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Iron in PDB 6myo: Avian Mitochondrial Complex II with Flutolanyl Bound

Enzymatic activity of Avian Mitochondrial Complex II with Flutolanyl Bound

All present enzymatic activity of Avian Mitochondrial Complex II with Flutolanyl Bound:
1.3.5.1;

Protein crystallography data

The structure of Avian Mitochondrial Complex II with Flutolanyl Bound, PDB code: 6myo was solved by E.A.Berry, L.-S.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.64 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.637, 83.783, 289.575, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.7

Other elements in 6myo:

The structure of Avian Mitochondrial Complex II with Flutolanyl Bound also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Potassium (K) 1 atom
Manganese (Mn) 1 atom

Iron Binding Sites:

The binding sites of Iron atom in the Avian Mitochondrial Complex II with Flutolanyl Bound (pdb code 6myo). 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 Mitochondrial Complex II with Flutolanyl Bound, PDB code: 6myo:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 6myo

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Iron binding site 1 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:45.7
occ:1.00
 FE1 B:FES1001 0.0 45.7 1.0
SG B:CYS85 2.1 43.7 1.0
S2 B:FES1001 2.2 50.7 1.0
S1 B:FES1001 2.2 45.1 1.0
SG B:CYS73 2.2 54.5 1.0
FE2 B:FES1001 2.9 54.8 1.0
CB B:CYS85 3.2 53.5 1.0
CB B:CYS73 3.4 38.8 1.0
N B:CYS73 4.0 44.5 1.0
N B:CYS85 4.1 59.4 1.0
CA B:CYS85 4.3 54.7 1.0
CA B:CYS73 4.3 45.8 1.0
CB B:LEU83 4.3 42.5 1.0
N B:GLY68 4.3 44.6 1.0
SG B:CYS65 4.3 48.5 1.0
CA B:GLY68 4.5 43.6 1.0
N B:ARG66 4.6 54.2 1.0
CA B:ARG66 4.7 60.4 1.0
CD2 B:LEU83 4.7 37.2 1.0
CD1 B:LEU83 4.7 37.2 1.0
N B:SER72 4.8 40.0 1.0
CG B:LEU83 4.8 39.9 1.0
SG B:CYS70 4.8 39.0 1.0
CD2 B:LEU45 4.9 53.9 1.0
N B:ALA84 4.9 43.6 1.0
C B:CYS73 5.0 46.4 1.0

Iron binding site 2 out of 10 in 6myo

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Iron binding site 2 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:54.8
occ:1.00
 FE2 B:FES1001 0.0 54.8 1.0
S2 B:FES1001 2.2 50.7 1.0
SG B:CYS65 2.2 48.5 1.0
S1 B:FES1001 2.3 45.1 1.0
SG B:CYS70 2.3 39.0 1.0
FE1 B:FES1001 2.9 45.7 1.0
CB B:CYS65 3.3 45.3 1.0
N B:CYS65 3.3 38.8 1.0
CB B:CYS70 3.4 35.6 1.0
N B:CYS70 3.5 37.3 1.0
CA B:CYS65 3.7 45.3 1.0
N B:ARG66 3.8 54.2 1.0
N B:GLY71 3.8 43.7 1.0
CA B:CYS70 3.8 34.9 1.0
N B:SER72 4.0 40.0 1.0
C B:CYS65 4.1 45.6 1.0
C B:CYS70 4.2 42.5 1.0
SG B:CYS85 4.2 43.7 1.0
N B:ILE69 4.4 45.1 1.0
N B:GLY68 4.4 44.6 1.0
N B:SER64 4.4 42.3 1.0
C B:SER64 4.5 40.2 1.0
OG B:SER72 4.5 48.0 1.0
CB B:SER72 4.5 37.0 1.0
CA B:ARG66 4.7 60.4 1.0
N B:GLU67 4.7 51.1 1.0
C B:ILE69 4.7 37.0 1.0
CA B:GLY68 4.7 43.6 1.0
CA B:GLY71 4.8 39.0 1.0
C B:GLY71 4.8 46.1 1.0
CA B:SER64 4.8 44.4 1.0
CA B:SER72 4.9 38.2 1.0
C B:GLY68 4.9 44.1 1.0
SG B:CYS73 4.9 54.5 1.0
N B:CYS73 4.9 44.5 1.0

Iron binding site 3 out of 10 in 6myo

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Iron binding site 3 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:44.1
occ:1.00
 FE1 B:SF41002 0.0 44.1 1.0
S4 B:SF41002 2.2 41.0 1.0
SG B:CYS164 2.2 45.7 1.0
S3 B:SF41002 2.2 47.4 1.0
S2 B:SF41002 2.2 40.0 1.0
FE2 B:SF41002 2.9 44.9 1.0
FE3 B:SF41002 3.0 43.7 1.0
FE4 B:SF41002 3.0 45.1 1.0
CB B:CYS164 3.0 32.6 1.0
N B:CYS164 3.7 38.4 1.0
S1 B:SF41002 3.8 42.5 1.0
CA B:CYS164 4.0 34.8 1.0
CB B:ALA182 4.1 31.6 1.0
CA B:ALA182 4.4 36.6 1.0
N B:CYS163 4.7 41.1 1.0
SG B:CYS158 4.7 40.4 1.0
N B:ALA182 4.8 37.7 1.0
SG B:CYS161 4.8 39.7 1.0
N B:SER165 4.8 43.0 1.0
C B:CYS163 4.9 41.5 1.0
CG B:PRO231 4.9 32.1 1.0
C B:CYS164 4.9 42.3 1.0
SG B:CYS225 5.0 47.1 1.0
CB B:CYS225 5.0 42.5 1.0

Iron binding site 4 out of 10 in 6myo

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Iron binding site 4 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:44.9
occ:1.00
 FE2 B:SF41002 0.0 44.9 1.0
S3 B:SF41002 2.2 47.4 1.0
SG B:CYS225 2.2 47.1 1.0
S4 B:SF41002 2.2 41.0 1.0
S1 B:SF41002 2.3 42.5 1.0
FE1 B:SF41002 2.9 44.1 1.0
FE3 B:SF41002 3.1 43.7 1.0
CB B:CYS225 3.1 42.5 1.0
FE4 B:SF41002 3.1 45.1 1.0
CA B:CYS225 3.8 39.1 1.0
S2 B:SF41002 3.9 40.0 1.0
CD B:PRO226 4.3 51.2 1.0
C B:CYS225 4.4 50.8 1.0
CB B:LEU229 4.5 40.4 1.0
CD1 B:LEU229 4.5 38.5 1.0
N B:PRO226 4.6 53.2 1.0
CG B:LEU229 4.6 37.3 1.0
N B:LYS227 4.7 50.9 1.0
CB B:LYS227 4.7 53.8 1.0
SG B:CYS164 4.9 45.7 1.0
CB B:CYS164 4.9 32.6 1.0
SG B:CYS161 5.0 39.7 1.0

Iron binding site 5 out of 10 in 6myo

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Iron binding site 5 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:43.7
occ:1.00
 FE3 B:SF41002 0.0 43.7 1.0
SG B:CYS158 2.2 40.4 1.0
S1 B:SF41002 2.2 42.5 1.0
S2 B:SF41002 2.2 40.0 1.0
S4 B:SF41002 2.3 41.0 1.0
FE4 B:SF41002 2.9 45.1 1.0
FE1 B:SF41002 3.0 44.1 1.0
FE2 B:SF41002 3.1 44.9 1.0
CB B:CYS158 3.2 39.3 1.0
CA B:CYS158 3.6 40.9 1.0
N B:ILE159 3.7 36.5 1.0
S3 B:SF41002 3.8 47.4 1.0
N B:LEU160 3.9 43.3 1.0
C B:CYS158 4.1 35.1 1.0
O B:HOH1133 4.2 31.6 1.0
CA B:LEU160 4.4 39.0 1.0
N B:CYS161 4.7 35.9 1.0
C B:ILE159 4.8 44.2 1.0
CA B:ILE159 4.8 35.8 1.0
CB B:ALA182 4.8 31.6 1.0
CD1 B:LEU229 4.8 38.5 1.0
CE B:MET185 4.9 33.7 1.0
SG B:CYS164 4.9 45.7 1.0
N B:CYS158 5.0 37.0 1.0

Iron binding site 6 out of 10 in 6myo

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Iron binding site 6 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:45.1
occ:1.00
 FE4 B:SF41002 0.0 45.1 1.0
S2 B:SF41002 2.2 40.0 1.0
S1 B:SF41002 2.2 42.5 1.0
SG B:CYS161 2.3 39.7 1.0
S3 B:SF41002 2.3 47.4 1.0
FE3 B:SF41002 2.9 43.7 1.0
FE1 B:SF41002 3.0 44.1 1.0
FE2 B:SF41002 3.1 44.9 1.0
N B:CYS161 3.4 35.9 1.0
CB B:CYS161 3.5 33.8 1.0
S4 B:SF41002 3.9 41.0 1.0
CA B:CYS161 3.9 37.8 1.0
N B:ALA162 4.0 37.5 1.0
CG1 B:ILE159 4.2 40.5 1.0
N B:CYS163 4.3 41.1 1.0
CD B:PRO226 4.4 51.2 1.0
C B:CYS161 4.4 37.8 1.0
N B:LEU160 4.4 43.3 1.0
C B:LEU160 4.5 49.5 1.0
CB B:CYS163 4.6 38.2 1.0
CA B:LEU160 4.7 39.0 1.0
CG B:PRO226 4.7 45.3 1.0
N B:ILE159 4.8 36.5 1.0
SG B:CYS158 4.8 40.4 1.0
CD1 B:ILE159 4.9 43.7 1.0
N B:CYS164 4.9 38.4 1.0
SG B:CYS225 4.9 47.1 1.0
SG B:CYS164 5.0 45.7 1.0
CA B:ALA162 5.0 36.9 1.0
C B:ILE159 5.0 44.2 1.0
CA B:CYS163 5.0 42.4 1.0

Iron binding site 7 out of 10 in 6myo

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Iron binding site 7 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:44.9
occ:1.00
 FE1 B:F3S1003 0.0 44.9 1.0
S1 B:F3S1003 2.2 32.4 1.0
SG B:CYS168 2.3 47.6 1.0
S2 B:F3S1003 2.3 41.1 1.0
S3 B:F3S1003 2.3 40.0 1.0
FE3 B:F3S1003 2.7 48.6 1.0
FE4 B:F3S1003 2.8 47.6 1.0
CB B:CYS168 3.1 47.0 1.0
CA B:CYS168 3.9 48.7 1.0
S4 B:F3S1003 4.0 38.6 1.0
OH B:TYR178 4.3 40.7 1.0
CB B:ILE218 4.4 33.8 1.0
C B:CYS168 4.7 43.0 1.0
CD1 B:ILE218 4.8 38.3 1.0
N B:ILE218 4.8 44.1 1.0
SG B:CYS221 4.8 44.0 1.0
CD B:PRO169 4.8 37.6 1.0
CB B:SER170 4.8 38.2 1.0
N B:PRO169 4.9 42.2 1.0
CE2 B:TYR178 4.9 34.7 1.0
CG1 B:ILE218 5.0 42.9 1.0

Iron binding site 8 out of 10 in 6myo

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Iron binding site 8 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:48.6
occ:1.00
 FE3 B:F3S1003 0.0 48.6 1.0
S1 B:F3S1003 2.2 32.4 1.0
S4 B:F3S1003 2.3 38.6 1.0
S3 B:F3S1003 2.3 40.0 1.0
SG B:CYS221 2.3 44.0 1.0
FE1 B:F3S1003 2.7 44.9 1.0
FE4 B:F3S1003 2.8 47.6 1.0
CB B:CYS221 3.4 37.1 1.0
N B:CYS221 3.9 47.0 1.0
S2 B:F3S1003 3.9 41.1 1.0
N B:MET219 4.0 49.0 1.0
CA B:MET219 4.3 45.8 1.0
CA B:CYS221 4.3 42.7 1.0
N B:ASN220 4.3 43.1 1.0
C B:MET219 4.6 43.9 1.0
CB B:PRO181 4.7 35.1 1.0
SG B:CYS168 4.7 47.6 1.0
CG B:PRO181 4.7 33.1 1.0
CA B:GLY232 4.8 38.1 1.0
N B:ILE218 4.8 44.1 1.0
SG B:CYS215 4.8 39.8 1.0
CB B:CYS168 4.9 47.0 1.0
CD1 B:ILE235 4.9 35.0 1.0
N B:GLY232 5.0 43.7 1.0
C B:ILE218 5.0 50.0 1.0

Iron binding site 9 out of 10 in 6myo

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Iron binding site 9 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:47.6
occ:1.00
 FE4 B:F3S1003 0.0 47.6 1.0
S2 B:F3S1003 2.2 41.1 1.0
S4 B:F3S1003 2.3 38.6 1.0
S3 B:F3S1003 2.3 40.0 1.0
SG B:CYS215 2.3 39.8 1.0
FE3 B:F3S1003 2.8 48.6 1.0
FE1 B:F3S1003 2.8 44.9 1.0
CB B:CYS215 3.4 38.0 1.0
N B:THR217 3.6 34.2 1.0
CA B:CYS215 3.8 40.5 1.0
OH B:TYR178 3.9 40.7 1.0
S1 B:F3S1003 4.0 32.4 1.0
CA B:THR217 4.0 35.9 1.0
O B:HOH1188 4.1 31.8 1.0
N B:HIS216 4.1 40.4 1.0
N B:ILE218 4.1 44.1 1.0
C B:CYS215 4.2 45.3 1.0
CD1 B:ILE235 4.3 35.0 1.0
C B:THR217 4.6 32.5 1.0
C B:HIS216 4.7 47.9 1.0
SG B:CYS168 4.7 47.6 1.0
SG B:CYS221 4.9 44.0 1.0
N B:MET219 5.0 49.0 1.0

Iron binding site 10 out of 10 in 6myo

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Iron binding site 10 out of 10 in the Avian Mitochondrial Complex II with Flutolanyl Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Avian Mitochondrial Complex II with Flutolanyl Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:46.5
occ:1.00
 FE C:HEM201 0.0 46.5 1.0
NE2 C:HIS98 1.9 39.1 1.0
NE2 D:HIS46 2.0 45.4 1.0
NA C:HEM201 2.0 51.9 1.0
NC C:HEM201 2.1 50.2 1.0
ND C:HEM201 2.1 55.5 1.0
NB C:HEM201 2.1 48.7 1.0
CE1 C:HIS98 2.9 38.3 1.0
CD2 C:HIS98 2.9 42.1 1.0
CE1 D:HIS46 3.0 46.9 1.0
CD2 D:HIS46 3.0 53.7 1.0
C1A C:HEM201 3.0 52.0 1.0
C1C C:HEM201 3.1 41.3 1.0
C4D C:HEM201 3.1 46.8 1.0
C4A C:HEM201 3.1 47.8 1.0
C4B C:HEM201 3.1 51.2 1.0
C4C C:HEM201 3.1 52.1 1.0
C1D C:HEM201 3.1 46.1 1.0
C1B C:HEM201 3.2 44.0 1.0
CHA C:HEM201 3.4 44.5 1.0
CHC C:HEM201 3.4 44.0 1.0
CHD C:HEM201 3.5 43.0 1.0
CHB C:HEM201 3.5 40.7 1.0
ND1 C:HIS98 4.0 37.9 1.0
CG C:HIS98 4.0 37.9 1.0
ND1 D:HIS46 4.1 47.6 1.0
CG D:HIS46 4.1 43.2 1.0
C2A C:HEM201 4.2 42.4 1.0
C3A C:HEM201 4.3 48.1 1.0
C2C C:HEM201 4.3 47.6 1.0
C3C C:HEM201 4.3 43.6 1.0
C3B C:HEM201 4.3 49.8 1.0
C3D C:HEM201 4.3 50.1 1.0
C2D C:HEM201 4.3 50.0 1.0
C2B C:HEM201 4.4 50.9 1.0
NE2 C:HIS42 5.0 40.4 1.0

Reference:

L.-S.Huang, E.A.Berry. Crystallographic Studies of the Binding of Ligands to the Ubiquinone Site of Mitochondrial Respiratory Complex II To Be Published.
Page generated: Wed Aug 7 02:28:24 2024

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