Iron in PDB 6myu: Avian Mitochondrial Complex II Crystallized in the Presence of Hqno

Enzymatic activity of Avian Mitochondrial Complex II Crystallized in the Presence of Hqno

All present enzymatic activity of Avian Mitochondrial Complex II Crystallized in the Presence of Hqno:
1.3.5.1;

Protein crystallography data

The structure of Avian Mitochondrial Complex II Crystallized in the Presence of Hqno, PDB code: 6myu 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) 47.78 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.029, 83.958, 290.540, 90.00, 90.00, 90.00
R / Rfree (%) 19.9 / 22.3

Other elements in 6myu:

The structure of Avian Mitochondrial Complex II Crystallized in the Presence of Hqno 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 Crystallized in the Presence of Hqno (pdb code 6myu). 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 Crystallized in the Presence of Hqno, PDB code: 6myu:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 6myu

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Iron binding site 1 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:35.6
occ:1.00
FE1 B:FES1001 0.0 35.6 1.0
S2 B:FES1001 2.2 34.7 1.0
S1 B:FES1001 2.2 35.0 1.0
SG B:CYS85 2.2 35.5 1.0
SG B:CYS73 2.4 37.2 1.0
FE2 B:FES1001 2.8 33.8 1.0
CB B:CYS85 3.3 40.6 1.0
CB B:CYS73 3.5 36.6 1.0
N B:CYS73 4.0 34.2 1.0
N B:CYS85 4.2 41.7 1.0
SG B:CYS65 4.2 37.4 1.0
N B:GLY68 4.3 38.6 1.0
CB B:LEU83 4.3 34.4 1.0
CA B:CYS85 4.3 40.8 1.0
CA B:CYS73 4.3 34.6 1.0
CA B:GLY68 4.4 36.8 1.0
N B:ARG66 4.6 44.8 1.0
CA B:ARG66 4.6 48.5 1.0
CD1 B:LEU83 4.7 30.8 1.0
N B:SER72 4.8 31.1 1.0
SG B:CYS70 4.8 35.5 1.0
CD2 B:LEU45 4.8 36.6 1.0
CG B:LEU83 4.9 31.1 1.0
CD2 B:LEU83 4.9 30.9 1.0

Iron binding site 2 out of 10 in 6myu

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Iron binding site 2 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1001

b:33.8
occ:1.00
FE2 B:FES1001 0.0 33.8 1.0
SG B:CYS65 2.2 37.4 1.0
S1 B:FES1001 2.2 35.0 1.0
S2 B:FES1001 2.2 34.7 1.0
SG B:CYS70 2.3 35.5 1.0
FE1 B:FES1001 2.8 35.6 1.0
CB B:CYS65 3.4 38.4 1.0
N B:CYS70 3.5 34.2 1.0
N B:CYS65 3.5 36.6 1.0
CB B:CYS70 3.5 30.6 1.0
N B:GLY71 3.7 30.0 1.0
CA B:CYS70 3.9 30.6 1.0
CA B:CYS65 3.9 36.3 1.0
N B:ARG66 3.9 44.8 1.0
N B:SER72 3.9 31.1 1.0
C B:CYS70 4.1 30.3 1.0
SG B:CYS85 4.2 35.5 1.0
N B:GLY68 4.3 38.6 1.0
C B:CYS65 4.3 40.8 1.0
N B:ILE69 4.3 35.9 1.0
CB B:SER72 4.5 32.1 1.0
CA B:GLY68 4.6 36.8 1.0
C B:SER64 4.6 39.3 1.0
N B:SER64 4.6 37.8 1.0
CA B:GLY71 4.6 29.8 1.0
C B:ILE69 4.7 32.6 1.0
N B:GLU67 4.7 45.8 1.0
CA B:ARG66 4.7 48.5 1.0
C B:GLY71 4.7 33.2 1.0
CA B:SER72 4.8 31.5 1.0
C B:GLY68 4.8 37.0 1.0
OG B:SER72 4.8 39.1 1.0
N B:CYS73 4.8 34.2 1.0
SG B:CYS73 4.9 37.2 1.0

Iron binding site 3 out of 10 in 6myu

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Iron binding site 3 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:33.2
occ:1.00
FE1 B:SF41002 0.0 33.2 1.0
S3 B:SF41002 2.2 33.1 1.0
SG B:CYS164 2.2 32.5 1.0
S4 B:SF41002 2.3 33.7 1.0
S2 B:SF41002 2.3 27.4 1.0
FE2 B:SF41002 2.6 33.0 1.0
FE3 B:SF41002 2.7 34.7 1.0
FE4 B:SF41002 2.8 34.8 1.0
CB B:CYS164 3.2 31.4 1.0
S1 B:SF41002 3.8 32.8 1.0
N B:CYS164 3.8 31.4 1.0
CB B:ALA182 4.0 26.9 1.0
CA B:CYS164 4.1 33.8 1.0
CA B:ALA182 4.4 26.6 1.0
SG B:CYS161 4.6 34.4 1.0
SG B:CYS158 4.7 32.7 1.0
SG B:CYS225 4.7 35.1 1.0
N B:ALA182 4.8 26.8 1.0
N B:CYS163 4.8 28.9 1.0
N B:ALA162 4.9 30.4 1.0
N B:SER165 5.0 31.4 1.0

Iron binding site 4 out of 10 in 6myu

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Iron binding site 4 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:33.0
occ:1.00
FE2 B:SF41002 0.0 33.0 1.0
S3 B:SF41002 2.2 33.1 1.0
S4 B:SF41002 2.2 33.7 1.0
SG B:CYS225 2.3 35.1 1.0
S1 B:SF41002 2.3 32.8 1.0
FE1 B:SF41002 2.6 33.2 1.0
FE3 B:SF41002 2.8 34.7 1.0
FE4 B:SF41002 2.8 34.8 1.0
CB B:CYS225 3.3 35.0 1.0
S2 B:SF41002 3.9 27.4 1.0
CA B:CYS225 3.9 35.0 1.0
CD B:PRO226 4.2 39.7 1.0
CD1 B:LEU229 4.5 29.8 1.0
C B:CYS225 4.6 36.3 1.0
CB B:LEU229 4.6 34.6 1.0
SG B:CYS164 4.6 32.5 1.0
CG B:LEU229 4.7 31.2 1.0
N B:PRO226 4.7 39.9 1.0
SG B:CYS161 4.7 34.4 1.0
CB B:LYS227 4.7 37.8 1.0
CB B:CYS164 4.8 31.4 1.0
N B:LYS227 4.8 38.1 1.0
CG B:PRO226 5.0 40.2 1.0

Iron binding site 5 out of 10 in 6myu

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Iron binding site 5 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno 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 32.8 1.0
S2 B:SF41002 2.3 27.4 1.0
S4 B:SF41002 2.4 33.7 1.0
SG B:CYS158 2.4 32.7 1.0
FE4 B:SF41002 2.7 34.8 1.0
FE1 B:SF41002 2.7 33.2 1.0
FE2 B:SF41002 2.8 33.0 1.0
CB B:CYS158 3.3 31.1 1.0
CA B:CYS158 3.7 32.7 1.0
S3 B:SF41002 3.8 33.1 1.0
N B:ILE159 3.9 36.8 1.0
N B:LEU160 4.0 35.4 1.0
O B:HOH1141 4.2 30.5 1.0
C B:CYS158 4.2 36.2 1.0
CA B:LEU160 4.6 36.1 1.0
CD1 B:LEU229 4.6 29.8 1.0
SG B:CYS164 4.7 32.5 1.0
N B:CYS161 4.8 32.5 1.0
CB B:ALA182 4.8 26.9 1.0
SG B:CYS161 4.8 34.4 1.0
CE B:MET185 4.8 33.8 1.0
SG B:CYS225 4.9 35.1 1.0
C B:ILE159 4.9 34.6 1.0
CA B:ILE159 5.0 33.4 1.0

Iron binding site 6 out of 10 in 6myu

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Iron binding site 6 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:34.8
occ:1.00
FE4 B:SF41002 0.0 34.8 1.0
S2 B:SF41002 2.2 27.4 1.0
SG B:CYS161 2.2 34.4 1.0
S1 B:SF41002 2.3 32.8 1.0
S3 B:SF41002 2.3 33.1 1.0
FE3 B:SF41002 2.7 34.7 1.0
FE1 B:SF41002 2.8 33.2 1.0
FE2 B:SF41002 2.8 33.0 1.0
N B:CYS161 3.6 32.5 1.0
CB B:CYS161 3.6 34.3 1.0
S4 B:SF41002 3.9 33.7 1.0
N B:ALA162 4.0 30.4 1.0
CA B:CYS161 4.0 34.4 1.0
N B:CYS163 4.3 28.9 1.0
CD B:PRO226 4.3 39.7 1.0
CG1 B:ILE159 4.3 32.6 1.0
C B:CYS161 4.4 33.2 1.0
N B:LEU160 4.5 35.4 1.0
CG B:PRO226 4.5 40.2 1.0
CB B:CYS163 4.6 34.3 1.0
C B:LEU160 4.6 35.9 1.0
SG B:CYS158 4.7 32.7 1.0
SG B:CYS225 4.7 35.1 1.0
SG B:CYS164 4.7 32.5 1.0
N B:CYS164 4.8 31.4 1.0
CA B:LEU160 4.8 36.1 1.0
N B:ILE159 4.8 36.8 1.0
CA B:ALA162 4.9 31.7 1.0
CA B:CYS163 5.0 31.5 1.0

Iron binding site 7 out of 10 in 6myu

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Iron binding site 7 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:36.9
occ:1.00
FE1 B:F3S1003 0.0 36.9 1.0
S1 B:F3S1003 2.2 33.1 1.0
SG B:CYS168 2.3 34.9 1.0
S3 B:F3S1003 2.3 31.9 1.0
S2 B:F3S1003 2.3 34.5 1.0
FE3 B:F3S1003 2.7 35.9 1.0
FE4 B:F3S1003 2.7 34.0 1.0
CB B:CYS168 3.1 37.5 1.0
S4 B:F3S1003 3.9 34.8 1.0
CA B:CYS168 4.0 38.5 1.0
OH B:TYR178 4.2 32.0 1.0
CB B:ILE218 4.6 31.5 1.0
CD1 B:ILE218 4.7 29.1 1.0
C B:CYS168 4.7 34.8 1.0
SG B:CYS221 4.8 33.9 1.0
CE2 B:TYR178 4.8 30.4 1.0
SG B:CYS215 4.8 30.2 1.0
CB B:SER170 4.9 37.8 1.0
N B:ILE218 4.9 32.5 1.0
CD B:PRO169 5.0 32.6 1.0
CZ B:TYR178 5.0 32.4 1.0
N B:PRO169 5.0 32.8 1.0
CD B:PRO181 5.0 29.9 1.0
N B:MET219 5.0 33.6 1.0

Iron binding site 8 out of 10 in 6myu

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Iron binding site 8 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:35.9
occ:1.00
FE3 B:F3S1003 0.0 35.9 1.0
S1 B:F3S1003 2.2 33.1 1.0
S4 B:F3S1003 2.3 34.8 1.0
SG B:CYS221 2.3 33.9 1.0
S3 B:F3S1003 2.3 31.9 1.0
FE1 B:F3S1003 2.7 36.9 1.0
FE4 B:F3S1003 2.7 34.0 1.0
CB B:CYS221 3.4 31.1 1.0
N B:MET219 3.9 33.6 1.0
S2 B:F3S1003 3.9 34.5 1.0
N B:CYS221 3.9 31.6 1.0
CA B:MET219 4.1 34.1 1.0
CA B:CYS221 4.3 31.6 1.0
N B:ASN220 4.4 31.9 1.0
C B:MET219 4.6 33.3 1.0
CB B:PRO181 4.7 28.6 1.0
SG B:CYS168 4.7 34.9 1.0
CB B:CYS168 4.8 37.5 1.0
CA B:GLY232 4.8 34.4 1.0
CG B:PRO181 4.8 29.1 1.0
SG B:CYS215 4.8 30.2 1.0
N B:ILE218 4.9 32.5 1.0

Iron binding site 9 out of 10 in 6myu

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Iron binding site 9 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:34.0
occ:1.00
FE4 B:F3S1003 0.0 34.0 1.0
S4 B:F3S1003 2.3 34.8 1.0
S2 B:F3S1003 2.3 34.5 1.0
SG B:CYS215 2.3 30.2 1.0
S3 B:F3S1003 2.3 31.9 1.0
FE1 B:F3S1003 2.7 36.9 1.0
FE3 B:F3S1003 2.7 35.9 1.0
CB B:CYS215 3.4 30.9 1.0
N B:THR217 3.8 34.5 1.0
CA B:CYS215 3.8 32.2 1.0
OH B:TYR178 3.9 32.0 1.0
S1 B:F3S1003 3.9 33.1 1.0
CA B:THR217 4.1 32.3 1.0
N B:HIS216 4.2 36.0 1.0
O B:HOH1186 4.2 33.5 1.0
N B:ILE218 4.2 32.5 1.0
C B:CYS215 4.3 34.9 1.0
CD1 B:ILE235 4.4 35.9 1.0
C B:THR217 4.6 33.4 1.0
SG B:CYS168 4.7 34.9 1.0
C B:HIS216 4.8 38.1 1.0
SG B:CYS221 4.8 33.9 1.0
N B:MET219 4.9 33.6 1.0

Iron binding site 10 out of 10 in 6myu

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Iron binding site 10 out of 10 in the Avian Mitochondrial Complex II Crystallized in the Presence of Hqno


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 Crystallized in the Presence of Hqno within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe201

b:36.4
occ:1.00
FE C:HEM201 0.0 36.4 1.0
NE2 D:HIS46 2.0 38.5 1.0
NE2 C:HIS98 2.0 35.9 1.0
NA C:HEM201 2.0 39.1 1.0
NC C:HEM201 2.0 40.7 1.0
ND C:HEM201 2.1 37.4 1.0
NB C:HEM201 2.1 40.1 1.0
CE1 D:HIS46 2.9 38.9 1.0
CD2 C:HIS98 2.9 37.1 1.0
C1A C:HEM201 3.0 41.9 1.0
CE1 C:HIS98 3.0 36.5 1.0
C1C C:HEM201 3.0 41.8 1.0
C4C C:HEM201 3.1 41.7 1.0
C4A C:HEM201 3.1 39.1 1.0
C4B C:HEM201 3.1 38.9 1.0
CD2 D:HIS46 3.1 40.3 1.0
C1D C:HEM201 3.1 36.3 1.0
C4D C:HEM201 3.1 40.9 1.0
C1B C:HEM201 3.1 38.9 1.0
CHC C:HEM201 3.4 41.8 1.0
CHA C:HEM201 3.4 40.8 1.0
CHD C:HEM201 3.4 37.4 1.0
CHB C:HEM201 3.5 38.5 1.0
ND1 D:HIS46 4.0 39.3 1.0
CG C:HIS98 4.1 36.4 1.0
ND1 C:HIS98 4.1 36.9 1.0
CG D:HIS46 4.2 39.3 1.0
C2A C:HEM201 4.2 40.3 1.0
C3A C:HEM201 4.3 39.0 1.0
C2C C:HEM201 4.3 42.8 1.0
C3C C:HEM201 4.3 42.9 1.0
C2D C:HEM201 4.3 39.5 1.0
C3B C:HEM201 4.3 38.8 1.0
C3D C:HEM201 4.3 43.4 1.0
C2B C:HEM201 4.4 41.1 1.0
NE2 C:HIS42 4.9 37.2 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: Sun Dec 13 16:44:27 2020

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