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Iron in PDB 1yq4: Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone

Enzymatic activity of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone

All present enzymatic activity of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone:
1.3.5.1;

Protein crystallography data

The structure of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone, PDB code: 1yq4 was solved by L.Huang, G.Sun, D.Cobessi, A.Wang, J.T.Shen, E.Y.Tung, V.E.Anderson, E.A.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.38 / 2.33
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.586, 83.487, 288.590, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.2

Iron Binding Sites:

The binding sites of Iron atom in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone (pdb code 1yq4). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone, PDB code: 1yq4:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 1yq4

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Iron binding site 1 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:37.8
occ:1.00
 FE1 B:FES1002 0.0 37.8 1.0
S2 B:FES1002 2.2 34.9 1.0
S1 B:FES1002 2.2 30.7 1.0
SG B:CYS73 2.2 46.2 1.0
SG B:CYS85 2.3 33.3 1.0
FE2 B:FES1002 2.7 32.6 1.0
CB B:CYS85 3.2 37.9 1.0
CB B:CYS73 3.2 35.7 1.0
N B:CYS73 3.9 35.0 1.0
CA B:CYS73 4.1 40.0 1.0
N B:CYS85 4.2 42.4 1.0
SG B:CYS65 4.2 37.0 1.0
N B:GLY68 4.3 36.2 1.0
CA B:CYS85 4.3 43.2 1.0
CB B:LEU83 4.4 25.1 1.0
N B:ARG66 4.5 38.6 1.0
CA B:GLY68 4.5 27.8 1.0
SG B:CYS70 4.6 34.0 1.0
CD2 B:LEU45 4.7 34.5 1.0
CA B:ARG66 4.8 49.1 1.0
N B:SER72 4.8 36.1 1.0
C B:CYS73 4.9 37.1 1.0
CD1 B:LEU83 5.0 13.6 1.0

Iron binding site 2 out of 10 in 1yq4

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Iron binding site 2 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:32.6
occ:1.00
 FE2 B:FES1002 0.0 32.6 1.0
S2 B:FES1002 2.2 34.9 1.0
SG B:CYS65 2.2 37.0 1.0
S1 B:FES1002 2.3 30.7 1.0
SG B:CYS70 2.3 34.0 1.0
FE1 B:FES1002 2.7 37.8 1.0
CB B:CYS65 3.1 38.5 1.0
CB B:CYS70 3.3 31.1 1.0
N B:CYS65 3.6 38.7 1.0
N B:ARG66 3.7 38.6 1.0
N B:CYS70 3.7 34.0 1.0
CA B:CYS65 3.7 32.7 1.0
N B:GLY71 3.8 33.0 1.0
CA B:CYS70 3.9 23.8 1.0
N B:SER72 4.0 36.1 1.0
C B:CYS65 4.1 29.9 1.0
C B:CYS70 4.2 31.8 1.0
SG B:CYS85 4.2 33.3 1.0
N B:GLY68 4.3 36.2 1.0
N B:ILE69 4.3 38.2 1.0
CB B:SER72 4.5 26.0 1.0
N B:SER64 4.6 38.0 1.0
C B:SER64 4.6 39.4 1.0
CA B:GLY68 4.6 27.8 1.0
N B:GLU67 4.7 43.4 1.0
OG B:SER72 4.7 40.4 1.0
CA B:ARG66 4.7 49.1 1.0
CA B:GLY71 4.7 35.2 1.0
N B:CYS73 4.7 35.0 1.0
C B:GLY71 4.8 34.3 1.0
SG B:CYS73 4.8 46.2 1.0
CA B:SER72 4.8 35.1 1.0
C B:ILE69 4.8 35.0 1.0
C B:GLY68 4.9 33.2 1.0

Iron binding site 3 out of 10 in 1yq4

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Iron binding site 3 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:38.7
occ:1.00
 FE1 B:SF41003 0.0 38.7 1.0
S3 B:SF41003 2.1 38.0 1.0
S4 B:SF41003 2.1 32.7 1.0
S2 B:SF41003 2.1 34.7 1.0
SG B:CYS164 2.3 39.2 1.0
FE2 B:SF41003 2.6 38.5 1.0
FE3 B:SF41003 2.7 34.6 1.0
FE4 B:SF41003 3.0 34.9 1.0
CB B:CYS164 3.2 20.9 1.0
S1 B:SF41003 3.5 37.2 1.0
N B:CYS164 4.0 20.3 1.0
CA B:CYS164 4.2 24.8 1.0
CB B:ALA182 4.4 25.8 1.0
CA B:ALA182 4.5 21.3 1.0
SG B:CYS158 4.6 33.1 1.0
SG B:CYS225 4.7 34.4 1.0
SG B:CYS161 4.7 34.7 1.0
N B:ALA182 4.8 31.3 1.0
N B:CYS163 4.8 26.2 1.0
CG B:PRO231 4.9 29.3 1.0
N B:SER165 4.9 30.7 1.0
CB B:CYS225 4.9 27.0 1.0
N B:ALA162 5.0 25.8 1.0

Iron binding site 4 out of 10 in 1yq4

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Iron binding site 4 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:38.5
occ:1.00
 FE2 B:SF41003 0.0 38.5 1.0
S3 B:SF41003 2.1 38.0 1.0
S1 B:SF41003 2.1 37.2 1.0
S4 B:SF41003 2.1 32.7 1.0
SG B:CYS225 2.3 34.4 1.0
FE1 B:SF41003 2.6 38.7 1.0
FE3 B:SF41003 2.7 34.6 1.0
FE4 B:SF41003 3.0 34.9 1.0
CB B:CYS225 3.3 27.0 1.0
S2 B:SF41003 3.5 34.7 1.0
CA B:CYS225 4.1 30.7 1.0
CD2 B:LEU229 4.1 45.6 1.0
CB B:LEU229 4.2 36.9 1.0
CD B:PRO226 4.4 40.9 1.0
SG B:CYS164 4.6 39.2 1.0
CG B:PRO226 4.7 43.0 1.0
C B:CYS225 4.7 42.9 1.0
CB B:CYS164 4.8 20.9 1.0
N B:PRO226 4.8 45.0 1.0
CE B:MET185 4.8 24.7 1.0
SG B:CYS158 4.9 33.1 1.0
N B:LYS227 4.9 40.4 1.0
CG B:LEU229 4.9 36.3 1.0
SG B:CYS161 4.9 34.7 1.0

Iron binding site 5 out of 10 in 1yq4

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Iron binding site 5 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:34.6
occ:1.00
 FE3 B:SF41003 0.0 34.6 1.0
S1 B:SF41003 2.0 37.2 1.0
S4 B:SF41003 2.1 32.7 1.0
S2 B:SF41003 2.1 34.7 1.0
SG B:CYS158 2.2 33.1 1.0
FE2 B:SF41003 2.7 38.5 1.0
FE1 B:SF41003 2.7 38.7 1.0
FE4 B:SF41003 2.9 34.9 1.0
CB B:CYS158 3.1 32.8 1.0
S3 B:SF41003 3.5 38.0 1.0
CA B:CYS158 3.6 31.6 1.0
N B:ILE159 3.8 33.4 1.0
N B:LEU160 4.0 28.0 1.0
C B:CYS158 4.1 33.5 1.0
O B:HOH1074 4.2 29.8 1.0
CE B:MET185 4.3 24.7 1.0
CD2 B:LEU229 4.5 45.6 1.0
CA B:LEU160 4.6 31.8 1.0
SG B:CYS164 4.8 39.2 1.0
SG B:CYS225 4.8 34.4 1.0
N B:CYS161 4.8 31.5 1.0
N B:CYS158 4.9 34.5 1.0
C B:ILE159 4.9 35.4 1.0
CA B:ILE159 5.0 30.4 1.0

Iron binding site 6 out of 10 in 1yq4

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Iron binding site 6 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:34.9
occ:1.00
 FE4 B:SF41003 0.0 34.9 1.0
S2 B:SF41003 2.1 34.7 1.0
S3 B:SF41003 2.1 38.0 1.0
S1 B:SF41003 2.1 37.2 1.0
SG B:CYS161 2.3 34.7 1.0
FE3 B:SF41003 2.9 34.6 1.0
FE2 B:SF41003 3.0 38.5 1.0
FE1 B:SF41003 3.0 38.7 1.0
CB B:CYS161 3.3 15.4 1.0
N B:CYS161 3.5 31.5 1.0
CA B:CYS161 3.9 23.6 1.0
N B:ALA162 4.0 25.8 1.0
S4 B:SF41003 4.0 32.7 1.0
CG B:PRO226 4.0 43.0 1.0
CG1 B:ILE159 4.1 33.3 1.0
CD B:PRO226 4.3 40.9 1.0
C B:CYS161 4.4 29.6 1.0
N B:CYS163 4.4 26.2 1.0
N B:LEU160 4.5 28.0 1.0
C B:LEU160 4.6 36.0 1.0
N B:ILE159 4.7 33.4 1.0
SG B:CYS158 4.7 33.1 1.0
SG B:CYS225 4.7 34.4 1.0
CA B:LEU160 4.8 31.8 1.0
CD1 B:ILE159 4.8 30.3 1.0
CB B:CYS163 4.8 28.6 1.0
C B:ILE159 4.9 35.4 1.0
SG B:CYS164 4.9 39.2 1.0
CA B:ALA162 4.9 18.4 1.0

Iron binding site 7 out of 10 in 1yq4

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Iron binding site 7 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:26.7
occ:1.00
 FE1 B:F3S1004 0.0 26.7 1.0
S2 B:F3S1004 2.0 30.2 1.0
S3 B:F3S1004 2.1 27.5 1.0
S1 B:F3S1004 2.2 28.9 1.0
SG B:CYS215 2.2 29.6 1.0
FE4 B:F3S1004 2.5 27.1 1.0
FE3 B:F3S1004 2.8 28.5 1.0
CB B:CYS215 3.3 17.3 1.0
CA B:CYS215 3.7 32.0 1.0
S4 B:F3S1004 3.7 27.6 1.0
OH B:TYR178 3.8 30.8 1.0
N B:THR217 3.8 29.0 1.0
CA B:THR217 4.2 28.6 1.0
N B:HIS216 4.2 27.4 1.0
N B:ILE218 4.2 27.7 1.0
C B:CYS215 4.2 31.2 1.0
O B:HOH1078 4.4 28.2 1.0
CD1 B:ILE235 4.5 24.1 1.0
SG B:CYS168 4.5 36.5 1.0
C B:THR217 4.7 31.9 1.0
SG B:CYS221 4.8 31.4 1.0
C B:HIS216 4.8 30.2 1.0
CZ B:TYR178 4.9 32.4 1.0

Iron binding site 8 out of 10 in 1yq4

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Iron binding site 8 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:28.5
occ:1.00
 FE3 B:F3S1004 0.0 28.5 1.0
S4 B:F3S1004 2.0 27.6 1.0
S1 B:F3S1004 2.1 28.9 1.0
S3 B:F3S1004 2.2 27.5 1.0
SG B:CYS221 2.3 31.4 1.0
FE4 B:F3S1004 2.6 27.1 1.0
FE1 B:F3S1004 2.8 26.7 1.0
CB B:CYS221 3.2 18.2 1.0
S2 B:F3S1004 3.8 30.2 1.0
N B:CYS221 3.8 34.5 1.0
N B:MET219 4.1 24.0 1.0
CA B:CYS221 4.1 29.7 1.0
CA B:MET219 4.2 28.4 1.0
N B:ASN220 4.3 27.3 1.0
CB B:PRO181 4.6 26.1 1.0
C B:MET219 4.6 31.0 1.0
SG B:CYS168 4.6 36.5 1.0
CA B:GLY232 4.7 30.1 1.0
CB B:CYS168 4.7 32.8 1.0
SG B:CYS215 4.7 29.6 1.0
CG B:PRO181 4.7 21.4 1.0
N B:ILE218 4.9 27.7 1.0
C B:ASN220 4.9 36.3 1.0
N B:GLY232 5.0 27.5 1.0

Iron binding site 9 out of 10 in 1yq4

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Iron binding site 9 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:27.1
occ:1.00
 FE4 B:F3S1004 0.0 27.1 1.0
S3 B:F3S1004 2.1 27.5 1.0
S2 B:F3S1004 2.1 30.2 1.0
S4 B:F3S1004 2.2 27.6 1.0
SG B:CYS168 2.2 36.5 1.0
FE1 B:F3S1004 2.5 26.7 1.0
FE3 B:F3S1004 2.6 28.5 1.0
CB B:CYS168 3.1 32.8 1.0
S1 B:F3S1004 3.7 28.9 1.0
CA B:CYS168 4.1 37.9 1.0
OH B:TYR178 4.2 30.8 1.0
CB B:ILE218 4.5 31.0 1.0
CB B:SER170 4.6 39.6 1.0
SG B:CYS215 4.7 29.6 1.0
CE2 B:TYR178 4.7 26.5 1.0
SG B:CYS221 4.8 31.4 1.0
CD1 B:ILE218 4.8 29.0 1.0
C B:CYS168 4.8 32.2 1.0
N B:ILE218 4.8 27.7 1.0
CG1 B:ILE218 5.0 34.4 1.0
CD B:PRO181 5.0 16.9 1.0
CZ B:TYR178 5.0 32.4 1.0

Iron binding site 10 out of 10 in 1yq4

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Iron binding site 10 out of 10 in the Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Avian Respiratory Complex II with 3-Nitropropionate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe143

b:40.0
occ:1.00
 FE C:HEM143 0.0 40.0 1.0
ND C:HEM143 1.9 41.1 1.0
NA C:HEM143 1.9 41.4 1.0
NE2 C:HIS98 2.0 34.3 1.0
NE2 D:HIS46 2.0 34.6 1.0
NB C:HEM143 2.0 40.4 1.0
NC C:HEM143 2.1 41.5 1.0
CD2 D:HIS46 2.9 37.2 1.0
C1A C:HEM143 2.9 40.4 1.0
CD2 C:HIS98 2.9 28.5 1.0
CE1 C:HIS98 3.0 42.2 1.0
C4D C:HEM143 3.0 46.1 1.0
C1D C:HEM143 3.0 42.4 1.0
C4A C:HEM143 3.0 43.2 1.0
C4B C:HEM143 3.0 42.4 1.0
CE1 D:HIS46 3.1 32.9 1.0
C4C C:HEM143 3.1 42.2 1.0
C1B C:HEM143 3.1 40.7 1.0
C1C C:HEM143 3.1 38.1 1.0
CHA C:HEM143 3.3 50.0 1.0
CHC C:HEM143 3.4 39.0 1.0
CHD C:HEM143 3.4 35.2 1.0
CHB C:HEM143 3.5 39.4 1.0
ND1 C:HIS98 4.0 25.2 1.0
CG C:HIS98 4.1 33.9 1.0
CG D:HIS46 4.1 18.1 1.0
ND1 D:HIS46 4.1 23.2 1.0
C2A C:HEM143 4.1 39.3 1.0
C3A C:HEM143 4.2 29.7 1.0
C2D C:HEM143 4.2 37.6 1.0
C3D C:HEM143 4.2 51.9 1.0
C3B C:HEM143 4.3 50.2 1.0
C3C C:HEM143 4.3 44.6 1.0
C2B C:HEM143 4.4 38.7 1.0
C2C C:HEM143 4.4 41.8 1.0

Reference:

L.Huang, G.Sun, D.Cobessi, A.C.Wang, J.T.Shen, E.Y.Tung, V.E.Anderson, E.A.Berry. 3-Nitropropionic Acid Is A Suicide Inhibitor of Mitochondrial Respiration That, Upon Oxidation By Complex II, Forms A Covalent Adduct with A Catalytic Base Arginine in the Active Site of the Enzyme J.Biol.Chem. V. 281 5965 2006.
ISSN: ISSN 0021-9258
PubMed: 16371358
DOI: 10.1074/JBC.M511270200
Page generated: Sat Aug 3 17:54:35 2024

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