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Iron in PDB 1nen: Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site

Enzymatic activity of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site

All present enzymatic activity of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site:
1.3.5.1; 1.3.99.1;

Protein crystallography data

The structure of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site, PDB code: 1nen was solved by V.Yankovskaya, R.Horsefield, S.Tornroth, C.Luna-Chavez, H.Miyoshi, C.Leger, B.Byrne, G.Cecchini, S.Iwata, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 2.90
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 138.800, 138.800, 521.900, 90.00, 90.00, 120.00
R / Rfree (%) 27.1 / 29.6

Other elements in 1nen:

The structure of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site (pdb code 1nen). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 10 binding sites of Iron where determined in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site, PDB code: 1nen:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 1nen

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Iron binding site 1 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:74.7
occ:1.00
 FE1 B:FES302 0.0 74.7 1.0
OD1 B:ASP63 2.1 62.9 1.0
S2 B:FES302 2.3 88.2 1.0
SG B:CYS75 2.3 70.9 1.0
S1 B:FES302 2.3 88.7 1.0
OD2 B:ASP63 2.6 56.6 1.0
CG B:ASP63 2.7 56.2 1.0
CB B:CYS75 2.7 73.6 1.0
FE2 B:FES302 2.7 79.8 1.0
N B:GLY58 4.0 64.8 1.0
CA B:CYS75 4.0 74.3 1.0
N B:CYS75 4.1 74.6 1.0
CB B:ASP63 4.2 60.8 1.0
CA B:GLY58 4.3 63.4 1.0
SG B:CYS55 4.4 77.1 1.0
N B:ASP63 4.5 67.0 1.0
CB B:LEU73 4.5 59.6 1.0
SG B:CYS60 4.5 63.5 1.0
N B:ARG56 4.6 73.8 1.0
CA B:ARG56 4.6 73.7 1.0
CD1 B:LEU73 4.7 61.6 1.0
C B:ARG56 4.7 73.6 1.0
N B:GLU57 4.7 72.8 1.0
CD2 B:LEU73 4.8 56.4 1.0
C B:CYS75 4.9 75.1 1.0
CA B:ASP63 4.9 68.4 1.0
CG B:LEU73 4.9 57.8 1.0
N B:VAL59 5.0 59.9 1.0

Iron binding site 2 out of 10 in 1nen

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Iron binding site 2 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:79.8
occ:1.00
 FE2 B:FES302 0.0 79.8 1.0
S2 B:FES302 2.2 88.2 1.0
S1 B:FES302 2.2 88.7 1.0
SG B:CYS60 2.2 63.5 1.0
SG B:CYS55 2.2 77.1 1.0
FE1 B:FES302 2.7 74.7 1.0
N B:CYS60 3.1 62.0 1.0
CB B:CYS60 3.2 65.6 1.0
CA B:CYS60 3.6 59.9 1.0
CB B:CYS55 3.7 75.6 1.0
N B:GLY61 3.7 60.5 1.0
OD1 B:ASP63 3.7 62.9 1.0
N B:ARG56 3.7 73.8 1.0
N B:VAL59 3.8 59.9 1.0
N B:CYS55 3.9 69.3 1.0
C B:CYS60 4.1 59.8 1.0
CA B:CYS55 4.1 72.7 1.0
C B:VAL59 4.2 64.3 1.0
N B:GLY58 4.3 64.8 1.0
C B:CYS55 4.3 74.1 1.0
N B:SER62 4.4 61.2 1.0
SG B:CYS75 4.5 70.9 1.0
N B:GLU57 4.5 72.8 1.0
C B:SER54 4.5 65.0 1.0
CA B:ARG56 4.6 73.7 1.0
CA B:VAL59 4.6 63.9 1.0
CA B:GLY58 4.6 63.4 1.0
C B:GLY58 4.7 59.8 1.0
N B:SER54 4.7 61.1 1.0
CA B:GLY61 4.8 61.7 1.0
CG B:ASP63 4.8 56.2 1.0
C B:ARG56 4.9 73.6 1.0
OG B:SER62 4.9 58.4 1.0
CA B:SER54 5.0 61.8 1.0
CB B:SER62 5.0 59.4 1.0

Iron binding site 3 out of 10 in 1nen

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Iron binding site 3 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:61.8
occ:1.00
 FE1 B:SF4303 0.0 61.8 1.0
SG B:CYS155 2.3 55.3 1.0
S3 B:SF4303 2.3 62.4 1.0
S4 B:SF4303 2.3 50.0 1.0
S2 B:SF4303 2.3 54.0 1.0
FE3 B:SF4303 2.6 52.8 1.0
FE2 B:SF4303 2.7 59.5 1.0
FE4 B:SF4303 2.8 63.0 1.0
CB B:CYS155 3.2 47.5 1.0
S1 B:SF4303 3.9 55.8 1.0
N B:CYS155 4.1 51.9 1.0
CB B:ALA173 4.3 46.9 1.0
CA B:CYS155 4.3 51.8 1.0
CA B:ALA173 4.5 51.5 1.0
SG B:CYS149 4.5 61.4 1.0
SG B:CYS216 4.6 60.3 1.0
N B:ALA173 4.7 51.9 1.0
SG B:CYS152 4.8 65.5 1.0
N B:CYS154 4.9 58.3 1.0
CG B:PRO222 5.0 62.0 1.0

Iron binding site 4 out of 10 in 1nen

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Iron binding site 4 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:59.5
occ:1.00
 FE2 B:SF4303 0.0 59.5 1.0
S3 B:SF4303 2.2 62.4 1.0
SG B:CYS149 2.2 61.4 1.0
S4 B:SF4303 2.3 50.0 1.0
S1 B:SF4303 2.3 55.8 1.0
FE4 B:SF4303 2.6 63.0 1.0
FE1 B:SF4303 2.7 61.8 1.0
FE3 B:SF4303 2.7 52.8 1.0
CB B:CYS149 3.4 57.5 1.0
CA B:CYS149 3.7 57.9 1.0
N B:ILE150 3.8 58.0 1.0
S2 B:SF4303 3.8 54.0 1.0
N B:LEU151 3.9 62.8 1.0
C B:CYS149 4.1 57.4 1.0
CD1 B:LEU220 4.3 55.4 1.0
CA B:LEU151 4.6 64.0 1.0
N B:CYS152 4.7 63.3 1.0
SG B:CYS152 4.7 65.5 1.0
SG B:CYS155 4.7 55.3 1.0
CD2 B:LEU176 4.8 45.1 1.0
CB B:ALA173 4.8 46.9 1.0
C B:ILE150 4.9 62.1 1.0
CA B:ILE150 4.9 61.8 1.0
SG B:CYS216 4.9 60.3 1.0
CG1 B:ILE150 5.0 60.5 1.0

Iron binding site 5 out of 10 in 1nen

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Iron binding site 5 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 5 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:52.8
occ:1.00
 FE3 B:SF4303 0.0 52.8 1.0
S2 B:SF4303 2.2 54.0 1.0
S4 B:SF4303 2.2 50.0 1.0
SG B:CYS216 2.2 60.3 1.0
S1 B:SF4303 2.3 55.8 1.0
FE1 B:SF4303 2.6 61.8 1.0
FE4 B:SF4303 2.7 63.0 1.0
FE2 B:SF4303 2.7 59.5 1.0
CB B:CYS216 3.4 69.1 1.0
S3 B:SF4303 3.8 62.4 1.0
CD1 B:LEU220 3.9 55.4 1.0
CA B:CYS216 4.1 70.2 1.0
CG B:LEU220 4.2 55.7 1.0
CB B:LEU220 4.3 60.3 1.0
CD B:PRO217 4.4 68.2 1.0
SG B:CYS152 4.5 65.5 1.0
C B:CYS216 4.7 71.9 1.0
SG B:CYS155 4.8 55.3 1.0
N B:PRO217 4.8 71.4 1.0
SG B:CYS149 4.8 61.4 1.0
CG B:LYS218 4.9 74.5 1.0
N B:LYS218 5.0 70.1 1.0

Iron binding site 6 out of 10 in 1nen

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Iron binding site 6 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 6 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:63.0
occ:1.00
 FE4 B:SF4303 0.0 63.0 1.0
S3 B:SF4303 2.2 62.4 1.0
SG B:CYS152 2.2 65.5 1.0
S1 B:SF4303 2.2 55.8 1.0
S2 B:SF4303 2.2 54.0 1.0
FE2 B:SF4303 2.6 59.5 1.0
FE3 B:SF4303 2.7 52.8 1.0
FE1 B:SF4303 2.8 61.8 1.0
N B:CYS152 3.5 63.3 1.0
CB B:CYS152 3.6 66.3 1.0
N B:ALA153 3.7 60.2 1.0
S4 B:SF4303 3.8 50.0 1.0
CA B:CYS152 4.0 63.8 1.0
N B:CYS154 4.1 58.3 1.0
C B:CYS152 4.3 61.0 1.0
SG B:CYS155 4.3 55.3 1.0
N B:LEU151 4.4 62.8 1.0
CG1 B:ILE150 4.5 60.5 1.0
C B:LEU151 4.6 65.6 1.0
SG B:CYS149 4.6 61.4 1.0
CA B:ALA153 4.6 58.1 1.0
CD B:PRO217 4.6 68.2 1.0
SG B:CYS216 4.6 60.3 1.0
CA B:LEU151 4.8 64.0 1.0
N B:ILE150 4.8 58.0 1.0
CB B:CYS154 4.8 59.1 1.0
N B:CYS155 4.8 51.9 1.0
C B:ALA153 4.9 57.9 1.0

Iron binding site 7 out of 10 in 1nen

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Iron binding site 7 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 7 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:59.0
occ:1.00
 FE1 B:F3S304 0.0 59.0 1.0
SG B:CYS206 2.2 59.4 1.0
S1 B:F3S304 2.2 51.9 1.0
S3 B:F3S304 2.3 65.1 1.0
S2 B:F3S304 2.3 44.6 1.0
FE3 B:F3S304 2.7 61.4 1.0
FE4 B:F3S304 2.8 56.1 1.0
CB B:CYS206 3.3 58.7 1.0
CA B:CYS206 3.7 55.6 1.0
S4 B:F3S304 3.8 54.9 1.0
N B:SER208 3.8 71.2 1.0
N B:HIS207 4.1 61.6 1.0
C B:CYS206 4.2 57.7 1.0
CA B:SER208 4.2 72.8 1.0
N B:ILE209 4.3 75.0 1.0
CD1 B:ILE226 4.4 34.5 1.0
CG2 B:THR223 4.7 60.3 1.0
C B:SER208 4.8 75.0 1.0
SG B:CYS212 4.8 73.9 1.0
SG B:CYS159 4.8 55.3 1.0
C B:HIS207 4.9 68.1 1.0

Iron binding site 8 out of 10 in 1nen

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Iron binding site 8 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 8 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:61.4
occ:1.00
 FE3 B:F3S304 0.0 61.4 1.0
SG B:CYS212 2.3 73.9 1.0
S1 B:F3S304 2.3 51.9 1.0
S4 B:F3S304 2.3 54.9 1.0
S3 B:F3S304 2.3 65.1 1.0
FE1 B:F3S304 2.7 59.0 1.0
FE4 B:F3S304 2.8 56.1 1.0
CG2 B:THR223 3.5 60.3 1.0
CB B:CYS212 3.5 72.7 1.0
S2 B:F3S304 3.9 44.6 1.0
N B:MET210 4.1 69.1 1.0
N B:CYS212 4.2 70.7 1.0
CG B:PRO172 4.3 54.9 1.0
CA B:MET210 4.3 70.1 1.0
CA B:CYS212 4.5 68.8 1.0
N B:ASN211 4.5 67.7 1.0
SG B:CYS206 4.7 59.4 1.0
CB B:THR223 4.7 62.4 1.0
C B:MET210 4.8 70.8 1.0
N B:ILE209 4.9 75.0 1.0
N B:THR223 4.9 62.0 1.0
CA B:THR223 4.9 62.5 1.0
SG B:CYS159 4.9 55.3 1.0
CB B:PRO172 5.0 51.7 1.0

Iron binding site 9 out of 10 in 1nen

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Iron binding site 9 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 9 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:56.1
occ:1.00
 FE4 B:F3S304 0.0 56.1 1.0
S4 B:F3S304 2.2 54.9 1.0
SG B:CYS159 2.3 55.3 1.0
S2 B:F3S304 2.3 44.6 1.0
S3 B:F3S304 2.3 65.1 1.0
FE1 B:F3S304 2.8 59.0 1.0
FE3 B:F3S304 2.8 61.4 1.0
CB B:CYS159 3.3 59.7 1.0
S1 B:F3S304 3.9 51.9 1.0
CG B:PRO172 4.2 54.9 1.0
CA B:CYS159 4.4 60.9 1.0
CE2 B:PHE169 4.7 60.3 1.0
SG B:CYS212 4.7 73.9 1.0
SG B:CYS206 4.8 59.4 1.0
CD B:PRO172 4.8 54.0 1.0
CZ B:PHE169 4.8 61.3 1.0
CB B:ILE209 4.9 68.3 1.0

Iron binding site 10 out of 10 in 1nen

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Iron binding site 10 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 10 of Complex II (Succinate Dehydrogenase) From E. Coli with Dinitrophenol-17 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe305

b:35.2
occ:1.00
 FE C:HEM305 0.0 35.2 1.0
NB C:HEM305 2.0 26.2 1.0
NA C:HEM305 2.1 24.0 1.0
NC C:HEM305 2.1 30.6 1.0
ND C:HEM305 2.1 30.2 1.0
NE2 C:HIS84 2.1 50.4 1.0
NE2 D:HIS71 2.2 49.1 1.0
C4B C:HEM305 2.9 33.0 1.0
C1A C:HEM305 3.0 30.4 1.0
C1C C:HEM305 3.0 37.7 1.0
C1B C:HEM305 3.0 26.5 1.0
C4D C:HEM305 3.0 33.8 1.0
C4A C:HEM305 3.1 24.4 1.0
C4C C:HEM305 3.1 30.6 1.0
C1D C:HEM305 3.1 34.4 1.0
CE1 C:HIS84 3.1 46.9 1.0
CD2 C:HIS84 3.1 51.2 1.0
CE1 D:HIS71 3.2 46.1 1.0
CD2 D:HIS71 3.2 48.8 1.0
CHC C:HEM305 3.4 38.4 1.0
CHA C:HEM305 3.4 31.3 1.0
CHB C:HEM305 3.5 18.6 1.0
CHD C:HEM305 3.5 34.6 1.0
C3B C:HEM305 4.2 36.0 1.0
C2B C:HEM305 4.2 32.7 1.0
ND1 C:HIS84 4.2 53.5 1.0
C2A C:HEM305 4.2 33.9 1.0
CG C:HIS84 4.3 53.9 1.0
C3A C:HEM305 4.3 27.7 1.0
C2C C:HEM305 4.3 31.6 1.0
ND1 D:HIS71 4.3 53.5 1.0
C3D C:HEM305 4.3 38.3 1.0
C3C C:HEM305 4.3 30.8 1.0
C2D C:HEM305 4.3 33.3 1.0
CG D:HIS71 4.3 56.6 1.0
CE1 C:HIS30 4.8 55.8 1.0

Reference:

V.Yankovskaya, R.Horsefield, S.Tornroth, C.Luna-Chavez, H.Miyoshi, C.Leger, B.Byrne, G.Cecchini, S.Iwata. Architecture of Succinate Dehydrogenase and Reactive Oxygen Species Generation Science V. 299 700 2003.
ISSN: ISSN 0036-8075
PubMed: 12560550
DOI: 10.1126/SCIENCE.1079605
Page generated: Sun Dec 13 14:25:26 2020

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