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Calcium 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:

Iron (Fe) 10 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 1nen

Go back to Calcium Binding Sites List in 1nen
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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
A:Ca590

b:0.8
occ:1.00
 O A:ALA390 2.8 80.8 1.0
O A:MET357 2.9 74.1 1.0
OH A:TYR355 3.1 93.2 1.0
O A:GLU388 3.2 82.7 1.0
O A:MET356 3.3 70.2 1.0
C A:MET357 3.5 75.3 1.0
CE2 A:TYR355 3.6 90.6 1.0
CZ A:TYR355 3.7 91.5 1.0
C A:ALA390 3.8 81.8 1.0
CA A:MET357 3.9 74.7 1.0
C A:GLU388 3.9 80.2 1.0
O A:HOH628 4.0 58.1 1.0
CA A:GLU388 4.0 81.2 1.0
O A:GLY387 4.2 79.8 1.0
O A:GLY358 4.2 84.6 1.0
C A:MET356 4.3 71.8 1.0
N A:GLY358 4.4 77.0 1.0
CA A:CYS391 4.4 81.0 1.0
N A:CYS391 4.5 82.1 1.0
N A:ALA390 4.5 78.4 1.0
C A:GLY358 4.5 81.1 1.0
N A:MET357 4.6 73.0 1.0
CD2 A:HIS395 4.7 80.4 1.0
CA A:ALA390 4.7 79.1 1.0
CG A:GLU388 4.8 81.8 1.0
CD2 A:TYR355 4.8 90.4 1.0
CE1 A:TYR355 4.9 90.2 1.0
CA A:GLY358 4.9 79.0 1.0
CB A:GLU388 4.9 82.1 1.0
CB A:CYS391 5.0 83.3 1.0
N A:ILE389 5.0 78.4 1.0

Calcium binding site 2 out of 2 in 1nen

Go back to Calcium Binding Sites List in 1nen
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca 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:Ca311

b:75.6
occ:1.00
 O B:ASP187 2.9 70.7 1.0
OG1 B:THR190 3.1 71.6 1.0
O B:HOH353 3.2 68.2 1.0
O B:HOH357 3.9 75.3 1.0
CB B:THR190 3.9 68.4 1.0
C B:ASP187 4.2 69.4 1.0
O B:ASP184 4.2 62.6 1.0
O B:LEU182 4.5 62.2 1.0
CG2 B:THR190 4.7 62.7 1.0
CA B:THR188 4.9 65.5 1.0
N B:THR190 4.9 63.4 1.0
N B:THR188 5.0 69.3 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: Thu Jul 11 12:49:37 2024

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