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Iron in PDB 2h89: Avian Respiratory Complex II with Malonate Bound

Enzymatic activity of Avian Respiratory Complex II with Malonate Bound

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

Protein crystallography data

The structure of Avian Respiratory Complex II with Malonate Bound, PDB code: 2h89 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) 50.74 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 70.520, 84.118, 292.212, 90.00, 90.00, 90.00
R / Rfree (%) 22.6 / 27.9

Other elements in 2h89:

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

Potassium (K) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Avian Respiratory Complex II with Malonate Bound (pdb code 2h89). 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 Malonate Bound, PDB code: 2h89:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 2h89

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Iron binding site 1 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:52.1
occ:1.00
 FE1 B:FES1002 0.0 52.1 1.0
SG B:CYS73 2.0 51.5 1.0
SG B:CYS85 2.1 45.1 1.0
S1 B:FES1002 2.2 44.6 1.0
S2 B:FES1002 2.2 48.3 1.0
FE2 B:FES1002 2.6 38.7 1.0
CB B:CYS85 3.2 47.2 1.0
CB B:CYS73 3.4 47.5 1.0
N B:CYS73 3.7 50.5 1.0
SG B:CYS65 4.1 47.7 1.0
CA B:CYS73 4.2 49.3 1.0
N B:GLY68 4.2 52.9 1.0
CA B:GLY68 4.3 50.3 1.0
N B:ARG66 4.3 52.7 1.0
N B:CYS85 4.4 50.6 1.0
CA B:CYS85 4.4 47.7 1.0
CA B:ARG66 4.5 56.9 1.0
SG B:CYS70 4.6 48.7 1.0
N B:SER72 4.6 49.0 1.0
CB B:LEU83 4.6 43.5 1.0
N B:GLU67 4.8 53.9 1.0
C B:SER72 4.8 49.1 1.0
CD2 B:LEU45 4.9 43.7 1.0
N B:GLY71 5.0 42.3 1.0
C B:ARG66 5.0 53.6 1.0

Iron binding site 2 out of 10 in 2h89

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Iron binding site 2 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1002

b:38.7
occ:1.00
 FE2 B:FES1002 0.0 38.7 1.0
SG B:CYS65 2.2 47.7 1.0
S2 B:FES1002 2.2 48.3 1.0
S1 B:FES1002 2.2 44.6 1.0
SG B:CYS70 2.2 48.7 1.0
FE1 B:FES1002 2.6 52.1 1.0
CB B:CYS65 3.3 46.8 1.0
CB B:CYS70 3.5 42.2 1.0
N B:CYS65 3.6 47.9 1.0
N B:CYS70 3.6 44.2 1.0
N B:ARG66 3.7 52.7 1.0
N B:GLY71 3.7 42.3 1.0
CA B:CYS65 3.8 46.9 1.0
N B:SER72 3.9 49.0 1.0
CA B:CYS70 3.9 42.3 1.0
C B:CYS70 4.2 41.9 1.0
SG B:CYS85 4.2 45.1 1.0
C B:CYS65 4.2 47.0 1.0
N B:ILE69 4.2 49.8 1.0
N B:GLY68 4.3 52.9 1.0
SG B:CYS73 4.4 51.5 1.0
CB B:SER72 4.4 50.8 1.0
OG B:SER72 4.5 57.8 1.0
CA B:GLY68 4.6 50.3 1.0
C B:SER64 4.6 48.7 1.0
CA B:GLY71 4.6 44.9 1.0
CA B:ARG66 4.6 56.9 1.0
N B:GLU67 4.6 53.9 1.0
N B:CYS73 4.7 50.5 1.0
N B:SER64 4.7 48.1 1.0
CA B:SER72 4.7 50.4 1.0
C B:GLY71 4.7 49.0 1.0
C B:ILE69 4.8 47.3 1.0
C B:GLY68 4.9 51.4 1.0
CA B:SER64 5.0 49.2 1.0

Iron binding site 3 out of 10 in 2h89

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Iron binding site 3 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:46.8
occ:1.00
 FE1 B:SF41003 0.0 46.8 1.0
S2 B:SF41003 2.2 42.5 1.0
S3 B:SF41003 2.2 51.3 1.0
S4 B:SF41003 2.3 47.1 1.0
SG B:CYS161 2.3 43.0 1.0
FE3 B:SF41003 2.6 39.9 1.0
FE2 B:SF41003 2.8 41.8 1.0
FE4 B:SF41003 3.0 49.3 1.0
N B:CYS161 3.6 45.7 1.0
CB B:CYS161 3.6 36.9 1.0
S1 B:SF41003 4.1 50.8 1.0
CA B:CYS161 4.1 44.4 1.0
CD B:PRO226 4.2 52.8 1.0
CG B:PRO226 4.2 53.0 1.0
N B:ALA162 4.3 42.8 1.0
SG B:CYS158 4.4 41.5 1.0
CG1 B:ILE159 4.4 41.9 1.0
SG B:CYS225 4.5 39.4 1.0
N B:CYS163 4.5 46.7 1.0
N B:LEU160 4.6 43.3 1.0
C B:CYS161 4.6 44.4 1.0
C B:LEU160 4.7 46.8 1.0
CB B:CYS163 4.7 49.5 1.0
SG B:CYS164 4.7 48.1 1.0
CA B:LEU160 4.8 46.0 1.0
N B:ILE159 4.9 47.4 1.0

Iron binding site 4 out of 10 in 2h89

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Iron binding site 4 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:41.8
occ:1.00
 FE2 B:SF41003 0.0 41.8 1.0
S1 B:SF41003 2.2 50.8 1.0
S3 B:SF41003 2.2 51.3 1.0
S4 B:SF41003 2.2 47.1 1.0
SG B:CYS225 2.4 39.4 1.0
FE4 B:SF41003 2.5 49.3 1.0
FE3 B:SF41003 2.5 39.9 1.0
FE1 B:SF41003 2.8 46.8 1.0
CB B:CYS225 3.4 39.2 1.0
S2 B:SF41003 3.7 42.5 1.0
CA B:CYS225 4.2 46.0 1.0
SG B:CYS164 4.3 48.1 1.0
CB B:LEU229 4.3 39.8 1.0
CD B:PRO226 4.4 52.8 1.0
SG B:CYS158 4.4 41.5 1.0
CD1 B:LEU229 4.6 39.3 1.0
CG B:LEU229 4.7 44.7 1.0
CB B:CYS164 4.7 42.7 1.0
SG B:CYS161 4.9 43.0 1.0
CE B:MET185 4.9 39.7 1.0
C B:CYS225 4.9 49.5 1.0
N B:PRO226 5.0 51.4 1.0
CD B:PRO231 5.0 40.3 1.0

Iron binding site 5 out of 10 in 2h89

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Iron binding site 5 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:39.9
occ:1.00
 FE3 B:SF41003 0.0 39.9 1.0
SG B:CYS158 2.1 41.5 1.0
S4 B:SF41003 2.2 47.1 1.0
S1 B:SF41003 2.2 50.8 1.0
S2 B:SF41003 2.3 42.5 1.0
FE2 B:SF41003 2.5 41.8 1.0
FE4 B:SF41003 2.6 49.3 1.0
FE1 B:SF41003 2.6 46.8 1.0
CB B:CYS158 3.5 42.8 1.0
S3 B:SF41003 3.6 51.3 1.0
CA B:CYS158 3.9 46.7 1.0
N B:ILE159 4.0 47.4 1.0
N B:LEU160 4.1 43.3 1.0
O B:HOH1027 4.4 47.5 1.0
C B:CYS158 4.4 46.5 1.0
SG B:CYS164 4.6 48.1 1.0
CA B:LEU160 4.6 46.0 1.0
CE B:MET185 4.6 39.7 1.0
SG B:CYS225 4.8 39.4 1.0
N B:CYS161 4.8 45.7 1.0
CD1 B:LEU229 4.8 39.3 1.0
SG B:CYS161 4.9 43.0 1.0
C B:ILE159 4.9 47.4 1.0
CA B:ILE159 5.0 43.6 1.0

Iron binding site 6 out of 10 in 2h89

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Iron binding site 6 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1003

b:49.3
occ:1.00
 FE4 B:SF41003 0.0 49.3 1.0
SG B:CYS164 2.1 48.1 1.0
S2 B:SF41003 2.2 42.5 1.0
S3 B:SF41003 2.2 51.3 1.0
S1 B:SF41003 2.3 50.8 1.0
FE2 B:SF41003 2.5 41.8 1.0
FE3 B:SF41003 2.6 39.9 1.0
FE1 B:SF41003 3.0 46.8 1.0
CB B:CYS164 3.2 42.7 1.0
S4 B:SF41003 3.8 47.1 1.0
N B:CYS164 4.0 42.7 1.0
CB B:ALA182 4.2 40.8 1.0
CA B:CYS164 4.2 43.3 1.0
CA B:ALA182 4.3 41.7 1.0
SG B:CYS158 4.3 41.5 1.0
N B:ALA182 4.6 42.7 1.0
SG B:CYS161 4.8 43.0 1.0
SG B:CYS225 4.8 39.4 1.0
O B:HOH1027 4.9 47.5 1.0
N B:CYS163 5.0 46.7 1.0
N B:SER165 5.0 42.9 1.0

Iron binding site 7 out of 10 in 2h89

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Iron binding site 7 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:37.8
occ:1.00
 FE1 B:F3S1004 0.0 37.8 1.0
S2 B:F3S1004 2.2 43.1 1.0
S3 B:F3S1004 2.2 37.0 1.0
SG B:CYS215 2.2 34.8 1.0
S1 B:F3S1004 2.3 35.7 1.0
FE4 B:F3S1004 2.6 36.0 1.0
FE3 B:F3S1004 2.9 31.5 1.0
CB B:CYS215 3.3 41.9 1.0
CA B:CYS215 3.6 40.2 1.0
N B:THR217 3.9 39.4 1.0
O B:HOH1051 3.9 68.0 1.0
OH B:TYR178 3.9 31.2 1.0
S4 B:F3S1004 4.0 36.6 1.0
N B:HIS216 4.1 42.6 1.0
C B:CYS215 4.1 42.5 1.0
N B:ILE218 4.2 44.7 1.0
CA B:THR217 4.2 37.7 1.0
SG B:CYS168 4.5 44.4 1.0
CD1 B:ILE235 4.6 38.1 1.0
C B:THR217 4.7 42.5 1.0
C B:HIS216 4.9 40.9 1.0
N B:MET219 4.9 44.4 1.0
O B:CYS215 4.9 39.5 1.0
N B:CYS215 5.0 40.1 1.0

Iron binding site 8 out of 10 in 2h89

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Iron binding site 8 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:31.5
occ:1.00
 FE3 B:F3S1004 0.0 31.5 1.0
S4 B:F3S1004 2.2 36.6 1.0
S1 B:F3S1004 2.2 35.7 1.0
S3 B:F3S1004 2.3 37.0 1.0
SG B:CYS221 2.5 37.4 1.0
FE4 B:F3S1004 2.5 36.0 1.0
FE1 B:F3S1004 2.9 37.8 1.0
CB B:CYS221 3.3 36.5 1.0
N B:CYS221 3.8 42.8 1.0
N B:MET219 4.0 44.4 1.0
S2 B:F3S1004 4.0 43.1 1.0
CA B:MET219 4.2 47.1 1.0
N B:ASN220 4.2 43.1 1.0
CA B:CYS221 4.2 37.6 1.0
SG B:CYS168 4.4 44.4 1.0
C B:MET219 4.5 49.5 1.0
CB B:CYS168 4.6 41.0 1.0
SG B:CYS215 4.8 34.8 1.0
CG B:PRO181 4.8 35.1 1.0
CB B:PRO181 4.8 34.7 1.0
CA B:GLY232 4.9 38.6 1.0
C B:ASN220 5.0 44.1 1.0

Iron binding site 9 out of 10 in 2h89

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Iron binding site 9 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe1004

b:36.0
occ:1.00
 FE4 B:F3S1004 0.0 36.0 1.0
SG B:CYS168 2.1 44.4 1.0
S3 B:F3S1004 2.2 37.0 1.0
S2 B:F3S1004 2.3 43.1 1.0
S4 B:F3S1004 2.3 36.6 1.0
FE3 B:F3S1004 2.5 31.5 1.0
FE1 B:F3S1004 2.6 37.8 1.0
CB B:CYS168 3.2 41.0 1.0
S1 B:F3S1004 3.6 35.7 1.0
CA B:CYS168 4.1 43.1 1.0
OH B:TYR178 4.4 31.2 1.0
CB B:ILE218 4.5 42.1 1.0
OG B:SER170 4.6 42.4 1.0
SG B:CYS215 4.8 34.8 1.0
C B:CYS168 4.8 42.2 1.0
CD B:PRO181 4.9 29.4 1.0
CD1 B:ILE218 4.9 45.4 1.0
SG B:CYS221 4.9 37.4 1.0
N B:ILE218 4.9 44.7 1.0
CD B:PRO169 4.9 42.8 1.0
N B:MET219 4.9 44.4 1.0

Iron binding site 10 out of 10 in 2h89

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Iron binding site 10 out of 10 in the Avian Respiratory Complex II with Malonate 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 Malonate Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe142

b:49.0
occ:1.00
 FE C:HEM142 0.0 49.0 1.0
NC C:HEM142 1.9 51.6 1.0
ND C:HEM142 2.0 49.7 1.0
NB C:HEM142 2.0 50.7 1.0
NA C:HEM142 2.0 49.7 1.0
NE2 C:HIS98 2.0 46.6 1.0
NE2 D:HIS46 2.0 46.4 1.0
CD2 C:HIS98 3.0 44.1 1.0
C1C C:HEM142 3.0 53.2 1.0
CD2 D:HIS46 3.0 43.0 1.0
C4B C:HEM142 3.0 53.3 1.0
C4C C:HEM142 3.0 53.4 1.0
C1A C:HEM142 3.0 50.9 1.0
CE1 C:HIS98 3.0 45.7 1.0
C4D C:HEM142 3.0 50.0 1.0
CE1 D:HIS46 3.0 43.6 1.0
C1D C:HEM142 3.1 50.2 1.0
C4A C:HEM142 3.1 50.8 1.0
C1B C:HEM142 3.1 53.2 1.0
CHC C:HEM142 3.3 54.7 1.0
CHA C:HEM142 3.4 50.4 1.0
CHD C:HEM142 3.4 51.5 1.0
CHB C:HEM142 3.5 51.3 1.0
ND1 C:HIS98 4.1 43.2 1.0
CG C:HIS98 4.1 41.0 1.0
ND1 D:HIS46 4.1 38.4 1.0
CG D:HIS46 4.2 34.1 1.0
C3C C:HEM142 4.2 53.4 1.0
C2C C:HEM142 4.2 55.3 1.0
C2A C:HEM142 4.2 48.7 1.0
C3B C:HEM142 4.3 54.3 1.0
C3A C:HEM142 4.3 49.9 1.0
C3D C:HEM142 4.3 51.1 1.0
C2D C:HEM142 4.3 47.5 1.0
C2B C:HEM142 4.3 53.1 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: Sat Aug 3 22:50:25 2024

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