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Iron in PDB 4ytp: Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide

Enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide

All present enzymatic activity of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide:
1.3.5.1;

Protein crystallography data

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide, PDB code: 4ytp 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 / 3.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 71.429, 84.008, 294.817, 90.00, 90.00, 90.00
R / Rfree (%) 20.6 / 26.9

Other elements in 4ytp:

The structure of Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide also contains other interesting chemical elements:

Fluorine (F) 3 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide (pdb code 4ytp). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide, PDB code: 4ytp:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 4ytp

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Iron binding site 1 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:66.4
occ:1.00
 FE1 B:FES301 0.0 66.4 1.0
SG B:CYS85 2.1 61.9 1.0
S2 B:FES301 2.2 58.3 1.0
S1 B:FES301 2.2 58.5 1.0
SG B:CYS73 2.3 54.6 1.0
FE2 B:FES301 2.9 66.7 1.0
CB B:CYS85 3.1 65.7 1.0
CB B:CYS73 3.6 58.4 1.0
N B:CYS85 4.0 69.6 1.0
SG B:CYS65 4.1 72.2 1.0
CB B:LEU83 4.1 71.2 1.0
CA B:CYS85 4.2 66.6 1.0
N B:CYS73 4.2 58.6 1.0
N B:GLY68 4.4 64.9 1.0
CA B:GLY68 4.4 62.1 1.0
CA B:CYS73 4.5 59.3 1.0
CD2 B:LEU83 4.5 70.3 1.0
N B:ARG66 4.6 67.0 1.0
CA B:ARG66 4.7 67.3 1.0
CD2 B:LEU45 4.7 59.5 1.0
CG B:LEU83 4.7 70.9 1.0
CD1 B:LEU83 4.8 71.4 1.0
N B:ALA84 4.9 71.9 1.0
SG B:CYS70 4.9 70.7 1.0
CA B:LEU83 4.9 71.6 1.0
N B:GLU67 5.0 65.5 1.0
N B:SER72 5.0 60.4 1.0

Iron binding site 2 out of 10 in 4ytp

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Iron binding site 2 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe301

b:66.7
occ:1.00
 FE2 B:FES301 0.0 66.7 1.0
SG B:CYS70 2.2 70.7 1.0
S1 B:FES301 2.2 58.5 1.0
S2 B:FES301 2.2 58.3 1.0
SG B:CYS65 2.3 72.2 1.0
FE1 B:FES301 2.9 66.4 1.0
N B:CYS65 3.2 64.9 1.0
CB B:CYS65 3.3 70.0 1.0
CB B:CYS70 3.7 65.2 1.0
CA B:CYS65 3.7 66.8 1.0
N B:ARG66 3.8 67.0 1.0
OG B:SER72 3.8 55.5 1.0
N B:GLY71 4.0 62.8 1.0
N B:SER72 4.1 60.4 1.0
N B:SER64 4.1 57.7 1.0
N B:CYS70 4.1 57.9 1.0
C B:CYS65 4.1 65.7 1.0
C B:SER64 4.1 59.4 1.0
SG B:CYS85 4.2 61.9 1.0
CB B:SER72 4.3 59.1 1.0
CA B:CYS70 4.3 61.9 1.0
CA B:SER64 4.5 57.8 1.0
C B:CYS70 4.5 62.5 1.0
N B:ILE69 4.6 60.6 1.0
N B:GLY68 4.6 64.9 1.0
CA B:ARG66 4.7 67.3 1.0
N B:GLU67 4.7 65.5 1.0
CA B:SER72 4.8 58.9 1.0
N B:CYS73 4.8 58.6 1.0
CB B:SER64 4.8 55.8 1.0
SG B:CYS73 4.8 54.6 1.0
CA B:GLY68 4.9 62.1 1.0
CA B:GLY71 4.9 62.0 1.0

Iron binding site 3 out of 10 in 4ytp

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Iron binding site 3 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:55.6
occ:1.00
 FE1 B:SF4302 0.0 55.6 1.0
SG B:CYS164 2.1 48.6 1.0
S3 B:SF4302 2.1 53.0 1.0
S4 B:SF4302 2.1 50.6 1.0
S2 B:SF4302 2.1 55.5 1.0
FE2 B:SF4302 3.0 56.3 1.0
FE4 B:SF4302 3.1 58.8 1.0
FE3 B:SF4302 3.2 57.6 1.0
CB B:CYS164 3.2 45.2 1.0
S1 B:SF4302 3.7 50.6 1.0
CB B:ALA182 3.9 46.7 1.0
CA B:ALA182 3.9 46.0 1.0
N B:CYS164 4.0 46.5 1.0
CA B:CYS164 4.2 46.4 1.0
N B:ALA182 4.4 44.3 1.0
SG B:CYS158 4.6 49.6 1.0
N B:SER165 4.7 45.0 1.0
CG B:PRO231 4.7 55.9 1.0
N B:ALA162 4.7 43.4 1.0
CA B:ALA162 4.8 44.9 1.0
N B:CYS163 4.9 43.4 1.0
SG B:CYS161 4.9 49.3 1.0
C B:CYS164 5.0 46.3 1.0

Iron binding site 4 out of 10 in 4ytp

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Iron binding site 4 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:56.3
occ:1.00
 FE2 B:SF4302 0.0 56.3 1.0
S4 B:SF4302 2.1 50.6 1.0
S3 B:SF4302 2.1 53.0 1.0
S1 B:SF4302 2.1 50.6 1.0
SG B:CYS158 2.2 49.6 1.0
FE1 B:SF4302 3.0 55.6 1.0
FE3 B:SF4302 3.1 57.6 1.0
FE4 B:SF4302 3.1 58.8 1.0
CB B:CYS158 3.2 49.5 1.0
CA B:CYS158 3.5 47.9 1.0
S2 B:SF4302 3.6 55.5 1.0
N B:ILE159 3.6 46.8 1.0
C B:CYS158 3.8 48.2 1.0
N B:LEU160 3.8 43.5 1.0
CD1 B:LEU229 4.2 56.5 1.0
CA B:LEU160 4.5 43.6 1.0
CA B:ILE159 4.6 45.8 1.0
O B:CYS158 4.6 53.7 1.0
N B:CYS161 4.7 47.1 1.0
C B:ILE159 4.7 45.0 1.0
N B:CYS158 4.9 45.7 1.0
CB B:ILE159 5.0 47.8 1.0
CA B:ALA182 5.0 46.0 1.0

Iron binding site 5 out of 10 in 4ytp

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Iron binding site 5 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:57.6
occ:1.00
 FE3 B:SF4302 0.0 57.6 1.0
S1 B:SF4302 2.1 50.6 1.0
S2 B:SF4302 2.1 55.5 1.0
S4 B:SF4302 2.1 50.6 1.0
SG B:CYS161 2.3 49.3 1.0
FE2 B:SF4302 3.1 56.3 1.0
FE4 B:SF4302 3.1 58.8 1.0
FE1 B:SF4302 3.2 55.6 1.0
CB B:CYS161 3.2 48.2 1.0
N B:CYS161 3.4 47.1 1.0
N B:ALA162 3.5 43.4 1.0
CD B:PRO226 3.6 72.4 1.0
CA B:CYS161 3.7 47.9 1.0
S3 B:SF4302 3.7 53.0 1.0
C B:CYS161 4.0 45.6 1.0
N B:CYS163 4.2 43.4 1.0
CG B:PRO226 4.2 73.3 1.0
C B:LEU160 4.5 45.5 1.0
N B:LEU160 4.5 43.5 1.0
CA B:ALA162 4.5 44.9 1.0
CB B:ILE159 4.7 47.8 1.0
CA B:LEU160 4.8 43.6 1.0
CB B:CYS163 4.8 43.3 1.0
N B:CYS164 4.8 46.5 1.0
SG B:CYS164 4.8 48.6 1.0
C B:ALA162 4.8 45.2 1.0
SG B:CYS225 4.9 69.6 1.0
N B:ILE159 4.9 46.8 1.0
N B:PRO226 5.0 71.2 1.0
SG B:CYS158 5.0 49.6 1.0

Iron binding site 6 out of 10 in 4ytp

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Iron binding site 6 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:58.8
occ:1.00
 FE4 B:SF4302 0.0 58.8 1.0
S2 B:SF4302 2.1 55.5 1.0
S1 B:SF4302 2.1 50.6 1.0
S3 B:SF4302 2.1 53.0 1.0
SG B:CYS225 2.5 69.6 1.0
FE1 B:SF4302 3.1 55.6 1.0
FE2 B:SF4302 3.1 56.3 1.0
FE3 B:SF4302 3.1 57.6 1.0
CB B:CYS225 3.2 68.0 1.0
S4 B:SF4302 3.7 50.6 1.0
CB B:LEU229 3.9 55.7 1.0
CD1 B:LEU229 3.9 56.5 1.0
CD B:PRO226 4.0 72.4 1.0
CA B:CYS225 4.0 67.4 1.0
CG B:LEU229 4.2 55.1 1.0
N B:PRO226 4.5 71.2 1.0
C B:CYS225 4.6 68.4 1.0
N B:LYS227 4.8 63.4 1.0
SG B:CYS164 4.8 48.6 1.0
CG B:LYS227 4.9 68.8 1.0
CB B:LYS227 4.9 65.5 1.0
CG B:PRO231 5.0 55.9 1.0
CB B:CYS164 5.0 45.2 1.0
CA B:LEU229 5.0 54.3 1.0
N B:LEU229 5.0 55.3 1.0

Iron binding site 7 out of 10 in 4ytp

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Iron binding site 7 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:49.9
occ:1.00
 FE1 B:F3S303 0.0 49.9 1.0
S1 B:F3S303 2.2 53.6 1.0
S3 B:F3S303 2.2 42.8 1.0
S2 B:F3S303 2.2 54.8 1.0
SG B:CYS215 2.5 44.6 1.0
FE4 B:F3S303 2.9 50.7 1.0
FE3 B:F3S303 2.9 52.3 1.0
CB B:CYS215 3.5 45.4 1.0
CA B:CYS215 3.6 44.0 1.0
N B:THR217 3.9 45.1 1.0
N B:HIS216 3.9 42.5 1.0
N B:ILE218 4.1 51.3 1.0
S4 B:F3S303 4.1 47.4 1.0
OH B:TYR178 4.2 65.7 1.0
C B:CYS215 4.2 41.2 1.0
CA B:THR217 4.2 46.0 1.0
SG B:CYS168 4.3 56.9 1.0
C B:HIS216 4.7 44.8 1.0
C B:THR217 4.7 48.0 1.0
N B:MET219 4.8 55.4 1.0
N B:CYS215 4.9 43.3 1.0
SG B:CYS221 4.9 49.3 1.0
CA B:HIS216 4.9 44.6 1.0

Iron binding site 8 out of 10 in 4ytp

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Iron binding site 8 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:52.3
occ:1.00
 FE3 B:F3S303 0.0 52.3 1.0
SG B:CYS168 1.8 56.9 1.0
S3 B:F3S303 2.2 42.8 1.0
S1 B:F3S303 2.2 53.6 1.0
S4 B:F3S303 2.2 47.4 1.0
FE4 B:F3S303 2.8 50.7 1.0
FE1 B:F3S303 2.9 49.9 1.0
CB B:CYS168 2.9 52.5 1.0
CA B:CYS168 3.7 51.0 1.0
S2 B:F3S303 4.1 54.8 1.0
CD1 B:ILE218 4.3 49.4 1.0
C B:CYS168 4.4 48.1 1.0
CB B:ILE218 4.4 48.0 1.0
CD B:PRO169 4.6 48.0 1.0
N B:PRO169 4.7 47.9 1.0
CB B:SER170 4.7 53.2 1.0
CG1 B:ILE218 4.8 48.2 1.0
SG B:CYS221 4.8 49.3 1.0
OH B:TYR178 4.8 65.7 1.0
N B:SER170 4.9 53.7 1.0
N B:CYS168 4.9 51.5 1.0
N B:MET219 5.0 55.4 1.0
CB B:CYS221 5.0 51.7 1.0
OG B:SER170 5.0 50.8 1.0

Iron binding site 9 out of 10 in 4ytp

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Iron binding site 9 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:50.7
occ:1.00
 FE4 B:F3S303 0.0 50.7 1.0
S3 B:F3S303 2.2 42.8 1.0
S4 B:F3S303 2.2 47.4 1.0
S2 B:F3S303 2.2 54.8 1.0
SG B:CYS221 2.3 49.3 1.0
FE3 B:F3S303 2.8 52.3 1.0
FE1 B:F3S303 2.9 49.9 1.0
CB B:CYS221 3.3 51.7 1.0
N B:MET219 3.6 55.4 1.0
N B:CYS221 3.7 52.0 1.0
CA B:MET219 3.9 55.1 1.0
S1 B:F3S303 3.9 53.6 1.0
CA B:CYS221 4.2 50.7 1.0
N B:ASN220 4.2 56.7 1.0
C B:MET219 4.3 56.7 1.0
SG B:CYS168 4.5 56.9 1.0
C B:ILE218 4.7 51.7 1.0
N B:ILE218 4.7 51.3 1.0
CA B:GLY232 4.8 51.9 1.0
C B:ASN220 4.9 54.0 1.0
SG B:CYS215 4.9 44.6 1.0
CB B:CYS168 5.0 52.5 1.0

Iron binding site 10 out of 10 in 4ytp

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Iron binding site 10 out of 10 in the Crystal Structure of Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)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 Porcine Heart Mitochondrial Complex II Bound with N-[(4-Tert-Butylphenyl)Methyl]-2-(Trifluoromethyl)Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe301

b:60.8
occ:1.00
 FE C:HEM301 0.0 60.8 1.0
ND C:HEM301 1.9 57.8 1.0
NA C:HEM301 2.0 58.1 1.0
NB C:HEM301 2.1 59.3 1.0
NC C:HEM301 2.1 62.5 1.0
NE2 C:HIS101 2.3 51.3 1.0
NE2 D:HIS79 2.3 49.3 1.0
C1D C:HEM301 2.9 55.3 1.0
C4D C:HEM301 2.9 55.4 1.0
C4A C:HEM301 3.0 61.2 1.0
C4B C:HEM301 3.0 60.2 1.0
C1A C:HEM301 3.0 57.0 1.0
C1B C:HEM301 3.0 62.5 1.0
CD2 C:HIS101 3.0 53.9 1.0
C4C C:HEM301 3.1 61.7 1.0
C1C C:HEM301 3.1 63.4 1.0
CE1 D:HIS79 3.2 50.5 1.0
CD2 D:HIS79 3.3 50.1 1.0
CE1 C:HIS101 3.4 52.8 1.0
CHD C:HEM301 3.4 57.8 1.0
CHA C:HEM301 3.4 56.0 1.0
CHB C:HEM301 3.4 64.6 1.0
CHC C:HEM301 3.4 60.7 1.0
C3D C:HEM301 4.2 53.2 1.0
C2D C:HEM301 4.2 54.2 1.0
C3A C:HEM301 4.2 60.0 1.0
C2A C:HEM301 4.2 59.6 1.0
CG C:HIS101 4.2 55.3 1.0
C2B C:HEM301 4.3 62.5 1.0
C3B C:HEM301 4.3 61.9 1.0
C3C C:HEM301 4.3 63.6 1.0
C2C C:HEM301 4.3 64.1 1.0
ND1 D:HIS79 4.4 52.4 1.0
ND1 C:HIS101 4.4 54.5 1.0
CG D:HIS79 4.4 51.4 1.0
NE2 C:HIS45 4.8 49.7 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 16:51:05 2024

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