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Iron in PDB 2h88: Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution

Enzymatic activity of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution

All present enzymatic activity of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution:
1.3.5.1;

Protein crystallography data

The structure of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution, PDB code: 2h88 was solved by L.S.Huang, J.T.Shen, A.C.Wang, E.A.Berry, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.14 / 1.74
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 119.972, 199.391, 68.063, 90.00, 90.35, 90.00
R / Rfree (%) 17.8 / 20.6

Other elements in 2h88:

The structure of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution 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 Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution (pdb code 2h88). 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 Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution, PDB code: 2h88:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 20 in 2h88

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Iron binding site 1 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:16.7
occ:1.00
FE1 B:FES1002 0.0 16.7 1.0
S2 B:FES1002 2.2 16.0 1.0
S1 B:FES1002 2.2 16.3 1.0
SG B:CYS73 2.2 17.5 1.0
SG B:CYS85 2.3 17.2 1.0
FE2 B:FES1002 2.7 14.9 1.0
CB B:CYS85 3.3 20.2 1.0
CB B:CYS73 3.4 13.0 1.0
N B:CYS73 4.0 15.8 1.0
N B:CYS85 4.2 17.8 1.0
SG B:CYS65 4.3 16.4 1.0
CA B:CYS73 4.3 15.2 1.0
CA B:CYS85 4.4 17.6 1.0
CB B:LEU83 4.4 15.8 1.0
N B:GLY68 4.5 19.3 1.0
CA B:GLY68 4.6 18.6 1.0
N B:ARG66 4.6 19.0 1.0
SG B:CYS70 4.8 15.2 1.0
CA B:ARG66 4.8 27.4 1.0
N B:SER72 4.8 15.5 1.0
CD2 B:LEU83 4.9 17.9 1.0
CD1 B:LEU83 5.0 19.6 1.0

Iron binding site 2 out of 20 in 2h88

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Iron binding site 2 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:14.9
occ:1.00
FE2 B:FES1002 0.0 14.9 1.0
S2 B:FES1002 2.2 16.0 1.0
S1 B:FES1002 2.2 16.3 1.0
SG B:CYS65 2.3 16.4 1.0
SG B:CYS70 2.3 15.2 1.0
FE1 B:FES1002 2.7 16.7 1.0
N B:CYS65 3.5 14.1 1.0
CB B:CYS65 3.6 15.2 1.0
CB B:CYS70 3.6 17.3 1.0
N B:CYS70 3.6 16.7 1.0
N B:GLY71 3.9 17.0 1.0
CA B:CYS65 3.9 14.5 1.0
N B:ARG66 4.0 19.0 1.0
CA B:CYS70 4.0 16.1 1.0
N B:SER72 4.0 15.5 1.0
SG B:CYS85 4.2 17.2 1.0
C B:CYS65 4.3 19.2 1.0
C B:CYS70 4.3 16.3 1.0
N B:SER64 4.4 14.9 1.0
N B:ILE69 4.5 14.2 1.0
N B:GLY68 4.5 19.3 1.0
C B:SER64 4.5 16.1 1.0
CB B:SER72 4.6 12.8 1.0
SG B:CYS73 4.7 17.5 1.0
N B:CYS73 4.8 15.8 1.0
CA B:GLY71 4.8 17.5 1.0
CA B:SER72 4.8 12.5 1.0
CA B:GLY68 4.8 18.6 1.0
C B:ILE69 4.8 17.7 1.0
C B:GLY71 4.8 18.6 1.0
N B:GLU67 4.8 26.8 1.0
OG B:SER72 4.8 17.2 1.0
CA B:ARG66 4.9 27.4 1.0
CA B:SER64 4.9 17.7 1.0
C B:GLY68 5.0 19.1 1.0

Iron binding site 3 out of 20 in 2h88

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Iron binding site 3 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:19.7
occ:1.00
FE1 B:SF41003 0.0 19.7 1.0
S3 B:SF41003 2.3 17.3 1.0
S2 B:SF41003 2.3 17.2 1.0
SG B:CYS161 2.3 19.9 1.0
S4 B:SF41003 2.3 19.9 1.0
FE4 B:SF41003 2.7 18.3 1.0
FE3 B:SF41003 2.8 19.7 1.0
FE2 B:SF41003 2.8 19.0 1.0
CB B:CYS161 3.7 12.7 1.0
N B:CYS161 3.7 18.5 1.0
S1 B:SF41003 3.9 19.3 1.0
N B:ALA162 4.0 16.7 1.0
CA B:CYS161 4.1 18.2 1.0
N B:CYS163 4.2 20.0 1.0
C B:CYS161 4.4 16.4 1.0
CG1 B:ILE159 4.5 19.4 1.0
CD B:PRO226 4.5 24.8 1.0
CB B:CYS163 4.6 20.6 1.0
CG B:PRO226 4.6 24.9 1.0
N B:LEU160 4.7 16.2 1.0
SG B:CYS158 4.7 18.8 1.0
SG B:CYS225 4.7 20.2 1.0
C B:LEU160 4.8 19.6 1.0
SG B:CYS164 4.8 21.6 1.0
N B:CYS164 4.8 16.3 1.0
CA B:ALA162 4.9 17.1 1.0
CA B:CYS163 5.0 18.8 1.0
N B:ILE159 5.0 19.6 1.0
CA B:LEU160 5.0 19.4 1.0

Iron binding site 4 out of 20 in 2h88

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Iron binding site 4 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:19.0
occ:1.00
FE2 B:SF41003 0.0 19.0 1.0
S3 B:SF41003 2.2 17.3 1.0
SG B:CYS225 2.3 20.2 1.0
S4 B:SF41003 2.3 19.9 1.0
S1 B:SF41003 2.3 19.3 1.0
FE4 B:SF41003 2.7 18.3 1.0
FE3 B:SF41003 2.8 19.7 1.0
FE1 B:SF41003 2.8 19.7 1.0
CB B:CYS225 3.3 20.8 1.0
S2 B:SF41003 3.9 17.2 1.0
CA B:CYS225 4.0 21.7 1.0
CD1 B:LEU229 4.4 20.3 1.0
CD B:PRO226 4.4 24.8 1.0
C B:CYS225 4.6 25.6 1.0
N B:PRO226 4.7 23.4 1.0
CB B:LEU229 4.7 17.0 1.0
CG B:LEU229 4.7 22.8 1.0
CB B:LYS227 4.8 27.0 1.0
SG B:CYS161 4.8 19.9 1.0
SG B:CYS164 4.8 21.6 1.0
N B:LYS227 4.8 20.5 1.0
CB B:CYS164 5.0 20.9 1.0
SG B:CYS158 5.0 18.8 1.0

Iron binding site 5 out of 20 in 2h88

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Iron binding site 5 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution 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 17.2 1.0
S4 B:SF41003 2.3 19.9 1.0
S1 B:SF41003 2.3 19.3 1.0
SG B:CYS158 2.3 18.8 1.0
FE4 B:SF41003 2.6 18.3 1.0
FE2 B:SF41003 2.8 19.0 1.0
FE1 B:SF41003 2.8 19.7 1.0
CB B:CYS158 3.4 20.4 1.0
S3 B:SF41003 3.8 17.3 1.0
CA B:CYS158 3.8 18.7 1.0
N B:ILE159 4.0 19.6 1.0
N B:LEU160 4.2 16.2 1.0
O B:HOH1683 4.3 24.8 1.0
C B:CYS158 4.3 18.2 1.0
CD1 B:LEU229 4.6 20.3 1.0
CA B:LEU160 4.7 19.4 1.0
SG B:CYS164 4.7 21.6 1.0
CE B:MET185 4.8 23.6 1.0
SG B:CYS225 4.9 20.2 1.0
N B:CYS161 4.9 18.5 1.0
CB B:ALA182 4.9 16.7 1.0
SG B:CYS161 5.0 19.9 1.0

Iron binding site 6 out of 20 in 2h88

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Iron binding site 6 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:18.3
occ:1.00
FE4 B:SF41003 0.0 18.3 1.0
S1 B:SF41003 2.2 19.3 1.0
S3 B:SF41003 2.2 17.3 1.0
S2 B:SF41003 2.3 17.2 1.0
SG B:CYS164 2.3 21.6 1.0
FE3 B:SF41003 2.6 19.7 1.0
FE2 B:SF41003 2.7 19.0 1.0
FE1 B:SF41003 2.7 19.7 1.0
CB B:CYS164 3.3 20.9 1.0
S4 B:SF41003 3.8 19.9 1.0
N B:CYS164 3.9 16.3 1.0
CB B:ALA182 4.2 16.7 1.0
CA B:CYS164 4.3 16.8 1.0
SG B:CYS158 4.6 18.8 1.0
CA B:ALA182 4.6 16.7 1.0
SG B:CYS161 4.7 19.9 1.0
SG B:CYS225 4.8 20.2 1.0
N B:CYS163 4.8 20.0 1.0
N B:ALA162 4.9 16.7 1.0
N B:ALA182 5.0 14.1 1.0

Iron binding site 7 out of 20 in 2h88

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Iron binding site 7 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:21.7
occ:1.00
FE1 B:F3S1004 0.0 21.7 1.0
S1 B:F3S1004 2.3 21.7 1.0
S2 B:F3S1004 2.3 20.7 1.0
S3 B:F3S1004 2.3 18.5 1.0
SG B:CYS215 2.3 23.9 1.0
FE4 B:F3S1004 2.7 22.1 1.0
FE3 B:F3S1004 2.8 21.2 1.0
CB B:CYS215 3.4 20.4 1.0
N B:THR217 3.8 23.0 1.0
CA B:CYS215 3.8 20.9 1.0
S4 B:F3S1004 4.0 20.9 1.0
OH B:TYR178 4.0 25.3 1.0
N B:HIS216 4.1 21.0 1.0
CA B:THR217 4.1 25.0 1.0
N B:ILE218 4.2 25.4 1.0
C B:CYS215 4.3 22.9 1.0
CD1 B:ILE235 4.4 21.2 1.0
O B:HOH1750 4.4 23.1 1.0
C B:THR217 4.7 27.4 1.0
SG B:CYS168 4.7 21.8 1.0
C B:HIS216 4.8 26.1 1.0
SG B:CYS221 4.9 22.4 1.0
N B:MET219 4.9 25.9 1.0

Iron binding site 8 out of 20 in 2h88

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Iron binding site 8 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:21.2
occ:1.00
FE3 B:F3S1004 0.0 21.2 1.0
S4 B:F3S1004 2.3 20.9 1.0
S1 B:F3S1004 2.3 21.7 1.0
S3 B:F3S1004 2.3 18.5 1.0
SG B:CYS221 2.3 22.4 1.0
FE4 B:F3S1004 2.7 22.1 1.0
FE1 B:F3S1004 2.8 21.7 1.0
CB B:CYS221 3.3 21.2 1.0
N B:MET219 3.9 25.9 1.0
S2 B:F3S1004 3.9 20.7 1.0
N B:CYS221 4.0 22.0 1.0
CA B:MET219 4.1 25.9 1.0
CA B:CYS221 4.3 21.2 1.0
N B:ASN220 4.4 22.7 1.0
C B:MET219 4.6 24.7 1.0
CB B:PRO181 4.6 15.9 1.0
SG B:CYS168 4.7 21.8 1.0
CG B:PRO181 4.7 17.1 1.0
CA B:GLY232 4.8 25.3 1.0
N B:ILE218 4.9 25.4 1.0
SG B:CYS215 4.9 23.9 1.0
CD1 B:ILE235 5.0 21.2 1.0

Iron binding site 9 out of 20 in 2h88

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Iron binding site 9 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:22.1
occ:1.00
FE4 B:F3S1004 0.0 22.1 1.0
S4 B:F3S1004 2.2 20.9 1.0
S3 B:F3S1004 2.3 18.5 1.0
S2 B:F3S1004 2.3 20.7 1.0
SG B:CYS168 2.3 21.8 1.0
FE3 B:F3S1004 2.7 21.2 1.0
FE1 B:F3S1004 2.7 21.7 1.0
CB B:CYS168 3.3 23.0 1.0
S1 B:F3S1004 3.9 21.7 1.0
CA B:CYS168 4.2 22.2 1.0
OH B:TYR178 4.3 25.3 1.0
CB B:ILE218 4.6 26.7 1.0
CE2 B:TYR178 4.8 19.4 1.0
CD1 B:ILE218 4.8 28.5 1.0
SG B:CYS221 4.8 22.4 1.0
C B:CYS168 4.9 22.5 1.0
N B:ILE218 4.9 25.4 1.0
SG B:CYS215 4.9 23.9 1.0
CB B:SER170 4.9 25.2 1.0
CD B:PRO181 4.9 17.7 1.0

Iron binding site 10 out of 20 in 2h88

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Iron binding site 10 out of 20 in the Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Avian Mitochondrial Respiratory Complex II at 1.8 Angstrom Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe142

b:28.1
occ:1.00
FE C:HEM142 0.0 28.1 1.0
NA C:HEM142 1.9 28.0 1.0
NB C:HEM142 2.0 28.3 1.0
NE2 C:HIS98 2.0 29.4 1.0
NC C:HEM142 2.0 32.0 1.0
ND C:HEM142 2.0 30.1 1.0
NE2 D:HIS46 2.1 28.1 1.0
CD2 C:HIS98 2.9 28.9 1.0
C1A C:HEM142 2.9 30.5 1.0
C4B C:HEM142 3.0 30.8 1.0
C4A C:HEM142 3.0 29.3 1.0
C4D C:HEM142 3.0 31.1 1.0
CD2 D:HIS46 3.0 28.0 1.0
CE1 C:HIS98 3.0 31.4 1.0
C1B C:HEM142 3.1 29.1 1.0
C1C C:HEM142 3.1 32.7 1.0
CE1 D:HIS46 3.1 32.4 1.0
C1D C:HEM142 3.1 32.6 1.0
C4C C:HEM142 3.1 30.8 1.0
CHA C:HEM142 3.3 30.4 1.0
CHC C:HEM142 3.4 29.5 1.0
CHB C:HEM142 3.5 29.2 1.0
CHD C:HEM142 3.5 29.8 1.0
CG C:HIS98 4.1 31.1 1.0
ND1 C:HIS98 4.1 28.8 1.0
C2A C:HEM142 4.2 32.8 1.0
CG D:HIS46 4.2 30.1 1.0
ND1 D:HIS46 4.2 32.2 1.0
C3A C:HEM142 4.2 32.4 1.0
C3B C:HEM142 4.3 30.5 1.0
C3D C:HEM142 4.3 34.5 1.0
C2B C:HEM142 4.3 30.9 1.0
C2D C:HEM142 4.3 33.1 1.0
C2C C:HEM142 4.4 33.1 1.0
C3C C:HEM142 4.4 33.4 1.0
O D:HOH2679 4.4 48.2 1.0
NE2 C:HIS42 4.9 30.9 1.0

Reference:

L.S.Huang, J.T.Shen, A.C.Wang, E.A.Berry. Crystallographic Studies of the Binding of Ligands to the Dicarboxylate Site of Complex II, and the Identity of the Ligand in the Biochim.Biophys.Acta V.1757 1073.
ISSN: ISSN 0006-3002
PubMed: 16935256
DOI: 10.1016/J.BBABIO.2006.06.015
Page generated: Sun Dec 13 14:45:53 2020

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