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Iron in PDB 6myq: Avian Mitochondrial Complex II with Ferulenol Bound

Enzymatic activity of Avian Mitochondrial Complex II with Ferulenol Bound

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

Protein crystallography data

The structure of Avian Mitochondrial Complex II with Ferulenol Bound, PDB code: 6myq 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) 28.34 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.910, 84.553, 290.523, 90.00, 90.00, 90.00
R / Rfree (%) 20.8 / 23.9

Other elements in 6myq:

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

Potassium (K) 2 atoms
Manganese (Mn) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 10 in 6myq

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Iron binding site 1 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:38.8
occ:1.00
 FE1 B:FES1001 0.0 38.8 1.0
S2 B:FES1001 2.2 36.2 1.0
S1 B:FES1001 2.2 36.5 1.0
SG B:CYS85 2.3 37.8 1.0
SG B:CYS73 2.4 37.0 1.0
FE2 B:FES1001 2.8 36.3 1.0
CB B:CYS85 3.4 42.7 1.0
CB B:CYS73 3.5 36.3 1.0
N B:CYS73 4.0 35.9 1.0
SG B:CYS65 4.2 40.1 1.0
N B:CYS85 4.2 40.3 1.0
CB B:LEU83 4.3 30.4 1.0
N B:GLY68 4.3 39.6 1.0
CA B:CYS73 4.4 35.1 1.0
CA B:CYS85 4.4 41.6 1.0
CA B:GLY68 4.5 39.8 1.0
N B:ARG66 4.6 34.4 1.0
CA B:ARG66 4.7 42.8 1.0
CD1 B:LEU83 4.7 29.5 1.0
SG B:CYS70 4.7 39.3 1.0
N B:SER72 4.8 31.7 1.0
CD2 B:LEU83 4.8 34.6 1.0
CG B:LEU83 4.8 29.6 1.0
N B:GLU67 4.9 42.3 1.0

Iron binding site 2 out of 10 in 6myq

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Iron binding site 2 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:36.3
occ:1.00
 FE2 B:FES1001 0.0 36.3 1.0
S1 B:FES1001 2.2 36.5 1.0
S2 B:FES1001 2.2 36.2 1.0
SG B:CYS65 2.2 40.1 1.0
SG B:CYS70 2.2 39.3 1.0
FE1 B:FES1001 2.8 38.8 1.0
CB B:CYS65 3.4 35.5 1.0
CB B:CYS70 3.4 30.7 1.0
N B:CYS70 3.5 35.4 1.0
N B:CYS65 3.5 36.9 1.0
N B:GLY71 3.6 31.1 1.0
CA B:CYS70 3.8 32.1 1.0
N B:ARG66 3.9 34.4 1.0
CA B:CYS65 3.9 31.9 1.0
N B:SER72 3.9 31.7 1.0
C B:CYS70 4.1 32.3 1.0
C B:CYS65 4.3 32.5 1.0
SG B:CYS85 4.3 37.8 1.0
N B:GLY68 4.3 39.6 1.0
N B:ILE69 4.4 41.4 1.0
CB B:SER72 4.5 30.7 1.0
N B:SER64 4.6 33.2 1.0
CA B:GLY71 4.6 31.8 1.0
C B:SER64 4.6 37.6 1.0
N B:GLU67 4.7 42.3 1.0
CA B:GLY68 4.7 39.8 1.0
C B:ILE69 4.7 35.5 1.0
C B:GLY71 4.7 39.0 1.0
OG B:SER72 4.8 44.5 1.0
CA B:ARG66 4.8 42.8 1.0
CA B:SER72 4.8 34.4 1.0
N B:CYS73 4.8 35.9 1.0
SG B:CYS73 4.9 37.0 1.0
C B:GLY68 4.9 42.8 1.0

Iron binding site 3 out of 10 in 6myq

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Iron binding site 3 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:38.1
occ:1.00
 FE1 B:SF41002 0.0 38.1 1.0
SG B:CYS164 2.2 40.3 1.0
S3 B:SF41002 2.2 39.9 1.0
S4 B:SF41002 2.3 35.1 1.0
S2 B:SF41002 2.3 34.0 1.0
FE2 B:SF41002 2.6 39.9 1.0
FE3 B:SF41002 2.7 34.7 1.0
FE4 B:SF41002 2.8 40.3 1.0
CB B:CYS164 3.1 36.0 1.0
S1 B:SF41002 3.8 28.6 1.0
N B:CYS164 3.8 34.1 1.0
CA B:CYS164 4.1 36.5 1.0
CB B:ALA182 4.2 25.9 1.0
CA B:ALA182 4.4 31.1 1.0
SG B:CYS158 4.6 32.7 1.0
SG B:CYS161 4.6 39.5 1.0
SG B:CYS225 4.6 40.9 1.0
N B:ALA182 4.8 32.1 1.0
N B:CYS163 4.8 34.4 1.0
CG B:PRO231 4.9 35.3 1.0
N B:SER165 5.0 37.8 1.0

Iron binding site 4 out of 10 in 6myq

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Iron binding site 4 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:39.9
occ:1.00
 FE2 B:SF41002 0.0 39.9 1.0
S4 B:SF41002 2.2 35.1 1.0
SG B:CYS225 2.2 40.9 1.0
S3 B:SF41002 2.2 39.9 1.0
S1 B:SF41002 2.3 28.6 1.0
FE1 B:SF41002 2.6 38.1 1.0
FE3 B:SF41002 2.8 34.7 1.0
FE4 B:SF41002 2.8 40.3 1.0
CB B:CYS225 3.4 41.7 1.0
S2 B:SF41002 3.9 34.0 1.0
CA B:CYS225 4.0 34.0 1.0
CD B:PRO226 4.2 43.9 1.0
CB B:LEU229 4.6 33.4 1.0
CD1 B:LEU229 4.6 30.7 1.0
SG B:CYS164 4.6 40.3 1.0
C B:CYS225 4.6 41.7 1.0
SG B:CYS161 4.7 39.5 1.0
N B:PRO226 4.7 43.4 1.0
CG B:LEU229 4.8 32.1 1.0
CB B:LYS227 4.8 36.6 1.0
CB B:CYS164 4.8 36.0 1.0
N B:LYS227 4.8 37.5 1.0
SG B:CYS158 4.9 32.7 1.0

Iron binding site 5 out of 10 in 6myq

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Iron binding site 5 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:34.7
occ:1.00
 FE3 B:SF41002 0.0 34.7 1.0
S1 B:SF41002 2.2 28.6 1.0
S2 B:SF41002 2.2 34.0 1.0
SG B:CYS158 2.2 32.7 1.0
S4 B:SF41002 2.3 35.1 1.0
FE4 B:SF41002 2.7 40.3 1.0
FE1 B:SF41002 2.7 38.1 1.0
FE2 B:SF41002 2.8 39.9 1.0
CB B:CYS158 3.4 31.0 1.0
CA B:CYS158 3.8 32.2 1.0
S3 B:SF41002 3.8 39.9 1.0
N B:LEU160 3.9 39.2 1.0
N B:ILE159 3.9 35.8 1.0
C B:CYS158 4.2 38.0 1.0
O B:HOH1154 4.3 32.2 1.0
CA B:LEU160 4.4 35.8 1.0
SG B:CYS164 4.7 40.3 1.0
N B:CYS161 4.7 37.7 1.0
CE B:MET185 4.7 40.6 1.0
CB B:ALA182 4.8 25.9 1.0
SG B:CYS161 4.8 39.5 1.0
SG B:CYS225 4.8 40.9 1.0
C B:ILE159 4.8 37.5 1.0
CD1 B:LEU229 4.9 30.7 1.0
CA B:ILE159 5.0 33.5 1.0

Iron binding site 6 out of 10 in 6myq

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Iron binding site 6 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:40.3
occ:1.00
 FE4 B:SF41002 0.0 40.3 1.0
S2 B:SF41002 2.2 34.0 1.0
SG B:CYS161 2.2 39.5 1.0
S1 B:SF41002 2.2 28.6 1.0
S3 B:SF41002 2.3 39.9 1.0
FE3 B:SF41002 2.7 34.7 1.0
FE1 B:SF41002 2.8 38.1 1.0
FE2 B:SF41002 2.8 39.9 1.0
N B:CYS161 3.5 37.7 1.0
CB B:CYS161 3.6 36.3 1.0
S4 B:SF41002 3.9 35.1 1.0
CA B:CYS161 4.0 35.9 1.0
N B:ALA162 4.1 33.4 1.0
CG1 B:ILE159 4.3 36.5 1.0
N B:CYS163 4.3 34.4 1.0
CD B:PRO226 4.3 43.9 1.0
N B:LEU160 4.3 39.2 1.0
C B:CYS161 4.4 35.1 1.0
C B:LEU160 4.6 37.2 1.0
SG B:CYS158 4.6 32.7 1.0
CB B:CYS163 4.6 34.6 1.0
CG B:PRO226 4.7 46.3 1.0
SG B:CYS225 4.7 40.9 1.0
CA B:LEU160 4.7 35.8 1.0
SG B:CYS164 4.7 40.3 1.0
N B:CYS164 4.8 34.1 1.0
N B:ILE159 4.8 35.8 1.0
CA B:ALA162 5.0 33.7 1.0

Iron binding site 7 out of 10 in 6myq

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Iron binding site 7 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:33.9
occ:1.00
 FE1 B:F3S1003 0.0 33.9 1.0
S1 B:F3S1003 2.2 30.7 1.0
SG B:CYS168 2.3 37.3 1.0
S3 B:F3S1003 2.3 34.0 1.0
S2 B:F3S1003 2.3 34.5 1.0
FE3 B:F3S1003 2.6 35.3 1.0
FE4 B:F3S1003 2.7 34.9 1.0
CB B:CYS168 3.2 40.3 1.0
S4 B:F3S1003 4.0 32.5 1.0
CA B:CYS168 4.0 42.2 1.0
OH B:TYR178 4.2 32.1 1.0
CB B:ILE218 4.5 33.6 1.0
CD1 B:ILE218 4.6 32.9 1.0
C B:CYS168 4.7 37.5 1.0
SG B:CYS215 4.8 31.9 1.0
CB B:SER170 4.8 36.3 1.0
SG B:CYS221 4.8 39.2 1.0
N B:ILE218 4.9 35.3 1.0
CD B:PRO169 4.9 30.3 1.0
CE2 B:TYR178 4.9 26.1 1.0
OG B:SER170 4.9 37.9 1.0
N B:MET219 5.0 37.3 1.0

Iron binding site 8 out of 10 in 6myq

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Iron binding site 8 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:35.3
occ:1.00
 FE3 B:F3S1003 0.0 35.3 1.0
S1 B:F3S1003 2.2 30.7 1.0
S4 B:F3S1003 2.3 32.5 1.0
S3 B:F3S1003 2.3 34.0 1.0
SG B:CYS221 2.3 39.2 1.0
FE1 B:F3S1003 2.6 33.9 1.0
FE4 B:F3S1003 2.7 34.9 1.0
CB B:CYS221 3.3 31.7 1.0
S2 B:F3S1003 3.8 34.5 1.0
N B:MET219 3.9 37.3 1.0
N B:CYS221 3.9 35.7 1.0
CA B:MET219 4.1 33.9 1.0
CA B:CYS221 4.3 36.7 1.0
N B:ASN220 4.4 31.2 1.0
C B:MET219 4.6 32.7 1.0
SG B:CYS168 4.6 37.3 1.0
SG B:CYS215 4.6 31.9 1.0
CB B:PRO181 4.7 32.1 1.0
CG B:PRO181 4.7 30.0 1.0
CA B:GLY232 4.8 36.2 1.0
N B:ILE218 4.8 35.3 1.0
CD1 B:ILE235 4.8 32.5 1.0
CB B:CYS168 4.9 40.3 1.0

Iron binding site 9 out of 10 in 6myq

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Iron binding site 9 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:34.9
occ:1.00
 FE4 B:F3S1003 0.0 34.9 1.0
SG B:CYS215 2.2 31.9 1.0
S4 B:F3S1003 2.2 32.5 1.0
S2 B:F3S1003 2.3 34.5 1.0
S3 B:F3S1003 2.3 34.0 1.0
FE3 B:F3S1003 2.7 35.3 1.0
FE1 B:F3S1003 2.7 33.9 1.0
CB B:CYS215 3.4 30.0 1.0
N B:THR217 3.7 34.6 1.0
CA B:CYS215 3.8 33.7 1.0
S1 B:F3S1003 3.9 30.7 1.0
OH B:TYR178 3.9 32.1 1.0
CA B:THR217 4.1 31.7 1.0
N B:ILE218 4.1 35.3 1.0
N B:HIS216 4.2 37.1 1.0
O B:HOH1167 4.2 31.5 1.0
CD1 B:ILE235 4.3 32.5 1.0
C B:CYS215 4.3 37.2 1.0
C B:THR217 4.6 32.3 1.0
SG B:CYS168 4.7 37.3 1.0
SG B:CYS221 4.7 39.2 1.0
C B:HIS216 4.7 42.2 1.0
N B:MET219 4.8 37.3 1.0

Iron binding site 10 out of 10 in 6myq

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Iron binding site 10 out of 10 in the Avian Mitochondrial Complex II with Ferulenol 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 Ferulenol Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:38.1
occ:1.00
 FE C:HEM201 0.0 38.1 1.0
NA C:HEM201 2.0 38.3 1.0
NE2 C:HIS98 2.0 32.8 1.0
NE2 D:HIS46 2.0 39.0 1.0
NB C:HEM201 2.0 42.1 1.0
NC C:HEM201 2.1 39.8 1.0
ND C:HEM201 2.1 35.5 1.0
CD2 C:HIS98 2.8 36.4 1.0
CE1 D:HIS46 2.9 41.9 1.0
C1A C:HEM201 3.0 41.8 1.0
C4A C:HEM201 3.0 38.5 1.0
CD2 D:HIS46 3.0 40.2 1.0
C4B C:HEM201 3.0 39.0 1.0
C1C C:HEM201 3.1 41.2 1.0
C1B C:HEM201 3.1 35.5 1.0
CE1 C:HIS98 3.1 36.3 1.0
C4C C:HEM201 3.1 42.8 1.0
C1D C:HEM201 3.1 34.3 1.0
C4D C:HEM201 3.1 40.0 1.0
CHC C:HEM201 3.4 36.9 1.0
CHB C:HEM201 3.4 35.4 1.0
CHA C:HEM201 3.5 40.4 1.0
CHD C:HEM201 3.5 33.5 1.0
CG C:HIS98 4.0 31.3 1.0
ND1 D:HIS46 4.1 38.5 1.0
ND1 C:HIS98 4.1 34.0 1.0
CG D:HIS46 4.1 40.1 1.0
C2A C:HEM201 4.2 39.6 1.0
C3A C:HEM201 4.2 40.9 1.0
C3B C:HEM201 4.3 41.9 1.0
C2B C:HEM201 4.3 40.1 1.0
C2C C:HEM201 4.3 42.9 1.0
C3C C:HEM201 4.3 43.3 1.0
C2D C:HEM201 4.4 35.0 1.0
C3D C:HEM201 4.4 41.2 1.0
NE2 C:HIS42 4.9 34.0 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 02:28:37 2024

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