Atomistry » Iron » PDB 1yev-1yqo » 1yq3
Atomistry »
  Iron »
    PDB 1yev-1yqo »
      1yq3 »

Iron in PDB 1yq3: Avian Respiratory Complex II with Oxaloacetate and Ubiquinone

Enzymatic activity of Avian Respiratory Complex II with Oxaloacetate and Ubiquinone

All present enzymatic activity of Avian Respiratory Complex II with Oxaloacetate and Ubiquinone:
1.3.5.1;

Protein crystallography data

The structure of Avian Respiratory Complex II with Oxaloacetate and Ubiquinone, PDB code: 1yq3 was solved by L.Huang, D.Cobessi, E.Y.Tung, E.A.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.66 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.008, 84.398, 289.496, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 22.3

Iron Binding Sites:

The binding sites of Iron atom in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone (pdb code 1yq3). 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 Respiratory Complex II with Oxaloacetate and Ubiquinone, PDB code: 1yq3:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 1 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:34.5
occ:1.00
 FE1 B:FES1002 0.0 34.5 1.0
S1 B:FES1002 2.2 33.9 1.0
S2 B:FES1002 2.2 34.4 1.0
SG B:CYS73 2.2 35.9 1.0
SG B:CYS85 2.3 33.1 1.0
FE2 B:FES1002 2.6 31.8 1.0
CB B:CYS85 3.2 33.4 1.0
CB B:CYS73 3.5 32.2 1.0
N B:CYS73 4.0 34.4 1.0
SG B:CYS65 4.2 33.2 1.0
N B:CYS85 4.2 36.1 1.0
N B:GLY68 4.3 38.3 1.0
CA B:CYS85 4.3 37.0 1.0
CA B:CYS73 4.4 34.9 1.0
CB B:LEU83 4.4 29.7 1.0
CA B:GLY68 4.4 35.1 1.0
N B:ARG66 4.6 38.4 1.0
SG B:CYS70 4.6 31.7 1.0
CD2 B:LEU45 4.8 39.0 1.0
N B:SER72 4.8 33.5 1.0
CA B:ARG66 4.9 45.7 1.0
CD1 B:LEU83 4.9 19.4 1.0

Iron binding site 2 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 2 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:31.8
occ:1.00
 FE2 B:FES1002 0.0 31.8 1.0
S1 B:FES1002 2.2 33.9 1.0
S2 B:FES1002 2.2 34.4 1.0
SG B:CYS70 2.2 31.7 1.0
SG B:CYS65 2.3 33.2 1.0
FE1 B:FES1002 2.6 34.5 1.0
N B:CYS65 3.5 30.8 1.0
CB B:CYS70 3.5 25.5 1.0
N B:CYS70 3.5 29.4 1.0
CB B:CYS65 3.5 33.0 1.0
N B:GLY71 3.8 25.3 1.0
N B:ARG66 3.8 38.4 1.0
CA B:CYS70 3.8 25.7 1.0
CA B:CYS65 3.9 31.7 1.0
N B:SER72 4.0 33.5 1.0
SG B:CYS85 4.1 33.1 1.0
C B:CYS70 4.2 25.6 1.0
C B:CYS65 4.3 32.7 1.0
N B:GLY68 4.3 38.3 1.0
N B:SER64 4.4 32.0 1.0
N B:ILE69 4.5 29.4 1.0
C B:SER64 4.5 34.3 1.0
SG B:CYS73 4.6 35.9 1.0
CA B:GLY68 4.6 35.1 1.0
OG B:SER72 4.6 31.7 1.0
CB B:SER72 4.6 27.9 1.0
CA B:GLY71 4.7 27.3 1.0
C B:ILE69 4.7 29.8 1.0
C B:GLY71 4.7 30.6 1.0
N B:CYS73 4.8 34.4 1.0
CA B:SER64 4.8 27.2 1.0
CA B:ARG66 4.8 45.7 1.0
CA B:SER72 4.9 29.9 1.0
C B:GLY68 4.9 31.4 1.0
N B:GLU67 4.9 39.2 1.0

Iron binding site 3 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 3 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:32.5
occ:1.00
 FE1 B:SF41003 0.0 32.5 1.0
S2 B:SF41003 2.2 31.8 1.0
S4 B:SF41003 2.2 36.4 1.0
S3 B:SF41003 2.3 31.5 1.0
SG B:CYS164 2.3 32.1 1.0
FE4 B:SF41003 2.4 31.9 1.0
FE3 B:SF41003 2.6 33.8 1.0
FE2 B:SF41003 2.8 35.2 1.0
CB B:CYS164 3.4 26.0 1.0
S1 B:SF41003 3.7 34.1 1.0
N B:CYS164 4.0 21.6 1.0
CB B:ALA182 4.1 27.2 1.0
CA B:CYS164 4.3 26.4 1.0
SG B:CYS158 4.3 31.3 1.0
CA B:ALA182 4.5 30.6 1.0
SG B:CYS225 4.7 36.8 1.0
SG B:CYS161 4.7 30.7 1.0
N B:CYS163 4.8 28.8 1.0
CG B:PRO231 4.8 25.7 1.0
N B:ALA162 4.8 26.0 1.0
N B:ALA182 4.9 29.3 1.0

Iron binding site 4 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 4 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:35.2
occ:1.00
 FE2 B:SF41003 0.0 35.2 1.0
SG B:CYS161 2.2 30.7 1.0
S4 B:SF41003 2.3 36.4 1.0
S3 B:SF41003 2.3 31.5 1.0
S1 B:SF41003 2.3 34.1 1.0
FE4 B:SF41003 2.7 31.9 1.0
FE1 B:SF41003 2.8 32.5 1.0
FE3 B:SF41003 2.8 33.8 1.0
CB B:CYS161 3.5 23.5 1.0
N B:CYS161 3.6 32.3 1.0
N B:ALA162 3.8 26.0 1.0
CA B:CYS161 4.0 29.4 1.0
S2 B:SF41003 4.1 31.8 1.0
CD B:PRO226 4.2 41.6 1.0
N B:CYS163 4.2 28.8 1.0
CG1 B:ILE159 4.3 24.3 1.0
C B:CYS161 4.4 30.9 1.0
N B:LEU160 4.5 29.0 1.0
SG B:CYS158 4.5 31.3 1.0
CG B:PRO226 4.6 44.5 1.0
C B:LEU160 4.7 31.9 1.0
SG B:CYS225 4.7 36.8 1.0
N B:ILE159 4.8 24.0 1.0
SG B:CYS164 4.8 32.1 1.0
CA B:ALA162 4.8 31.9 1.0
CB B:CYS163 4.8 30.7 1.0
CA B:LEU160 4.8 30.3 1.0
CD1 B:ILE159 4.9 21.7 1.0
N B:CYS164 4.9 21.6 1.0

Iron binding site 5 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 5 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:33.8
occ:1.00
 FE3 B:SF41003 0.0 33.8 1.0
S4 B:SF41003 2.2 36.4 1.0
S1 B:SF41003 2.2 34.1 1.0
S2 B:SF41003 2.3 31.8 1.0
SG B:CYS225 2.3 36.8 1.0
FE1 B:SF41003 2.6 32.5 1.0
FE4 B:SF41003 2.7 31.9 1.0
FE2 B:SF41003 2.8 35.2 1.0
CB B:CYS225 3.4 31.9 1.0
S3 B:SF41003 3.9 31.5 1.0
CD B:PRO226 4.1 41.6 1.0
CA B:CYS225 4.1 36.6 1.0
CD2 B:LEU229 4.3 26.4 1.0
CB B:LEU229 4.4 33.2 1.0
SG B:CYS164 4.7 32.1 1.0
SG B:CYS158 4.7 31.3 1.0
C B:CYS225 4.7 41.1 1.0
N B:PRO226 4.7 42.8 1.0
SG B:CYS161 4.8 30.7 1.0
CB B:LYS227 4.8 40.3 1.0
N B:LYS227 4.9 39.9 1.0

Iron binding site 6 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 6 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:31.9
occ:1.00
 FE4 B:SF41003 0.0 31.9 1.0
SG B:CYS158 2.2 31.3 1.0
S3 B:SF41003 2.3 31.5 1.0
S1 B:SF41003 2.3 34.1 1.0
S2 B:SF41003 2.3 31.8 1.0
FE1 B:SF41003 2.4 32.5 1.0
FE3 B:SF41003 2.7 33.8 1.0
FE2 B:SF41003 2.7 35.2 1.0
CB B:CYS158 3.5 28.8 1.0
S4 B:SF41003 3.6 36.4 1.0
CA B:CYS158 3.8 24.4 1.0
N B:ILE159 4.0 24.0 1.0
N B:LEU160 4.1 29.0 1.0
O B:HOH1024 4.2 28.9 1.0
C B:CYS158 4.3 23.5 1.0
SG B:CYS164 4.6 32.1 1.0
CA B:LEU160 4.6 30.3 1.0
CE B:MET185 4.6 22.4 1.0
CB B:ALA182 4.7 27.2 1.0
N B:CYS161 4.8 32.3 1.0
SG B:CYS161 4.9 30.7 1.0
SG B:CYS225 4.9 36.8 1.0
CD2 B:LEU229 4.9 26.4 1.0
C B:ILE159 5.0 30.6 1.0

Iron binding site 7 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 7 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:28.6
occ:1.00
 FE1 B:F3S1004 0.0 28.6 1.0
S2 B:F3S1004 2.1 29.4 1.0
S3 B:F3S1004 2.2 28.6 1.0
SG B:CYS215 2.2 31.5 1.0
S1 B:F3S1004 2.3 31.2 1.0
FE4 B:F3S1004 2.5 30.0 1.0
FE3 B:F3S1004 2.8 30.3 1.0
CB B:CYS215 3.4 28.2 1.0
CA B:CYS215 3.7 32.3 1.0
N B:THR217 3.8 31.2 1.0
S4 B:F3S1004 4.0 31.8 1.0
OH B:TYR178 4.0 27.8 1.0
CA B:THR217 4.2 31.1 1.0
N B:HIS216 4.2 34.3 1.0
O B:HOH1053 4.3 29.4 1.0
C B:CYS215 4.3 32.3 1.0
N B:ILE218 4.3 32.1 1.0
CD1 B:ILE235 4.5 25.9 1.0
SG B:CYS168 4.6 33.0 1.0
SG B:CYS221 4.7 32.1 1.0
C B:THR217 4.7 32.9 1.0
C B:HIS216 4.8 35.9 1.0

Iron binding site 8 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 8 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:30.3
occ:1.00
 FE3 B:F3S1004 0.0 30.3 1.0
S4 B:F3S1004 2.2 31.8 1.0
S1 B:F3S1004 2.2 31.2 1.0
SG B:CYS221 2.3 32.1 1.0
S3 B:F3S1004 2.3 28.6 1.0
FE4 B:F3S1004 2.6 30.0 1.0
FE1 B:F3S1004 2.8 28.6 1.0
CB B:CYS221 3.3 28.8 1.0
N B:CYS221 3.8 36.8 1.0
S2 B:F3S1004 3.8 29.4 1.0
N B:MET219 3.9 30.6 1.0
CA B:CYS221 4.1 32.1 1.0
CA B:MET219 4.1 34.5 1.0
N B:ASN220 4.3 33.2 1.0
C B:MET219 4.5 32.7 1.0
SG B:CYS168 4.6 33.0 1.0
SG B:CYS215 4.6 31.5 1.0
CB B:PRO181 4.7 25.6 1.0
CG B:PRO181 4.7 29.7 1.0
CA B:GLY232 4.7 36.0 1.0
C B:ASN220 4.9 36.1 1.0
CB B:CYS168 4.9 35.7 1.0
N B:ILE218 5.0 32.1 1.0

Iron binding site 9 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 9 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:30.0
occ:1.00
 FE4 B:F3S1004 0.0 30.0 1.0
S3 B:F3S1004 2.1 28.6 1.0
S2 B:F3S1004 2.2 29.4 1.0
SG B:CYS168 2.3 33.0 1.0
S4 B:F3S1004 2.3 31.8 1.0
FE1 B:F3S1004 2.5 28.6 1.0
FE3 B:F3S1004 2.6 30.3 1.0
CB B:CYS168 3.3 35.7 1.0
S1 B:F3S1004 3.8 31.2 1.0
CA B:CYS168 4.1 33.3 1.0
OH B:TYR178 4.3 27.8 1.0
CB B:ILE218 4.5 28.5 1.0
SG B:CYS215 4.6 31.5 1.0
SG B:CYS221 4.7 32.1 1.0
C B:CYS168 4.8 34.6 1.0
CD1 B:ILE218 4.8 23.4 1.0
CG B:PRO181 4.9 29.7 1.0
CE2 B:TYR178 4.9 27.0 1.0
CD B:PRO181 4.9 25.2 1.0
CD B:PRO169 4.9 35.1 1.0
N B:ILE218 4.9 32.1 1.0
CB B:SER170 4.9 33.6 1.0
CG1 B:ILE218 5.0 26.5 1.0

Iron binding site 10 out of 10 in 1yq3

Go back to Iron Binding Sites List in 1yq3
Iron binding site 10 out of 10 in the Avian Respiratory Complex II with Oxaloacetate and Ubiquinone


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 Oxaloacetate and Ubiquinone within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe143

b:34.9
occ:1.00
 FE C:HEM143 0.0 34.9 1.0
NB C:HEM143 1.8 37.5 1.0
ND C:HEM143 1.9 36.2 1.0
NE2 D:HIS46 2.0 36.7 1.0
NE2 C:HIS98 2.0 36.6 1.0
NA C:HEM143 2.0 36.4 1.0
NC C:HEM143 2.1 37.0 1.0
CD2 D:HIS46 2.9 31.3 1.0
C4B C:HEM143 2.9 38.0 1.0
CD2 C:HIS98 3.0 31.9 1.0
C1D C:HEM143 3.0 36.5 1.0
C1A C:HEM143 3.0 35.5 1.0
C4C C:HEM143 3.1 35.1 1.0
CE1 D:HIS46 3.1 40.4 1.0
C4D C:HEM143 3.1 37.5 1.0
CE1 C:HIS98 3.1 37.2 1.0
C1B C:HEM143 3.1 34.3 1.0
C4A C:HEM143 3.1 35.8 1.0
C1C C:HEM143 3.1 36.2 1.0
CHC C:HEM143 3.3 32.6 1.0
CHD C:HEM143 3.4 33.8 1.0
CHA C:HEM143 3.5 36.7 1.0
CHB C:HEM143 3.6 32.3 1.0
CG D:HIS46 4.1 33.2 1.0
CG C:HIS98 4.1 35.0 1.0
ND1 D:HIS46 4.1 34.0 1.0
ND1 C:HIS98 4.2 27.6 1.0
C2A C:HEM143 4.2 36.4 1.0
C3A C:HEM143 4.2 36.6 1.0
C3B C:HEM143 4.2 37.9 1.0
C2D C:HEM143 4.3 34.6 1.0
C3D C:HEM143 4.3 35.6 1.0
C2B C:HEM143 4.3 36.3 1.0
C3C C:HEM143 4.4 36.1 1.0
C2C C:HEM143 4.5 37.0 1.0

Reference:

L.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: Sun Dec 13 14:38:02 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy