Iron in PDB 6myr: Avian Mitochondrial Complex II with Thiapronil Bound

Enzymatic activity of Avian Mitochondrial Complex II with Thiapronil Bound

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

Protein crystallography data

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

Resolution Low / High (Å) 47.93 / 2.15
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.361, 84.622, 293.337, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 23.8

Other elements in 6myr:

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

Potassium (K) 1 atom
Chlorine (Cl) 1 atom

Iron Binding Sites:

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

Iron binding site 1 out of 10 in 6myr

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

b:55.6
occ:1.00
 FE1 B:FES1001 0.0 55.6 1.0
S2 B:FES1001 2.2 56.6 1.0
SG B:CYS85 2.2 54.3 1.0
S1 B:FES1001 2.2 55.3 1.0
SG B:CYS73 2.3 58.6 1.0
FE2 B:FES1001 2.9 55.2 1.0
CB B:CYS73 3.4 56.9 1.0
CB B:CYS85 3.5 54.3 1.0
N B:CYS73 3.9 54.5 1.0
CA B:CYS73 4.2 54.9 1.0
N B:CYS85 4.2 56.6 1.0
SG B:CYS65 4.3 59.4 1.0
CB B:LEU83 4.3 52.2 1.0
CA B:CYS85 4.5 57.2 1.0
N B:GLY68 4.6 54.0 1.0
CD2 B:LEU83 4.6 50.4 1.0
N B:ARG66 4.6 64.5 1.0
N B:SER72 4.7 49.5 1.0
CA B:GLY68 4.7 52.8 1.0
CA B:ARG66 4.8 65.7 1.0
CD1 B:LEU83 4.8 47.5 1.0
CG B:LEU83 4.8 52.1 1.0
C B:CYS73 4.9 54.0 1.0
SG B:CYS70 4.9 52.7 1.0
CD2 B:LEU45 4.9 62.7 1.0
N B:ALA84 5.0 53.8 1.0

Iron binding site 2 out of 10 in 6myr

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

b:55.2
occ:1.00
 FE2 B:FES1001 0.0 55.2 1.0
S1 B:FES1001 2.2 55.3 1.0
S2 B:FES1001 2.2 56.6 1.0
SG B:CYS65 2.2 59.4 1.0
SG B:CYS70 2.3 52.7 1.0
FE1 B:FES1001 2.9 55.6 1.0
CB B:CYS65 3.3 56.3 1.0
N B:CYS65 3.3 54.7 1.0
CB B:CYS70 3.5 47.6 1.0
N B:CYS70 3.6 49.2 1.0
N B:GLY71 3.7 49.7 1.0
CA B:CYS65 3.7 57.7 1.0
N B:ARG66 3.8 64.5 1.0
N B:SER72 3.9 49.5 1.0
CA B:CYS70 3.9 47.2 1.0
C B:CYS65 4.2 61.7 1.0
C B:CYS70 4.2 48.1 1.0
SG B:CYS85 4.3 54.3 1.0
CB B:SER72 4.4 51.9 1.0
N B:ILE69 4.4 51.5 1.0
C B:SER64 4.4 60.3 1.0
N B:GLY68 4.5 54.0 1.0
N B:SER64 4.5 53.9 1.0
CA B:GLY71 4.7 48.3 1.0
C B:GLY71 4.7 52.5 1.0
CA B:SER72 4.7 51.0 1.0
C B:ILE69 4.8 49.7 1.0
CA B:ARG66 4.8 65.7 1.0
N B:GLU67 4.8 65.1 1.0
N B:CYS73 4.9 54.5 1.0
CA B:GLY68 4.9 52.8 1.0
CA B:SER64 4.9 57.2 1.0
SG B:CYS73 5.0 58.6 1.0
CB B:SER64 5.0 57.2 1.0

Iron binding site 3 out of 10 in 6myr

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

b:52.0
occ:1.00
 FE1 B:SF41002 0.0 52.0 1.0
SG B:CYS164 2.2 49.6 1.0
S3 B:SF41002 2.2 54.1 1.0
S4 B:SF41002 2.3 44.1 1.0
S2 B:SF41002 2.3 47.6 1.0
FE2 B:SF41002 2.7 51.1 1.0
FE4 B:SF41002 2.7 49.6 1.0
FE3 B:SF41002 2.7 45.6 1.0
CB B:CYS164 3.2 47.1 1.0
N B:CYS164 3.8 52.2 1.0
S1 B:SF41002 3.8 46.9 1.0
CB B:ALA182 4.1 40.3 1.0
CA B:CYS164 4.1 48.3 1.0
SG B:CYS161 4.5 46.2 1.0
CA B:ALA182 4.5 42.3 1.0
N B:CYS163 4.7 50.3 1.0
SG B:CYS158 4.7 49.3 1.0
SG B:CYS225 4.8 56.5 1.0
N B:ALA162 4.8 43.6 1.0
N B:ALA182 4.9 46.3 1.0
C B:CYS163 4.9 52.0 1.0

Iron binding site 4 out of 10 in 6myr

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

b:51.1
occ:1.00
 FE2 B:SF41002 0.0 51.1 1.0
S4 B:SF41002 2.2 44.1 1.0
S3 B:SF41002 2.3 54.1 1.0
S1 B:SF41002 2.3 46.9 1.0
SG B:CYS225 2.3 56.5 1.0
FE1 B:SF41002 2.7 52.0 1.0
FE3 B:SF41002 2.7 45.6 1.0
FE4 B:SF41002 2.8 49.6 1.0
CB B:CYS225 3.3 56.6 1.0
S2 B:SF41002 3.9 47.6 1.0
CA B:CYS225 3.9 55.2 1.0
CD B:PRO226 4.3 50.3 1.0
CD1 B:LEU229 4.5 50.9 1.0
SG B:CYS161 4.6 46.2 1.0
C B:CYS225 4.6 55.2 1.0
CB B:LEU229 4.6 53.1 1.0
SG B:CYS164 4.7 49.6 1.0
N B:PRO226 4.7 54.8 1.0
CB B:LYS227 4.8 51.1 1.0
N B:LYS227 4.8 49.1 1.0
CG B:LEU229 4.8 52.8 1.0
CB B:CYS164 4.9 47.1 1.0
SG B:CYS158 5.0 49.3 1.0

Iron binding site 5 out of 10 in 6myr

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

b:45.6
occ:1.00
 FE3 B:SF41002 0.0 45.6 1.0
S1 B:SF41002 2.2 46.9 1.0
S2 B:SF41002 2.3 47.6 1.0
S4 B:SF41002 2.3 44.1 1.0
SG B:CYS158 2.4 49.3 1.0
FE4 B:SF41002 2.7 49.6 1.0
FE2 B:SF41002 2.7 51.1 1.0
FE1 B:SF41002 2.7 52.0 1.0
CB B:CYS158 3.3 40.7 1.0
CA B:CYS158 3.8 42.5 1.0
S3 B:SF41002 3.9 54.1 1.0
N B:ILE159 3.9 49.4 1.0
N B:LEU160 4.0 49.4 1.0
C B:CYS158 4.2 49.3 1.0
O B:HOH1156 4.3 47.8 1.0
CA B:LEU160 4.6 45.9 1.0
CD1 B:LEU229 4.7 50.9 1.0
N B:CYS161 4.7 43.0 1.0
SG B:CYS164 4.7 49.6 1.0
CB B:ALA182 4.8 40.3 1.0
SG B:CYS161 4.8 46.2 1.0
CE B:MET185 4.8 52.3 1.0
C B:ILE159 4.9 47.6 1.0
SG B:CYS225 4.9 56.5 1.0
CA B:ILE159 4.9 45.2 1.0

Iron binding site 6 out of 10 in 6myr

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

b:49.6
occ:1.00
 FE4 B:SF41002 0.0 49.6 1.0
SG B:CYS161 2.2 46.2 1.0
S2 B:SF41002 2.2 47.6 1.0
S1 B:SF41002 2.3 46.9 1.0
S3 B:SF41002 2.3 54.1 1.0
FE3 B:SF41002 2.7 45.6 1.0
FE1 B:SF41002 2.7 52.0 1.0
FE2 B:SF41002 2.8 51.1 1.0
N B:CYS161 3.5 43.0 1.0
CB B:CYS161 3.5 45.9 1.0
S4 B:SF41002 3.9 44.1 1.0
CA B:CYS161 4.0 44.6 1.0
N B:ALA162 4.0 43.6 1.0
N B:CYS163 4.3 50.3 1.0
CG1 B:ILE159 4.3 45.6 1.0
C B:CYS161 4.4 47.3 1.0
CD B:PRO226 4.4 50.3 1.0
N B:LEU160 4.4 49.4 1.0
C B:LEU160 4.6 45.8 1.0
CB B:CYS163 4.7 49.7 1.0
SG B:CYS158 4.7 49.3 1.0
CA B:LEU160 4.7 45.9 1.0
CG B:PRO226 4.8 48.5 1.0
SG B:CYS164 4.8 49.6 1.0
SG B:CYS225 4.8 56.5 1.0
N B:ILE159 4.8 49.4 1.0
N B:CYS164 4.9 52.2 1.0
CA B:ALA162 4.9 47.5 1.0
C B:ILE159 5.0 47.6 1.0

Iron binding site 7 out of 10 in 6myr

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

b:51.5
occ:1.00
 FE1 B:F3S1003 0.0 51.5 1.0
SG B:CYS168 2.2 49.6 1.0
S1 B:F3S1003 2.2 50.9 1.0
S3 B:F3S1003 2.3 52.0 1.0
S2 B:F3S1003 2.3 56.1 1.0
FE3 B:F3S1003 2.6 49.4 1.0
FE4 B:F3S1003 2.7 49.9 1.0
CB B:CYS168 3.3 49.0 1.0
S4 B:F3S1003 3.9 44.9 1.0
CA B:CYS168 4.1 50.2 1.0
OH B:TYR178 4.3 42.8 1.0
CB B:ILE218 4.5 54.1 1.0
SG B:CYS215 4.7 44.6 1.0
SG B:CYS221 4.8 52.2 1.0
N B:ILE218 4.8 53.3 1.0
N B:MET219 4.9 53.8 1.0
C B:CYS168 4.9 52.6 1.0
CD1 B:ILE218 4.9 51.2 1.0
CE2 B:TYR178 4.9 41.4 1.0
CB B:SER170 5.0 54.0 1.0

Iron binding site 8 out of 10 in 6myr

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

b:49.4
occ:1.00
 FE3 B:F3S1003 0.0 49.4 1.0
S1 B:F3S1003 2.2 50.9 1.0
S4 B:F3S1003 2.3 44.9 1.0
S3 B:F3S1003 2.3 52.0 1.0
SG B:CYS221 2.4 52.2 1.0
FE1 B:F3S1003 2.6 51.5 1.0
FE4 B:F3S1003 2.7 49.9 1.0
CB B:CYS221 3.4 53.2 1.0
N B:MET219 3.9 53.8 1.0
S2 B:F3S1003 3.9 56.1 1.0
N B:CYS221 3.9 54.6 1.0
CA B:MET219 4.1 48.1 1.0
CA B:CYS221 4.3 53.9 1.0
N B:ASN220 4.5 45.7 1.0
SG B:CYS168 4.6 49.6 1.0
C B:MET219 4.6 48.5 1.0
CB B:PRO181 4.7 49.7 1.0
SG B:CYS215 4.7 44.6 1.0
CG B:PRO181 4.7 47.2 1.0
CA B:GLY232 4.8 52.5 1.0
N B:ILE218 4.9 53.3 1.0
CD1 B:ILE235 4.9 46.5 1.0

Iron binding site 9 out of 10 in 6myr

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

b:49.9
occ:1.00
 FE4 B:F3S1003 0.0 49.9 1.0
SG B:CYS215 2.2 44.6 1.0
S4 B:F3S1003 2.2 44.9 1.0
S2 B:F3S1003 2.3 56.1 1.0
S3 B:F3S1003 2.3 52.0 1.0
FE1 B:F3S1003 2.7 51.5 1.0
FE3 B:F3S1003 2.7 49.4 1.0
CB B:CYS215 3.3 43.6 1.0
N B:THR217 3.7 49.5 1.0
CA B:CYS215 3.8 48.3 1.0
OH B:TYR178 3.9 42.8 1.0
S1 B:F3S1003 4.0 50.9 1.0
N B:HIS216 4.0 50.3 1.0
CA B:THR217 4.1 49.8 1.0
C B:CYS215 4.2 48.8 1.0
N B:ILE218 4.2 53.3 1.0
CD1 B:ILE235 4.3 46.5 1.0
O B:HOH1144 4.3 46.8 1.0
SG B:CYS168 4.6 49.6 1.0
C B:THR217 4.7 51.2 1.0
C B:HIS216 4.8 54.4 1.0
N B:MET219 4.9 53.8 1.0
SG B:CYS221 4.9 52.2 1.0

Iron binding site 10 out of 10 in 6myr

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

b:54.4
occ:1.00
 FE C:HEM201 0.0 54.4 1.0
NA C:HEM201 2.0 52.1 1.0
NE2 D:HIS46 2.0 54.4 1.0
NB C:HEM201 2.1 59.1 1.0
NC C:HEM201 2.1 52.6 1.0
NE2 C:HIS98 2.1 53.9 1.0
ND C:HEM201 2.1 54.5 1.0
CD2 C:HIS98 3.0 54.8 1.0
C4A C:HEM201 3.0 54.9 1.0
CE1 D:HIS46 3.0 55.8 1.0
C1A C:HEM201 3.0 57.6 1.0
CD2 D:HIS46 3.1 57.9 1.0
C1B C:HEM201 3.1 57.2 1.0
C4B C:HEM201 3.1 60.1 1.0
C4D C:HEM201 3.1 53.5 1.0
C4C C:HEM201 3.1 57.6 1.0
C1C C:HEM201 3.1 59.6 1.0
C1D C:HEM201 3.1 53.8 1.0
CE1 C:HIS98 3.1 52.8 1.0
CHB C:HEM201 3.4 54.8 1.0
CHA C:HEM201 3.4 53.5 1.0
CHC C:HEM201 3.5 58.5 1.0
CHD C:HEM201 3.5 53.5 1.0
ND1 D:HIS46 4.1 56.9 1.0
CG C:HIS98 4.1 54.5 1.0
CG D:HIS46 4.2 56.6 1.0
ND1 C:HIS98 4.2 54.5 1.0
C3A C:HEM201 4.2 53.6 1.0
C2A C:HEM201 4.2 53.5 1.0
C2B C:HEM201 4.3 60.7 1.0
C3B C:HEM201 4.3 62.6 1.0
C3D C:HEM201 4.3 55.8 1.0
C2D C:HEM201 4.3 53.0 1.0
C3C C:HEM201 4.3 62.9 1.0
C2C C:HEM201 4.3 61.9 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: Sun Dec 13 16:44:25 2020

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