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Iron in PDB 2fbw: Avian Respiratory Complex II with Carboxin Bound

Enzymatic activity of Avian Respiratory Complex II with Carboxin Bound

All present enzymatic activity of Avian Respiratory Complex II with Carboxin Bound:
1.3.5.1;

Protein crystallography data

The structure of Avian Respiratory Complex II with Carboxin Bound, PDB code: 2fbw was solved by L.S.Huang, G.Sun, D.Cobessi, A.C.Wang, J.T.Shen, E.Y.Tung, V.E.Anderson, E.A.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 64.09 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 118.700, 200.753, 67.631, 90.00, 90.06, 90.00
R / Rfree (%) 18.7 / 22.7

Other elements in 2fbw:

The structure of Avian Respiratory Complex II with Carboxin Bound also contains other interesting chemical elements:

Potassium (K) 4 atoms

Iron Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20;

Binding sites:

The binding sites of Iron atom in the Avian Respiratory Complex II with Carboxin Bound (pdb code 2fbw). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 20 binding sites of Iron where determined in the Avian Respiratory Complex II with Carboxin Bound, PDB code: 2fbw:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 2fbw

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Iron binding site 1 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:17.8
occ:1.00
 FE1 B:FES1002 0.0 17.8 1.0
S2 B:FES1002 2.2 16.4 1.0
S1 B:FES1002 2.2 16.4 1.0
SG B:CYS73 2.2 18.4 1.0
SG B:CYS85 2.2 19.3 1.0
FE2 B:FES1002 2.8 14.8 1.0
CB B:CYS85 3.2 17.6 1.0
CB B:CYS73 3.5 17.9 1.0
N B:CYS73 3.9 13.6 1.0
N B:CYS85 4.1 19.3 1.0
SG B:CYS65 4.2 15.3 1.0
CA B:CYS73 4.3 15.5 1.0
CA B:CYS85 4.3 19.9 1.0
N B:GLY68 4.5 19.3 1.0
CB B:LEU83 4.5 12.2 1.0
CA B:GLY68 4.5 14.2 1.0
CD2 B:LEU45 4.6 17.8 1.0
SG B:CYS70 4.7 16.0 1.0
N B:ARG66 4.8 20.6 1.0
N B:SER72 4.8 10.4 1.0
CD2 B:LEU83 5.0 19.3 1.0

Iron binding site 2 out of 20 in 2fbw

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Iron binding site 2 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:14.8
occ:1.00
 FE2 B:FES1002 0.0 14.8 1.0
S1 B:FES1002 2.2 16.4 1.0
S2 B:FES1002 2.2 16.4 1.0
SG B:CYS70 2.2 16.0 1.0
SG B:CYS65 2.3 15.3 1.0
FE1 B:FES1002 2.8 17.8 1.0
CB B:CYS70 3.3 13.9 1.0
N B:CYS65 3.4 16.2 1.0
CB B:CYS65 3.5 5.8 1.0
N B:CYS70 3.6 16.0 1.0
N B:GLY71 3.7 13.2 1.0
CA B:CYS70 3.8 18.0 1.0
CA B:CYS65 3.9 16.3 1.0
N B:SER72 4.0 10.4 1.0
N B:ARG66 4.1 20.6 1.0
C B:CYS70 4.2 17.6 1.0
SG B:CYS85 4.2 19.3 1.0
CB B:SER72 4.3 15.4 1.0
C B:CYS65 4.3 17.1 1.0
N B:SER64 4.4 14.5 1.0
N B:ILE69 4.5 16.6 1.0
C B:SER64 4.5 14.4 1.0
N B:GLY68 4.6 19.3 1.0
OG B:SER72 4.6 20.8 1.0
CA B:SER72 4.7 13.8 1.0
N B:CYS73 4.7 13.6 1.0
SG B:CYS73 4.7 18.4 1.0
CA B:GLY71 4.7 15.6 1.0
CA B:GLY68 4.8 14.2 1.0
C B:GLY71 4.8 17.0 1.0
C B:ILE69 4.8 18.1 1.0
CA B:SER64 4.9 15.6 1.0
C B:GLY68 5.0 15.4 1.0

Iron binding site 3 out of 20 in 2fbw

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Iron binding site 3 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:18.4
occ:1.00
 FE1 B:SF41003 0.0 18.4 1.0
S2 B:SF41003 2.2 17.6 1.0
S4 B:SF41003 2.2 17.0 1.0
SG B:CYS164 2.2 24.2 1.0
S3 B:SF41003 2.3 17.0 1.0
FE2 B:SF41003 2.7 17.7 1.0
FE3 B:SF41003 2.7 19.7 1.0
FE4 B:SF41003 2.8 21.4 1.0
CB B:CYS164 3.3 17.7 1.0
S1 B:SF41003 3.8 19.0 1.0
N B:CYS164 4.0 20.0 1.0
CB B:ALA182 4.1 13.3 1.0
CA B:CYS164 4.2 18.7 1.0
CA B:ALA182 4.5 16.2 1.0
SG B:CYS158 4.5 19.0 1.0
SG B:CYS161 4.6 20.4 1.0
SG B:CYS225 4.8 22.1 1.0
N B:CYS163 4.8 19.3 1.0
N B:ALA182 4.9 17.7 1.0
N B:ALA162 4.9 18.5 1.0

Iron binding site 4 out of 20 in 2fbw

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Iron binding site 4 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:17.7
occ:1.00
 FE2 B:SF41003 0.0 17.7 1.0
S3 B:SF41003 2.2 17.0 1.0
S4 B:SF41003 2.3 17.0 1.0
S1 B:SF41003 2.3 19.0 1.0
SG B:CYS158 2.3 19.0 1.0
FE1 B:SF41003 2.7 18.4 1.0
FE4 B:SF41003 2.7 21.4 1.0
FE3 B:SF41003 2.8 19.7 1.0
CB B:CYS158 3.3 13.2 1.0
CA B:CYS158 3.7 16.6 1.0
S2 B:SF41003 3.8 17.6 1.0
N B:ILE159 3.9 15.8 1.0
N B:LEU160 4.0 19.6 1.0
C B:CYS158 4.2 17.9 1.0
O B:HOH1725 4.5 25.1 1.0
CA B:LEU160 4.6 20.1 1.0
SG B:CYS164 4.7 24.2 1.0
CD2 B:LEU229 4.8 18.1 1.0
N B:CYS161 4.8 16.8 1.0
CB B:ALA182 4.8 13.3 1.0
SG B:CYS225 4.9 22.1 1.0
SG B:CYS161 4.9 20.4 1.0
CE B:MET185 4.9 20.9 1.0
C B:ILE159 4.9 19.6 1.0

Iron binding site 5 out of 20 in 2fbw

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Iron binding site 5 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:19.7
occ:1.00
 FE3 B:SF41003 0.0 19.7 1.0
S2 B:SF41003 2.2 17.6 1.0
S4 B:SF41003 2.2 17.0 1.0
SG B:CYS225 2.2 22.1 1.0
S1 B:SF41003 2.3 19.0 1.0
FE1 B:SF41003 2.7 18.4 1.0
FE2 B:SF41003 2.8 17.7 1.0
FE4 B:SF41003 2.8 21.4 1.0
CB B:CYS225 3.3 17.6 1.0
S3 B:SF41003 3.9 17.0 1.0
CA B:CYS225 3.9 20.2 1.0
CD B:PRO226 4.2 26.9 1.0
CD2 B:LEU229 4.3 18.1 1.0
CB B:LEU229 4.6 20.4 1.0
C B:CYS225 4.6 22.7 1.0
SG B:CYS164 4.7 24.2 1.0
CB B:LYS227 4.7 29.6 1.0
N B:PRO226 4.7 23.0 1.0
SG B:CYS161 4.7 20.4 1.0
N B:LYS227 4.8 24.2 1.0
CB B:CYS164 4.9 17.7 1.0
CG B:PRO226 5.0 26.6 1.0
CG B:LYS227 5.0 32.0 1.0

Iron binding site 6 out of 20 in 2fbw

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Iron binding site 6 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:21.4
occ:1.00
 FE4 B:SF41003 0.0 21.4 1.0
S3 B:SF41003 2.2 17.0 1.0
S1 B:SF41003 2.2 19.0 1.0
SG B:CYS161 2.3 20.4 1.0
S2 B:SF41003 2.3 17.6 1.0
FE2 B:SF41003 2.7 17.7 1.0
FE1 B:SF41003 2.8 18.4 1.0
FE3 B:SF41003 2.8 19.7 1.0
CB B:CYS161 3.6 13.6 1.0
N B:CYS161 3.6 16.8 1.0
S4 B:SF41003 3.8 17.0 1.0
N B:ALA162 4.0 18.5 1.0
CA B:CYS161 4.1 16.6 1.0
CD B:PRO226 4.3 26.9 1.0
N B:CYS163 4.3 19.3 1.0
CG1 B:ILE159 4.4 14.9 1.0
C B:CYS161 4.5 17.1 1.0
N B:LEU160 4.6 19.6 1.0
SG B:CYS158 4.6 19.0 1.0
CG B:PRO226 4.6 26.6 1.0
CB B:CYS163 4.7 20.7 1.0
SG B:CYS225 4.7 22.1 1.0
C B:LEU160 4.7 18.9 1.0
SG B:CYS164 4.7 24.2 1.0
CA B:LEU160 4.8 20.1 1.0
N B:ILE159 4.9 15.8 1.0
N B:CYS164 4.9 20.0 1.0
CA B:ALA162 4.9 19.3 1.0

Iron binding site 7 out of 20 in 2fbw

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Iron binding site 7 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:19.9
occ:1.00
 FE1 B:F3S1004 0.0 19.9 1.0
SG B:CYS215 2.2 20.2 1.0
S1 B:F3S1004 2.2 25.5 1.0
S2 B:F3S1004 2.2 18.5 1.0
S3 B:F3S1004 2.3 20.1 1.0
FE4 B:F3S1004 2.7 19.2 1.0
FE3 B:F3S1004 2.8 19.3 1.0
CB B:CYS215 3.4 18.4 1.0
CA B:CYS215 3.8 22.1 1.0
N B:THR217 3.8 26.3 1.0
OH B:TYR178 3.9 22.6 1.0
S4 B:F3S1004 4.0 17.8 1.0
N B:HIS216 4.1 19.0 1.0
CA B:THR217 4.1 22.8 1.0
CD1 B:ILE235 4.2 17.1 1.0
C B:CYS215 4.2 22.0 1.0
N B:ILE218 4.3 21.3 1.0
O B:HOH1793 4.6 22.5 1.0
C B:THR217 4.7 24.5 1.0
SG B:CYS168 4.7 20.4 1.0
SG B:CYS221 4.8 22.9 1.0
C B:HIS216 4.8 23.9 1.0
N B:MET219 4.9 22.6 1.0

Iron binding site 8 out of 20 in 2fbw

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Iron binding site 8 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:19.3
occ:1.00
 FE3 B:F3S1004 0.0 19.3 1.0
S4 B:F3S1004 2.2 17.8 1.0
S1 B:F3S1004 2.3 25.5 1.0
S3 B:F3S1004 2.3 20.1 1.0
SG B:CYS221 2.3 22.9 1.0
FE4 B:F3S1004 2.6 19.2 1.0
FE1 B:F3S1004 2.8 19.9 1.0
CB B:CYS221 3.3 18.6 1.0
S2 B:F3S1004 3.9 18.5 1.0
N B:CYS221 3.9 21.3 1.0
N B:MET219 3.9 22.6 1.0
CA B:MET219 4.1 22.8 1.0
CA B:CYS221 4.2 23.1 1.0
N B:ASN220 4.3 25.0 1.0
C B:MET219 4.5 24.2 1.0
SG B:CYS168 4.6 20.4 1.0
CB B:PRO181 4.7 14.6 1.0
CD1 B:ILE235 4.8 17.1 1.0
CA B:GLY232 4.8 18.4 1.0
SG B:CYS215 4.8 20.2 1.0
CG B:PRO181 4.9 14.2 1.0
CB B:CYS168 5.0 17.3 1.0
N B:ILE218 5.0 21.3 1.0

Iron binding site 9 out of 20 in 2fbw

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Iron binding site 9 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:19.2
occ:1.00
 FE4 B:F3S1004 0.0 19.2 1.0
S4 B:F3S1004 2.2 17.8 1.0
S3 B:F3S1004 2.2 20.1 1.0
SG B:CYS168 2.2 20.4 1.0
S2 B:F3S1004 2.2 18.5 1.0
FE3 B:F3S1004 2.6 19.3 1.0
FE1 B:F3S1004 2.7 19.9 1.0
CB B:CYS168 3.2 17.3 1.0
S1 B:F3S1004 3.8 25.5 1.0
CA B:CYS168 4.1 17.4 1.0
OH B:TYR178 4.1 22.6 1.0
CB B:ILE218 4.6 22.3 1.0
CE2 B:TYR178 4.7 20.2 1.0
SG B:CYS221 4.7 22.9 1.0
SG B:CYS215 4.8 20.2 1.0
C B:CYS168 4.8 20.6 1.0
CB B:SER170 4.9 23.3 1.0
CZ B:TYR178 4.9 16.4 1.0
CD B:PRO169 4.9 19.8 1.0
CD B:PRO181 4.9 15.8 1.0

Iron binding site 10 out of 20 in 2fbw

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Iron binding site 10 out of 20 in the Avian Respiratory Complex II with Carboxin Bound


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Avian Respiratory Complex II with Carboxin Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe143

b:29.8
occ:1.00
 FE C:HEM143 0.0 29.8 1.0
NA C:HEM143 1.9 28.2 1.0
NC C:HEM143 2.0 31.5 1.0
NE2 C:HIS98 2.0 28.6 1.0
NE2 D:HIS46 2.0 28.7 1.0
NB C:HEM143 2.0 27.8 1.0
ND C:HEM143 2.0 31.9 1.0
CD2 C:HIS98 2.9 26.7 1.0
C1A C:HEM143 3.0 28.7 1.0
CD2 D:HIS46 3.0 25.5 1.0
C4A C:HEM143 3.0 32.2 1.0
CE1 D:HIS46 3.0 31.5 1.0
CE1 C:HIS98 3.0 29.3 1.0
C1C C:HEM143 3.0 30.2 1.0
C4C C:HEM143 3.0 33.0 1.0
C4B C:HEM143 3.0 29.2 1.0
C4D C:HEM143 3.1 24.3 1.0
C1B C:HEM143 3.1 31.0 1.0
C1D C:HEM143 3.1 31.3 1.0
CHA C:HEM143 3.4 23.2 1.0
CHC C:HEM143 3.4 29.1 1.0
CHB C:HEM143 3.4 30.4 1.0
CHD C:HEM143 3.4 32.6 1.0
CG C:HIS98 4.1 29.5 1.0
ND1 C:HIS98 4.1 26.4 1.0
ND1 D:HIS46 4.1 33.5 1.0
CG D:HIS46 4.1 29.9 1.0
C2A C:HEM143 4.2 33.1 1.0
C3A C:HEM143 4.2 32.6 1.0
C2C C:HEM143 4.3 32.6 1.0
C3C C:HEM143 4.3 32.8 1.0
C3B C:HEM143 4.3 33.5 1.0
C3D C:HEM143 4.3 32.0 1.0
C2B C:HEM143 4.3 30.9 1.0
C2D C:HEM143 4.3 31.7 1.0
CE1 C:HIS42 5.0 30.3 1.0

Reference:

L.S.Huang, G.Sun, D.Cobessi, A.C.Wang, J.T.Shen, E.Y.Tung, V.E.Anderson, E.A.Berry. 3-Nitropropionic Acid Is A Suicide Inhibitor of Mitochondrial Respiration That, Upon Oxidation By Complex II, Forms A Covalent Adduct with A Catalytic Base Arginine in the Active Site of the Enzyme. J.Biol.Chem. V. 281 5965 2006.
ISSN: ISSN 0021-9258
PubMed: 16371358
DOI: 10.1074/JBC.M511270200
Page generated: Sat Aug 3 21:14:23 2024

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