 1.0
CG B:PRO205 4.6 33.0 1.0
CB B:PRO205 4.7 32.4 1.0
CB B:ALA256 4.8 41.1 1.0
SG B:CYS192 4.8 38.7 1.0
C B:ASN244 4.9 36.6 1.0
CD1 B:ILE259 4.9 37.7 1.0
CA B:ALA256 4.9 39.3 1.0
N B:ILE242 4.9 36.7 1.0
SG B:CYS239 4.9 41.7 1.0
C B:ILE242 4.9 34.8 1.0
N B:THR246 5.0 40.2 1.0

Iron binding site 9 out of 20 in 4ysx

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Iron binding site 9 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:35.6
occ:1.00
 FE4 B:F3S303 0.0 35.6 1.0
S3 B:F3S303 2.1 38.7 1.0
S4 B:F3S303 2.2 36.6 1.0
S2 B:F3S303 2.2 36.4 1.0
SG B:CYS192 2.3 38.7 1.0
FE1 B:F3S303 2.8 37.2 1.0
FE3 B:F3S303 2.8 36.0 1.0
CB B:CYS192 3.2 33.5 1.0
S1 B:F3S303 3.9 38.5 1.0
CA B:CYS192 4.0 33.2 1.0
OH B:TYR202 4.2 33.1 1.0
CB B:ILE242 4.4 35.8 1.0
CD1 B:ILE242 4.6 39.1 1.0
C B:CYS192 4.7 34.6 1.0
CE2 B:TYR202 4.7 32.9 1.0
CD B:PRO205 4.8 31.2 1.0
CG1 B:ILE242 4.8 37.2 1.0
SG B:CYS245 4.9 35.2 1.0
CG B:PRO205 4.9 33.0 1.0
N B:ILE242 4.9 36.7 1.0
CD B:PRO193 5.0 32.5 1.0
CB B:SER194 5.0 33.9 1.0
CZ B:TYR202 5.0 34.8 1.0
SG B:CYS239 5.0 41.7 1.0
N B:MET243 5.0 35.4 1.0

Iron binding site 10 out of 20 in 4ysx

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Iron binding site 10 out of 20 in the Crystal Structure of Mitochondrial Rhodoquinol-Fumarate Reductase From Ascaris Suum with the Specific Inhibitor NN23


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 the Specific Inhibitor NN23 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:43.0
occ:1.00
 FE C:HEM201 0.0 43.0 1.0
ND C:HEM201 1.9 45.0 1.0
NA C:HEM201 2.0 46.0 1.0
NC C:HEM201 2.1 44.9 1.0
NE2 D:HIS95 2.1 39.1 1.0
NB C:HEM201 2.1 45.9 1.0
NE2 C:HIS131 2.2 44.0 1.0
C1D C:HEM201 2.9 43.2 1.0
C4D C:HEM201 2.9 43.9 1.0
C1A C:HEM201 3.0 46.4 1.0
C4A C:HEM201 3.0 49.1 1.0
CE1 D:HIS95 3.0 38.5 1.0
C1C C:HEM201 3.0 45.0 1.0
C4B C:HEM201 3.1 44.5 1.0
C1B C:HEM201 3.1 48.8 1.0
CD2 D:HIS95 3.1 39.9 1.0
CD2 C:HIS131 3.1 42.5 1.0
C4C C:HEM201 3.1 47.1 1.0
CE1 C:HIS131 3.2 43.8 1.0
CHA C:HEM201 3.4 45.3 1.0
CHD C:HEM201 3.4 46.4 1.0
CHC C:HEM201 3.4 45.1 1.0
CHB C:HEM201 3.4 51.1 1.0
ND1 D:HIS95 4.2 38.0 1.0
C2D C:HEM201 4.2 43.7 1.0
C3D C:HEM201 4.2 48.4 1.0
CG D:HIS95 4.2 39.6 1.0
C3A C:HEM201 4.2 48.0 1.0
C2A C:HEM201 4.2 48.4 1.0
C2C C:HEM201 4.2 45.5 1.0
ND1 C:HIS131 4.2 42.9 1.0
CG C:HIS131 4.2 41.3 1.0
C3C C:HEM201 4.3 46.6 1.0
C2B C:HEM201 4.3 47.1 1.0
C3B C:HEM201 4.3 49.0 1.0
NE2 C:HIS75 4.9 40.1 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 16:40:02 2024

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