Atomistry » Calcium » PDB 1n7s-1nm9 » 1nen
Atomistry »
  Calcium »
    PDB 1n7s-1nm9 »
      1nen »

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: Sat Dec 12 03:08:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy