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Iron in PDB 2acz: Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site

Enzymatic activity of Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site

All present enzymatic activity of Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site:
1.3.99.1;

Protein crystallography data

The structure of Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site, PDB code: 2acz was solved by R.Horsefield, V.Yankovskaya, G.Sexton, W.Whittingham, K.Shiomi, S.Omura, 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 / 3.10
Space group H 3 2
Cell size a, b, c (Å), α, β, γ (°) 138.759, 138.759, 521.873, 90.00, 90.00, 120.00
R / Rfree (%) 26.4 / 30.8

Other elements in 2acz:

The structure of Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site (pdb code 2acz). 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site, PDB code: 2acz:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 2acz

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Iron binding site 1 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:53.4
occ:1.00
 FE1 B:FES302 0.0 53.4 1.0
OD2 B:ASP63 2.2 56.9 1.0
S2 B:FES302 2.2 58.3 1.0
S1 B:FES302 2.3 60.2 1.0
OD1 B:ASP63 2.5 56.1 1.0
SG B:CYS75 2.6 58.2 1.0
CG B:ASP63 2.6 55.4 1.0
FE2 B:FES302 2.7 57.5 1.0
CB B:CYS75 3.1 58.5 1.0
N B:ASP63 3.8 54.6 1.0
CB B:ASP63 4.0 55.1 1.0
N B:CYS75 4.2 59.5 1.0
CA B:CYS75 4.3 58.5 1.0
N B:GLY58 4.4 65.9 1.0
CA B:ASP63 4.5 56.2 1.0
CA B:GLY58 4.5 64.3 1.0
N B:ARG56 4.5 62.2 1.0
SG B:CYS60 4.5 55.9 1.0
N B:SER62 4.6 52.2 1.0
SG B:CYS55 4.6 56.0 1.0
CA B:ARG56 4.6 65.6 1.0
CD1 B:LEU73 4.7 52.2 1.0
CB B:SER62 4.8 50.7 1.0
CD2 B:LEU73 4.8 54.9 1.0
C B:SER62 4.9 53.1 1.0
CB B:LEU73 4.9 59.0 1.0
C B:ARG56 4.9 66.5 1.0
CA B:SER62 4.9 52.2 1.0
N B:GLY61 5.0 50.9 1.0

Iron binding site 2 out of 10 in 2acz

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Iron binding site 2 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:57.5
occ:1.00
 FE2 B:FES302 0.0 57.5 1.0
S2 B:FES302 2.2 58.3 1.0
S1 B:FES302 2.2 60.2 1.0
SG B:CYS55 2.3 56.0 1.0
SG B:CYS60 2.5 55.9 1.0
FE1 B:FES302 2.7 53.4 1.0
CB B:CYS60 3.3 56.4 1.0
N B:ARG56 3.3 62.2 1.0
N B:CYS60 3.4 56.2 1.0
CB B:CYS55 3.4 57.8 1.0
N B:CYS55 3.5 55.9 1.0
CA B:CYS55 3.8 58.2 1.0
CA B:CYS60 3.8 54.7 1.0
C B:CYS55 3.9 60.3 1.0
N B:VAL59 4.0 60.4 1.0
N B:GLY61 4.1 50.9 1.0
C B:SER54 4.2 52.0 1.0
N B:GLY58 4.2 65.9 1.0
CA B:ARG56 4.2 65.6 1.0
C B:CYS60 4.3 53.0 1.0
SG B:CYS75 4.4 58.2 1.0
N B:SER54 4.4 47.1 1.0
N B:SER62 4.4 52.2 1.0
C B:VAL59 4.5 58.2 1.0
N B:GLU57 4.5 66.4 1.0
CB B:SER62 4.5 50.7 1.0
OD2 B:ASP63 4.6 56.9 1.0
CA B:GLY58 4.6 64.3 1.0
C B:ARG56 4.7 66.5 1.0
CA B:SER54 4.7 49.2 1.0
C B:GLY58 4.7 62.5 1.0
CA B:VAL59 4.8 59.3 1.0
O B:SER54 4.9 51.4 1.0
CB B:SER54 5.0 48.0 1.0
CB B:CYS75 5.0 58.5 1.0

Iron binding site 3 out of 10 in 2acz

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Iron binding site 3 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:45.1
occ:1.00
 FE1 B:SF4303 0.0 45.1 1.0
S2 B:SF4303 2.3 48.2 1.0
S3 B:SF4303 2.3 45.3 1.0
S4 B:SF4303 2.3 46.5 1.0
SG B:CYS155 2.5 43.5 1.0
FE2 B:SF4303 2.7 46.1 1.0
FE3 B:SF4303 2.7 42.9 1.0
FE4 B:SF4303 2.8 49.7 1.0
CB B:CYS155 3.4 42.5 1.0
S1 B:SF4303 3.9 49.0 1.0
N B:CYS155 4.0 45.1 1.0
CB B:ALA173 4.4 51.4 1.0
CA B:CYS155 4.4 44.1 1.0
SG B:CYS149 4.7 53.6 1.0
CA B:ALA173 4.7 51.0 1.0
N B:CYS154 4.7 46.2 1.0
SG B:CYS216 4.8 51.2 1.0
SG B:CYS152 4.8 51.8 1.0
CG B:PRO222 4.9 53.9 1.0
N B:ALA173 4.9 50.1 1.0
CB B:CYS216 5.0 47.7 1.0

Iron binding site 4 out of 10 in 2acz

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Iron binding site 4 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:46.1
occ:1.00
 FE2 B:SF4303 0.0 46.1 1.0
S3 B:SF4303 2.2 45.3 1.0
S1 B:SF4303 2.2 49.0 1.0
S4 B:SF4303 2.3 46.5 1.0
SG B:CYS216 2.4 51.2 1.0
FE1 B:SF4303 2.7 45.1 1.0
FE4 B:SF4303 2.7 49.7 1.0
FE3 B:SF4303 2.7 42.9 1.0
CB B:CYS216 3.4 47.7 1.0
S2 B:SF4303 3.8 48.2 1.0
CA B:CYS216 4.0 48.0 1.0
CD1 B:LEU220 4.1 53.1 1.0
CB B:LEU220 4.4 53.6 1.0
CG B:LEU220 4.4 51.3 1.0
C B:CYS216 4.5 47.5 1.0
CD B:PRO217 4.5 48.4 1.0
N B:PRO217 4.6 48.3 1.0
N B:LYS218 4.7 55.5 1.0
SG B:CYS152 4.7 51.8 1.0
SG B:CYS149 4.9 53.6 1.0
CB B:LYS218 4.9 58.1 1.0
SG B:CYS155 5.0 43.5 1.0

Iron binding site 5 out of 10 in 2acz

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Iron binding site 5 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:42.9
occ:1.00
 FE3 B:SF4303 0.0 42.9 1.0
S4 B:SF4303 2.2 46.5 1.0
S2 B:SF4303 2.2 48.2 1.0
S1 B:SF4303 2.3 49.0 1.0
SG B:CYS149 2.3 53.6 1.0
FE4 B:SF4303 2.6 49.7 1.0
FE1 B:SF4303 2.7 45.1 1.0
FE2 B:SF4303 2.7 46.1 1.0
CB B:CYS149 3.2 50.4 1.0
CA B:CYS149 3.7 51.3 1.0
S3 B:SF4303 3.7 45.3 1.0
N B:ILE150 4.0 52.2 1.0
N B:LEU151 4.2 46.8 1.0
CD1 B:LEU220 4.3 53.1 1.0
C B:CYS149 4.3 52.0 1.0
CB B:ALA173 4.8 51.4 1.0
CA B:LEU151 4.8 46.5 1.0
N B:CYS152 4.8 46.8 1.0
SG B:CYS152 4.9 51.8 1.0
SG B:CYS155 4.9 43.5 1.0
N B:CYS149 5.0 51.9 1.0
SG B:CYS216 5.0 51.2 1.0

Iron binding site 6 out of 10 in 2acz

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Iron binding site 6 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:49.7
occ:1.00
 FE4 B:SF4303 0.0 49.7 1.0
S2 B:SF4303 2.2 48.2 1.0
S1 B:SF4303 2.2 49.0 1.0
S3 B:SF4303 2.2 45.3 1.0
SG B:CYS152 2.4 51.8 1.0
FE3 B:SF4303 2.6 42.9 1.0
FE2 B:SF4303 2.7 46.1 1.0
FE1 B:SF4303 2.8 45.1 1.0
N B:CYS152 3.6 46.8 1.0
CB B:CYS152 3.6 46.1 1.0
S4 B:SF4303 3.8 46.5 1.0
N B:ALA153 4.0 46.1 1.0
CA B:CYS152 4.1 47.0 1.0
N B:CYS154 4.2 46.2 1.0
CG1 B:ILE150 4.3 52.8 1.0
C B:CYS152 4.3 46.7 1.0
SG B:CYS149 4.3 53.6 1.0
CB B:CYS154 4.5 49.1 1.0
N B:LEU151 4.6 46.8 1.0
CD B:PRO217 4.6 48.4 1.0
C B:LEU151 4.7 46.7 1.0
SG B:CYS216 4.8 51.2 1.0
SG B:CYS155 4.8 43.5 1.0
N B:ILE150 4.8 52.2 1.0
CA B:LEU151 4.9 46.5 1.0
CA B:ALA153 4.9 45.4 1.0
CA B:CYS154 4.9 47.7 1.0
CD1 B:ILE150 5.0 53.6 1.0

Iron binding site 7 out of 10 in 2acz

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Iron binding site 7 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:39.0
occ:1.00
 FE1 B:F3S304 0.0 39.0 1.0
S1 B:F3S304 2.2 42.0 1.0
S2 B:F3S304 2.3 33.4 1.0
S3 B:F3S304 2.3 41.1 1.0
SG B:CYS206 2.6 52.3 1.0
FE3 B:F3S304 2.7 39.8 1.0
FE4 B:F3S304 2.7 39.4 1.0
CB B:CYS206 3.3 48.7 1.0
CA B:CYS206 3.7 48.8 1.0
S4 B:F3S304 4.0 41.7 1.0
CG2 B:THR223 4.2 51.8 1.0
CD1 B:ILE226 4.2 40.7 1.0
N B:HIS207 4.3 52.2 1.0
N B:SER208 4.4 53.1 1.0
C B:CYS206 4.4 49.8 1.0
CZ B:PHE169 4.7 54.8 1.0
SG B:CYS212 4.7 46.9 1.0
SG B:CYS159 4.8 49.9 1.0
CA B:SER208 4.8 52.7 1.0
N B:ILE209 4.9 51.6 1.0
N B:CYS206 5.0 46.8 1.0

Iron binding site 8 out of 10 in 2acz

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Iron binding site 8 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:39.8
occ:1.00
 FE3 B:F3S304 0.0 39.8 1.0
S1 B:F3S304 2.3 42.0 1.0
S4 B:F3S304 2.3 41.7 1.0
S3 B:F3S304 2.3 41.1 1.0
SG B:CYS212 2.4 46.9 1.0
FE1 B:F3S304 2.7 39.0 1.0
FE4 B:F3S304 2.8 39.4 1.0
CG2 B:THR223 3.4 51.8 1.0
CB B:CYS212 3.6 53.0 1.0
S2 B:F3S304 3.7 33.4 1.0
N B:MET210 3.8 54.4 1.0
CA B:MET210 4.0 56.5 1.0
N B:CYS212 4.1 55.3 1.0
C B:MET210 4.4 57.7 1.0
CA B:CYS212 4.5 53.4 1.0
N B:ASN211 4.5 57.2 1.0
CG B:PRO172 4.7 46.1 1.0
CB B:THR223 4.8 53.5 1.0
N B:ILE209 4.8 51.6 1.0
SG B:CYS206 5.0 52.3 1.0
SG B:CYS159 5.0 49.9 1.0
C B:ILE209 5.0 53.5 1.0

Iron binding site 9 out of 10 in 2acz

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Iron binding site 9 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:39.4
occ:1.00
 FE4 B:F3S304 0.0 39.4 1.0
S4 B:F3S304 2.2 41.7 1.0
S2 B:F3S304 2.3 33.4 1.0
S3 B:F3S304 2.3 41.1 1.0
SG B:CYS159 2.3 49.9 1.0
FE1 B:F3S304 2.7 39.0 1.0
FE3 B:F3S304 2.8 39.8 1.0
CB B:CYS159 3.2 54.0 1.0
S1 B:F3S304 3.6 42.0 1.0
CA B:CYS159 4.1 54.3 1.0
CG B:PRO172 4.5 46.1 1.0
CE2 B:PHE169 4.7 53.4 1.0
SG B:CYS212 4.8 46.9 1.0
C B:CYS159 4.9 52.0 1.0
CB B:SER161 4.9 50.1 1.0
CZ B:PHE169 4.9 54.8 1.0
CB B:ILE209 5.0 50.2 1.0

Iron binding site 10 out of 10 in 2acz

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Iron binding site 10 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Atpenin A5 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 Atpenin A5 Inhibitor Co-Crystallized at the Ubiquinone Binding Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe130

b:28.2
occ:1.00
 FE C:HEB130 0.0 28.2 1.0
NB C:HEB130 2.0 26.7 1.0
NC C:HEB130 2.0 25.7 1.0
NA C:HEB130 2.1 22.4 1.0
ND C:HEB130 2.1 26.7 1.0
NE2 C:HIS84 2.2 44.6 1.0
NE2 D:HIS71 2.2 41.7 1.0
C4B C:HEB130 3.0 28.5 1.0
C1C C:HEB130 3.0 28.9 1.0
C1A C:HEB130 3.0 23.0 1.0
CD2 D:HIS71 3.1 39.8 1.0
C1B C:HEB130 3.1 26.5 1.0
C4A C:HEB130 3.1 23.5 1.0
C4D C:HEB130 3.1 26.9 1.0
C4C C:HEB130 3.1 29.2 1.0
C1D C:HEB130 3.1 27.3 1.0
CD2 C:HIS84 3.1 41.9 1.0
CE1 C:HIS84 3.2 42.2 1.0
CE1 D:HIS71 3.3 41.4 1.0
CHC C:HEB130 3.4 27.7 1.0
CHA C:HEB130 3.4 24.4 1.0
CHB C:HEB130 3.5 22.6 1.0
CHD C:HEB130 3.5 29.0 1.0
CG D:HIS71 4.2 40.9 1.0
C3B C:HEB130 4.2 29.6 1.0
C2A C:HEB130 4.3 25.3 1.0
C2C C:HEB130 4.3 30.9 1.0
C3C C:HEB130 4.3 32.1 1.0
C2B C:HEB130 4.3 26.7 1.0
C3A C:HEB130 4.3 24.6 1.0
CG C:HIS84 4.3 43.4 1.0
ND1 C:HIS84 4.3 44.5 1.0
ND1 D:HIS71 4.3 43.8 1.0
C3D C:HEB130 4.3 26.5 1.0
C2D C:HEB130 4.3 24.4 1.0

Reference:

R.Horsefield, V.Yankovskaya, G.Sexton, W.Whittingham, K.Shiomi, S.Omura, B.Byrne, G.Cecchini, S.Iwata. Structural and Computational Analysis of the Quinone-Binding Site of Complex II (Succinate-Ubiquinone Oxidoreductase): A Mechanism of Electron Transfer and Proton Conduction During Ubiquinone Reduction. J.Biol.Chem. V. 281 7309 2006.
ISSN: ISSN 0021-9258
PubMed: 16407191
DOI: 10.1074/JBC.M508173200
Page generated: Sun Dec 13 14:39:28 2020

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