Calcium in PDB 1nek: 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;

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

The structure of Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound also contains other interesting chemical elements:

Iron

(Fe)

10 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound, PDB code: 1nek:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Complex II (Succinate Dehydrogenase) From E. Coli with Ubiquinone Bound


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 Ubiquinone Bound within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca590 b:45.9 occ:1.00 O A:MET357 2.9 43.0 1.0 O A:ALA390 2.9 47.0 1.0 O A:GLU388 3.0 47.5 1.0 O A:MET356 3.0 42.6 1.0 OH A:TYR355 3.2 60.8 1.0 C A:MET357 3.3 40.6 1.0 O A:GLY358 3.6 39.0 1.0 CA A:MET357 3.6 40.3 1.0 CE2 A:TYR355 3.6 54.8 1.0 CZ A:TYR355 3.7 55.6 1.0 C A:ALA390 3.8 48.7 1.0 C A:GLU388 3.8 44.9 1.0 C A:MET356 4.0 42.8 1.0 CA A:GLU388 4.0 44.8 1.0 N A:GLY358 4.1 38.2 1.0 C A:GLY358 4.1 38.0 1.0 N A:MET357 4.3 43.1 1.0 O A:HOH628 4.3 49.0 1.0 O A:GLY387 4.3 47.6 1.0 CA A:CYS391 4.4 48.8 1.0 N A:CYS391 4.4 49.0 1.0 N A:ALA390 4.5 45.5 1.0 CG A:GLU388 4.6 47.5 1.0 CA A:GLY358 4.6 35.6 1.0 CA A:ALA390 4.7 48.2 1.0 CD2 A:TYR355 4.7 53.1 1.0 CB A:MET357 4.8 40.1 1.0 CB A:GLU388 4.9 44.7 1.0 CE1 A:TYR355 4.9 52.3 1.0 CD2 A:HIS395 4.9 54.6 1.0 N A:GLY359 4.9 33.8 1.0 CB A:CYS391 4.9 49.9 1.0 N A:ILE389 4.9 42.4 1.0 CE A:MET356 5.0 54.2 1.0

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


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 Ubiquinone Bound within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca311 b:59.8 occ:1.00 OG1 B:THR190 2.9 32.0 1.0 O B:ASP187 3.0 31.1 1.0 O B:HOH352 3.2 57.2 1.0 O B:HOH356 3.6 52.9 1.0 CB B:THR190 3.8 23.9 1.0 C B:ASP187 4.2 28.4 1.0 O B:ASP184 4.4 30.4 1.0 O B:LEU182 4.4 28.3 1.0 CG2 B:THR190 4.6 9.4 1.0 CA B:THR188 4.8 25.4 1.0 N B:THR190 4.9 24.2 1.0 CA B:THR190 5.0 23.6 1.0 N B:THR188 5.0 28.6 1.0

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