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Iron in PDB 6myt: Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket

Enzymatic activity of Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket

All present enzymatic activity of Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket:
1.3.5.1;

Protein crystallography data

The structure of Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket, PDB code: 6myt 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) 25.19 / 2.27
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 69.992, 83.817, 290.344, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 26

Other elements in 6myt:

The structure of Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket also contains other interesting chemical elements:

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

Iron Binding Sites:

The binding sites of Iron atom in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket (pdb code 6myt). 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 Atpenin A5 Bound, Sidechain in Pocket, PDB code: 6myt:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 6myt

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Iron binding site 1 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:45.8
occ:1.00
 FE1 B:FES1001 0.0 45.8 1.0
SG B:CYS73 2.2 48.0 1.0
S2 B:FES1001 2.2 48.9 1.0
S1 B:FES1001 2.2 45.0 1.0
SG B:CYS85 2.2 50.7 1.0
FE2 B:FES1001 3.0 41.2 1.0
CB B:CYS85 3.2 46.8 1.0
CB B:CYS73 3.4 44.8 1.0
N B:CYS73 4.0 39.0 1.0
N B:CYS85 4.1 49.7 1.0
CA B:CYS73 4.3 45.2 1.0
CA B:CYS85 4.3 47.8 1.0
SG B:CYS65 4.3 49.4 1.0
N B:GLY68 4.3 39.7 1.0
CB B:LEU83 4.4 43.3 1.0
CA B:GLY68 4.6 39.0 1.0
CA B:ARG66 4.6 57.1 1.0
N B:ARG66 4.6 54.8 1.0
N B:SER72 4.7 50.6 1.0
CD2 B:LEU83 4.8 40.8 1.0
CD2 B:LEU45 4.8 58.0 1.0
N B:GLU67 4.8 50.1 1.0
SG B:CYS70 4.9 46.4 1.0
CD1 B:LEU83 4.9 37.9 1.0
CG B:LEU83 4.9 41.2 1.0
C B:CYS73 4.9 46.2 1.0
N B:ALA84 5.0 46.7 1.0

Iron binding site 2 out of 10 in 6myt

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Iron binding site 2 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:41.2
occ:1.00
 FE2 B:FES1001 0.0 41.2 1.0
SG B:CYS65 2.1 49.4 1.0
S1 B:FES1001 2.2 45.0 1.0
S2 B:FES1001 2.2 48.9 1.0
SG B:CYS70 2.2 46.4 1.0
FE1 B:FES1001 3.0 45.8 1.0
CB B:CYS65 3.2 46.0 1.0
CB B:CYS70 3.4 41.6 1.0
N B:CYS65 3.4 45.7 1.0
N B:CYS70 3.6 45.2 1.0
N B:GLY71 3.6 45.9 1.0
CA B:CYS65 3.7 45.6 1.0
N B:ARG66 3.8 54.8 1.0
CA B:CYS70 3.8 43.7 1.0
N B:SER72 4.1 50.6 1.0
C B:CYS65 4.1 50.9 1.0
C B:CYS70 4.1 46.8 1.0
N B:GLY68 4.3 39.7 1.0
N B:ILE69 4.4 50.8 1.0
SG B:CYS85 4.4 50.7 1.0
C B:SER64 4.5 47.4 1.0
N B:GLU67 4.5 50.1 1.0
CA B:GLY71 4.6 46.6 1.0
N B:SER64 4.6 50.3 1.0
CA B:ARG66 4.7 57.1 1.0
CB B:SER72 4.7 47.4 1.0
OG B:SER72 4.7 50.2 1.0
CA B:GLY68 4.7 39.0 1.0
C B:ILE69 4.7 37.8 1.0
C B:GLY71 4.8 49.8 1.0
CB B:SER64 4.9 55.3 1.0
CA B:SER64 4.9 49.4 1.0
C B:GLY68 4.9 52.1 1.0
SG B:CYS73 4.9 48.0 1.0
CA B:SER72 5.0 49.2 1.0

Iron binding site 3 out of 10 in 6myt

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Iron binding site 3 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:45.7
occ:1.00
 FE1 B:SF41002 0.0 45.7 1.0
SG B:CYS164 2.2 47.9 1.0
S3 B:SF41002 2.3 48.3 1.0
S4 B:SF41002 2.3 37.9 1.0
S2 B:SF41002 2.3 34.9 1.0
FE2 B:SF41002 2.7 42.6 1.0
FE4 B:SF41002 2.7 45.8 1.0
FE3 B:SF41002 2.8 41.3 1.0
CB B:CYS164 3.1 42.4 1.0
N B:CYS164 3.8 44.8 1.0
S1 B:SF41002 3.9 39.1 1.0
CA B:CYS164 4.0 37.6 1.0
CB B:ALA182 4.2 42.6 1.0
CA B:ALA182 4.5 33.4 1.0
SG B:CYS161 4.6 40.0 1.0
SG B:CYS158 4.6 49.1 1.0
N B:CYS163 4.7 39.6 1.0
SG B:CYS225 4.8 46.0 1.0
N B:SER165 4.9 38.5 1.0
N B:ALA162 4.9 40.7 1.0
C B:CYS163 4.9 44.9 1.0
C B:CYS164 5.0 36.1 1.0

Iron binding site 4 out of 10 in 6myt

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Iron binding site 4 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:42.6
occ:1.00
 FE2 B:SF41002 0.0 42.6 1.0
S4 B:SF41002 2.3 37.9 1.0
S3 B:SF41002 2.3 48.3 1.0
S1 B:SF41002 2.3 39.1 1.0
SG B:CYS225 2.3 46.0 1.0
FE1 B:SF41002 2.7 45.7 1.0
FE3 B:SF41002 2.7 41.3 1.0
FE4 B:SF41002 2.7 45.8 1.0
CB B:CYS225 3.3 44.3 1.0
S2 B:SF41002 3.9 34.9 1.0
CA B:CYS225 4.0 45.0 1.0
CD B:PRO226 4.4 47.8 1.0
CD1 B:LEU229 4.5 38.4 1.0
CB B:LEU229 4.6 37.4 1.0
C B:CYS225 4.6 46.9 1.0
CB B:LYS227 4.6 53.1 1.0
SG B:CYS161 4.7 40.0 1.0
SG B:CYS164 4.7 47.9 1.0
CG B:LEU229 4.7 39.2 1.0
N B:PRO226 4.8 49.7 1.0
CB B:CYS164 4.8 42.4 1.0
N B:LYS227 4.8 47.4 1.0
SG B:CYS158 4.9 49.1 1.0

Iron binding site 5 out of 10 in 6myt

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Iron binding site 5 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:41.3
occ:1.00
 FE3 B:SF41002 0.0 41.3 1.0
SG B:CYS158 2.2 49.1 1.0
S1 B:SF41002 2.3 39.1 1.0
S2 B:SF41002 2.3 34.9 1.0
S4 B:SF41002 2.3 37.9 1.0
FE4 B:SF41002 2.7 45.8 1.0
FE2 B:SF41002 2.7 42.6 1.0
FE1 B:SF41002 2.8 45.7 1.0
CB B:CYS158 3.2 44.6 1.0
CA B:CYS158 3.6 46.7 1.0
S3 B:SF41002 3.9 48.3 1.0
N B:ILE159 3.9 47.2 1.0
N B:LEU160 4.1 47.2 1.0
C B:CYS158 4.2 47.9 1.0
O B:HOH1110 4.2 36.3 1.0
CE B:MET185 4.6 49.3 1.0
CD1 B:LEU229 4.6 38.4 1.0
CA B:LEU160 4.7 48.7 1.0
SG B:CYS164 4.7 47.9 1.0
N B:CYS161 4.9 43.1 1.0
SG B:CYS225 4.9 46.0 1.0
SG B:CYS161 4.9 40.0 1.0
N B:CYS158 4.9 44.0 1.0
C B:ILE159 5.0 48.8 1.0

Iron binding site 6 out of 10 in 6myt

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Iron binding site 6 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:45.8
occ:1.00
 FE4 B:SF41002 0.0 45.8 1.0
SG B:CYS161 2.3 40.0 1.0
S1 B:SF41002 2.3 39.1 1.0
S2 B:SF41002 2.3 34.9 1.0
S3 B:SF41002 2.3 48.3 1.0
FE3 B:SF41002 2.7 41.3 1.0
FE1 B:SF41002 2.7 45.7 1.0
FE2 B:SF41002 2.7 42.6 1.0
N B:CYS161 3.6 43.1 1.0
CB B:CYS161 3.6 45.4 1.0
S4 B:SF41002 3.9 37.9 1.0
CA B:CYS161 4.1 43.9 1.0
N B:ALA162 4.1 40.7 1.0
N B:CYS163 4.3 39.6 1.0
CG1 B:ILE159 4.3 42.6 1.0
N B:LEU160 4.4 47.2 1.0
C B:CYS161 4.4 42.2 1.0
CD B:PRO226 4.5 47.8 1.0
SG B:CYS158 4.6 49.1 1.0
C B:LEU160 4.6 48.0 1.0
SG B:CYS225 4.7 46.0 1.0
CB B:CYS163 4.7 43.7 1.0
N B:ILE159 4.8 47.2 1.0
SG B:CYS164 4.8 47.9 1.0
CA B:LEU160 4.8 48.7 1.0
N B:CYS164 4.9 44.8 1.0
CG B:PRO226 4.9 46.5 1.0

Iron binding site 7 out of 10 in 6myt

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Iron binding site 7 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:44.5
occ:1.00
 FE1 B:F3S1003 0.0 44.5 1.0
SG B:CYS168 2.1 50.2 1.0
S1 B:F3S1003 2.2 40.7 1.0
S2 B:F3S1003 2.3 44.0 1.0
S3 B:F3S1003 2.3 42.2 1.0
FE3 B:F3S1003 2.7 41.6 1.0
FE4 B:F3S1003 2.7 41.4 1.0
CB B:CYS168 3.1 48.4 1.0
CA B:CYS168 3.9 49.0 1.0
S4 B:F3S1003 4.0 37.7 1.0
OH B:TYR178 4.2 38.7 1.0
CB B:ILE218 4.6 37.2 1.0
CD B:PRO169 4.7 44.2 1.0
C B:CYS168 4.7 45.1 1.0
SG B:CYS221 4.8 43.7 1.0
CD1 B:ILE218 4.8 37.5 1.0
SG B:CYS215 4.8 39.3 1.0
N B:PRO169 4.9 44.2 1.0
N B:MET219 5.0 51.3 1.0
CE2 B:TYR178 5.0 33.2 1.0

Iron binding site 8 out of 10 in 6myt

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Iron binding site 8 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:41.6
occ:1.00
 FE3 B:F3S1003 0.0 41.6 1.0
S1 B:F3S1003 2.2 40.7 1.0
S4 B:F3S1003 2.3 37.7 1.0
S3 B:F3S1003 2.3 42.2 1.0
SG B:CYS221 2.3 43.7 1.0
FE1 B:F3S1003 2.7 44.5 1.0
FE4 B:F3S1003 2.7 41.4 1.0
CB B:CYS221 3.3 42.3 1.0
N B:CYS221 3.9 42.7 1.0
N B:MET219 3.9 51.3 1.0
S2 B:F3S1003 3.9 44.0 1.0
CA B:MET219 4.1 48.5 1.0
CA B:CYS221 4.2 44.6 1.0
N B:ASN220 4.4 43.4 1.0
CB B:PRO181 4.6 46.4 1.0
C B:MET219 4.6 40.7 1.0
SG B:CYS168 4.6 50.2 1.0
SG B:CYS215 4.7 39.3 1.0
CA B:GLY232 4.7 40.2 1.0
CG B:PRO181 4.7 33.3 1.0
CD1 B:ILE235 5.0 39.1 1.0
N B:ILE218 5.0 43.6 1.0

Iron binding site 9 out of 10 in 6myt

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Iron binding site 9 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:41.4
occ:1.00
 FE4 B:F3S1003 0.0 41.4 1.0
SG B:CYS215 2.2 39.3 1.0
S4 B:F3S1003 2.3 37.7 1.0
S2 B:F3S1003 2.3 44.0 1.0
S3 B:F3S1003 2.3 42.2 1.0
FE3 B:F3S1003 2.7 41.6 1.0
FE1 B:F3S1003 2.7 44.5 1.0
CB B:CYS215 3.2 35.6 1.0
CA B:CYS215 3.6 39.7 1.0
N B:THR217 3.8 40.4 1.0
S1 B:F3S1003 3.9 40.7 1.0
OH B:TYR178 4.0 38.7 1.0
N B:HIS216 4.1 40.5 1.0
C B:CYS215 4.1 40.4 1.0
CA B:THR217 4.2 38.7 1.0
N B:ILE218 4.2 43.6 1.0
CD1 B:ILE235 4.3 39.1 1.0
SG B:CYS168 4.4 50.2 1.0
C B:THR217 4.7 38.1 1.0
N B:MET219 4.8 51.3 1.0
SG B:CYS221 4.8 43.7 1.0
C B:HIS216 4.8 47.6 1.0
O B:HOH1113 4.9 36.5 1.0
N B:CYS215 5.0 35.3 1.0

Iron binding site 10 out of 10 in 6myt

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Iron binding site 10 out of 10 in the Avian Mitochondrial Complex II with Atpenin A5 Bound, Sidechain in Pocket


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 Atpenin A5 Bound, Sidechain in Pocket within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:43.9
occ:1.00
 FE C:HEM201 0.0 43.9 1.0
NE2 C:HIS98 1.9 41.9 1.0
NA C:HEM201 2.0 50.0 1.0
NB C:HEM201 2.0 52.4 1.0
NC C:HEM201 2.1 45.5 1.0
ND C:HEM201 2.1 49.7 1.0
NE2 D:HIS46 2.2 42.2 1.0
CE1 C:HIS98 2.9 45.6 1.0
CD2 C:HIS98 2.9 46.0 1.0
CE1 D:HIS46 3.0 45.1 1.0
C1A C:HEM201 3.0 51.9 1.0
C4A C:HEM201 3.0 50.3 1.0
C4B C:HEM201 3.1 47.2 1.0
C1B C:HEM201 3.1 49.6 1.0
C4D C:HEM201 3.1 50.0 1.0
C1C C:HEM201 3.1 47.6 1.0
C1D C:HEM201 3.1 50.9 1.0
C4C C:HEM201 3.1 50.2 1.0
CD2 D:HIS46 3.2 45.9 1.0
CHA C:HEM201 3.4 51.1 1.0
CHB C:HEM201 3.4 49.4 1.0
CHC C:HEM201 3.4 47.1 1.0
CHD C:HEM201 3.5 52.1 1.0
ND1 C:HIS98 4.0 46.5 1.0
CG C:HIS98 4.0 45.5 1.0
ND1 D:HIS46 4.2 45.0 1.0
C2A C:HEM201 4.2 53.0 1.0
C3A C:HEM201 4.2 52.1 1.0
C3B C:HEM201 4.3 52.4 1.0
C2B C:HEM201 4.3 50.1 1.0
CG D:HIS46 4.3 44.0 1.0
C2D C:HEM201 4.3 56.7 1.0
C3D C:HEM201 4.3 57.0 1.0
C2C C:HEM201 4.3 48.7 1.0
C3C C:HEM201 4.3 48.9 1.0
NE2 C:HIS42 4.9 42.2 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 02:30:16 2024

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