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Iron in PDB 1nek: Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound

Enzymatic activity of Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound

All present enzymatic activity of Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound:
1.3.5.1; 1.3.99.1;

Protein crystallography data

The structure of Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound, PDB code: 1nek 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 / 2.60
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 (%) 24.7 / 28.9

Other elements in 1nek:

The structure of Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound 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 Ubiquinone Bound (pdb code 1nek). 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 Ubiquinone Bound, PDB code: 1nek:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iron binding site 1 out of 10 in 1nek

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Iron binding site 1 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:36.5
occ:1.00
 FE1 B:FES302 0.0 36.5 1.0
OD1 B:ASP63 2.1 34.1 1.0
S2 B:FES302 2.3 47.4 1.0
SG B:CYS75 2.3 33.0 1.0
S1 B:FES302 2.3 43.2 1.0
OD2 B:ASP63 2.4 24.8 1.0
CG B:ASP63 2.6 28.3 1.0
FE2 B:FES302 2.7 37.3 1.0
CB B:CYS75 2.8 29.8 1.0
N B:GLY58 3.9 41.5 1.0
CA B:CYS75 4.1 27.4 1.0
CB B:ASP63 4.1 28.8 1.0
N B:CYS75 4.2 32.2 1.0
CA B:GLY58 4.2 36.5 1.0
SG B:CYS55 4.3 37.4 1.0
N B:ASP63 4.4 23.1 1.0
SG B:CYS60 4.5 37.2 1.0
N B:ARG56 4.5 39.0 1.0
CA B:ARG56 4.5 40.7 1.0
CB B:LEU73 4.5 23.7 1.0
C B:ARG56 4.6 43.8 1.0
N B:GLU57 4.8 47.4 1.0
CA B:ASP63 4.8 27.8 1.0
CD1 B:LEU73 4.9 13.8 1.0
CD2 B:LEU73 5.0 13.7 1.0
N B:VAL59 5.0 30.2 1.0
C B:CYS75 5.0 27.3 1.0
O B:ARG56 5.0 47.5 1.0

Iron binding site 2 out of 10 in 1nek

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Iron binding site 2 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe302

b:37.3
occ:1.00
 FE2 B:FES302 0.0 37.3 1.0
S2 B:FES302 2.2 47.4 1.0
SG B:CYS55 2.2 37.4 1.0
S1 B:FES302 2.2 43.2 1.0
SG B:CYS60 2.3 37.2 1.0
FE1 B:FES302 2.7 36.5 1.0
CB B:CYS60 3.1 26.4 1.0
N B:CYS60 3.1 22.5 1.0
CB B:CYS55 3.5 40.3 1.0
CA B:CYS60 3.5 25.4 1.0
N B:ARG56 3.7 39.0 1.0
N B:GLY61 3.7 25.4 1.0
OD1 B:ASP63 3.7 34.1 1.0
N B:CYS55 3.8 33.9 1.0
N B:VAL59 3.9 30.2 1.0
CA B:CYS55 4.0 38.0 1.0
C B:CYS60 4.1 25.5 1.0
N B:GLY58 4.2 41.5 1.0
C B:CYS55 4.2 40.1 1.0
C B:VAL59 4.2 27.3 1.0
N B:SER62 4.4 24.9 1.0
C B:SER54 4.4 24.9 1.0
SG B:CYS75 4.5 33.0 1.0
N B:GLU57 4.5 47.4 1.0
CA B:ARG56 4.5 40.7 1.0
CA B:GLY58 4.5 36.5 1.0
CA B:VAL59 4.6 31.6 1.0
N B:SER54 4.6 18.2 1.0
C B:GLY58 4.7 33.0 1.0
CG B:ASP63 4.7 28.3 1.0
CA B:GLY61 4.8 22.4 1.0
CB B:SER62 4.8 30.0 1.0
C B:ARG56 4.8 43.8 1.0
CA B:SER54 4.9 19.8 1.0
OD2 B:ASP63 5.0 24.8 1.0

Iron binding site 3 out of 10 in 1nek

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Iron binding site 3 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:27.4
occ:1.00
 FE1 B:SF4303 0.0 27.4 1.0
SG B:CYS155 2.2 27.3 1.0
S3 B:SF4303 2.3 24.5 1.0
S4 B:SF4303 2.3 23.6 1.0
S2 B:SF4303 2.3 24.6 1.0
FE3 B:SF4303 2.6 26.9 1.0
FE2 B:SF4303 2.7 25.3 1.0
FE4 B:SF4303 2.8 35.0 1.0
CB B:CYS155 3.2 19.9 1.0
S1 B:SF4303 3.9 29.6 1.0
N B:CYS155 4.1 25.4 1.0
CB B:ALA173 4.1 20.6 1.0
CA B:CYS155 4.3 19.6 1.0
CA B:ALA173 4.4 22.0 1.0
SG B:CYS149 4.5 21.0 1.0
SG B:CYS216 4.6 29.0 1.0
N B:ALA173 4.6 24.0 1.0
N B:CYS154 4.8 27.6 1.0
SG B:CYS152 4.8 34.6 1.0
N B:ALA153 4.9 27.2 1.0
CG B:PRO222 5.0 28.0 1.0

Iron binding site 4 out of 10 in 1nek

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Iron binding site 4 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:25.3
occ:1.00
 FE2 B:SF4303 0.0 25.3 1.0
SG B:CYS149 2.2 21.0 1.0
S3 B:SF4303 2.2 24.5 1.0
S4 B:SF4303 2.3 23.6 1.0
S1 B:SF4303 2.3 29.6 1.0
FE4 B:SF4303 2.6 35.0 1.0
FE1 B:SF4303 2.7 27.4 1.0
FE3 B:SF4303 2.7 26.9 1.0
CB B:CYS149 3.3 24.4 1.0
CA B:CYS149 3.7 28.5 1.0
S2 B:SF4303 3.8 24.6 1.0
N B:ILE150 3.9 30.7 1.0
N B:LEU151 4.0 30.8 1.0
C B:CYS149 4.2 30.9 1.0
CD1 B:LEU220 4.2 32.1 1.0
CA B:LEU151 4.6 33.8 1.0
CB B:ALA173 4.6 20.6 1.0
N B:CYS152 4.6 34.4 1.0
SG B:CYS152 4.7 34.6 1.0
SG B:CYS155 4.8 27.3 1.0
C B:ILE150 4.8 28.4 1.0
SG B:CYS216 4.9 29.0 1.0
CA B:ILE150 4.9 29.8 1.0
CD2 B:LEU176 4.9 7.9 1.0
CG1 B:ILE150 5.0 34.6 1.0

Iron binding site 5 out of 10 in 1nek

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Iron binding site 5 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:26.9
occ:1.00
 FE3 B:SF4303 0.0 26.9 1.0
S2 B:SF4303 2.2 24.6 1.0
S4 B:SF4303 2.2 23.6 1.0
SG B:CYS216 2.3 29.0 1.0
S1 B:SF4303 2.3 29.6 1.0
FE1 B:SF4303 2.6 27.4 1.0
FE4 B:SF4303 2.7 35.0 1.0
FE2 B:SF4303 2.7 25.3 1.0
CB B:CYS216 3.6 22.5 1.0
S3 B:SF4303 3.8 24.5 1.0
CD1 B:LEU220 3.8 32.1 1.0
CG B:LEU220 4.2 31.2 1.0
CA B:CYS216 4.2 25.4 1.0
CD B:PRO217 4.2 33.6 1.0
CB B:LEU220 4.3 31.2 1.0
SG B:CYS152 4.5 34.6 1.0
SG B:CYS155 4.7 27.3 1.0
N B:PRO217 4.8 33.1 1.0
CG B:LYS218 4.8 37.2 1.0
SG B:CYS149 4.8 21.0 1.0
C B:CYS216 4.9 28.9 1.0
CB B:CYS155 5.0 19.9 1.0

Iron binding site 6 out of 10 in 1nek

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Iron binding site 6 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe303

b:35.0
occ:1.00
 FE4 B:SF4303 0.0 35.0 1.0
S3 B:SF4303 2.2 24.5 1.0
S1 B:SF4303 2.2 29.6 1.0
S2 B:SF4303 2.2 24.6 1.0
SG B:CYS152 2.3 34.6 1.0
FE2 B:SF4303 2.6 25.3 1.0
FE3 B:SF4303 2.7 26.9 1.0
FE1 B:SF4303 2.8 27.4 1.0
N B:CYS152 3.5 34.4 1.0
N B:ALA153 3.6 27.2 1.0
CB B:CYS152 3.6 29.2 1.0
S4 B:SF4303 3.8 23.6 1.0
CA B:CYS152 3.9 28.5 1.0
N B:CYS154 4.0 27.6 1.0
C B:CYS152 4.1 26.8 1.0
SG B:CYS155 4.5 27.3 1.0
CA B:ALA153 4.5 24.2 1.0
CD B:PRO217 4.5 33.6 1.0
SG B:CYS149 4.5 21.0 1.0
CG1 B:ILE150 4.5 34.6 1.0
N B:LEU151 4.5 30.8 1.0
C B:LEU151 4.6 32.6 1.0
SG B:CYS216 4.7 29.0 1.0
CB B:CYS154 4.8 32.4 1.0
C B:ALA153 4.8 24.8 1.0
CA B:LEU151 4.8 33.8 1.0
N B:CYS155 4.8 25.4 1.0
N B:ILE150 4.9 30.7 1.0
CA B:CYS154 5.0 29.5 1.0

Iron binding site 7 out of 10 in 1nek

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Iron binding site 7 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:22.3
occ:1.00
 FE1 B:F3S304 0.0 22.3 1.0
SG B:CYS206 2.2 21.3 1.0
S1 B:F3S304 2.2 16.1 1.0
S3 B:F3S304 2.3 29.2 1.0
S2 B:F3S304 2.3 14.3 1.0
FE3 B:F3S304 2.7 21.0 1.0
FE4 B:F3S304 2.8 23.4 1.0
CB B:CYS206 3.4 26.5 1.0
S4 B:F3S304 3.8 23.5 1.0
CA B:CYS206 3.8 27.0 1.0
N B:SER208 3.9 22.2 1.0
N B:HIS207 4.1 29.5 1.0
C B:CYS206 4.3 27.6 1.0
CA B:SER208 4.3 22.3 1.0
N B:ILE209 4.3 27.5 1.0
CD1 B:ILE226 4.6 6.6 1.0
CG2 B:THR223 4.8 17.8 1.0
SG B:CYS212 4.8 23.4 1.0
SG B:CYS159 4.8 31.0 1.0
C B:SER208 4.9 27.2 1.0
C B:HIS207 4.9 21.8 1.0
CZ B:PHE169 5.0 11.7 1.0

Iron binding site 8 out of 10 in 1nek

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Iron binding site 8 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:21.0
occ:1.00
 FE3 B:F3S304 0.0 21.0 1.0
SG B:CYS212 2.2 23.4 1.0
S1 B:F3S304 2.3 16.1 1.0
S4 B:F3S304 2.3 23.5 1.0
S3 B:F3S304 2.3 29.2 1.0
FE1 B:F3S304 2.7 22.3 1.0
FE4 B:F3S304 2.8 23.4 1.0
CB B:CYS212 3.4 31.2 1.0
CG2 B:THR223 3.5 17.8 1.0
S2 B:F3S304 3.9 14.3 1.0
N B:MET210 4.0 33.2 1.0
N B:CYS212 4.1 35.1 1.0
CA B:MET210 4.3 32.2 1.0
CG B:PRO172 4.3 20.3 1.0
CA B:CYS212 4.4 30.1 1.0
N B:ASN211 4.4 35.0 1.0
CB B:THR223 4.7 25.8 1.0
SG B:CYS206 4.7 21.3 1.0
C B:MET210 4.8 35.0 1.0
SG B:CYS159 4.8 31.0 1.0
N B:ILE209 4.9 27.5 1.0
CA B:THR223 4.9 31.8 1.0
N B:THR223 4.9 30.9 1.0
CB B:PRO172 4.9 23.6 1.0

Iron binding site 9 out of 10 in 1nek

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Iron binding site 9 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe304

b:23.4
occ:1.00
 FE4 B:F3S304 0.0 23.4 1.0
S4 B:F3S304 2.2 23.5 1.0
SG B:CYS159 2.2 31.0 1.0
S2 B:F3S304 2.3 14.3 1.0
S3 B:F3S304 2.3 29.2 1.0
FE1 B:F3S304 2.8 22.3 1.0
FE3 B:F3S304 2.8 21.0 1.0
CB B:CYS159 3.4 32.0 1.0
S1 B:F3S304 3.9 16.1 1.0
CG B:PRO172 4.2 20.3 1.0
CA B:CYS159 4.4 30.1 1.0
CE2 B:PHE169 4.6 20.8 1.0
CZ B:PHE169 4.7 11.7 1.0
SG B:CYS212 4.7 23.4 1.0
SG B:CYS206 4.8 21.3 1.0
CD B:PRO172 4.8 25.1 1.0
CD1 B:ILE209 4.8 23.7 1.0
CB B:ILE209 4.9 24.3 1.0
OG B:SER161 4.9 20.0 1.0
CB B:SER161 4.9 19.1 1.0

Iron binding site 10 out of 10 in 1nek

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Iron binding site 10 out of 10 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Fe305

b:10.8
occ:1.00
 FE C:HEM305 0.0 10.8 1.0
NB C:HEM305 2.0 1.8 1.0
NC C:HEM305 2.0 1.8 1.0
ND C:HEM305 2.1 1.8 1.0
NA C:HEM305 2.1 1.8 1.0
NE2 C:HIS84 2.1 20.4 1.0
NE2 D:HIS71 2.3 16.8 1.0
C4B C:HEM305 2.9 6.0 1.0
C1B C:HEM305 3.0 2.6 1.0
C1C C:HEM305 3.0 7.0 1.0
C1A C:HEM305 3.0 5.4 1.0
C4D C:HEM305 3.0 8.7 1.0
C4A C:HEM305 3.0 1.8 1.0
C4C C:HEM305 3.1 1.8 1.0
C1D C:HEM305 3.1 6.0 1.0
CE1 C:HIS84 3.1 18.6 1.0
CD2 C:HIS84 3.1 7.5 1.0
CE1 D:HIS71 3.2 9.6 1.0
CD2 D:HIS71 3.3 12.8 1.0
CHC C:HEM305 3.3 5.7 1.0
CHB C:HEM305 3.4 1.8 1.0
CHA C:HEM305 3.4 1.8 1.0
CHD C:HEM305 3.5 3.8 1.0
C3B C:HEM305 4.1 2.4 1.0
C2B C:HEM305 4.2 1.8 1.0
ND1 C:HIS84 4.2 24.6 1.0
C3C C:HEM305 4.3 4.5 1.0
C2C C:HEM305 4.3 4.6 1.0
C2A C:HEM305 4.3 2.0 1.0
C3A C:HEM305 4.3 1.8 1.0
CG C:HIS84 4.3 18.4 1.0
C3D C:HEM305 4.3 2.6 1.0
C2D C:HEM305 4.3 3.6 1.0
ND1 D:HIS71 4.3 19.4 1.0
CG D:HIS71 4.4 17.8 1.0
CE1 C:HIS30 4.7 23.5 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: Sat Aug 3 11:32:16 2024

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