Calcium in PDB 6h6n: Ubij-SCP2 Ubiquinone Synthesis Protein

The structure of Ubij-SCP2 Ubiquinone Synthesis Protein, PDB code: 6h6n was solved by C.D.Fyfe, P.Legrand, L.Pecqueur, L.Ciccone, M.Lombard, M.Fontecave, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.29 / 2.12
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.300, 67.930, 73.080, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 22.9

The structure of Ubij-SCP2 Ubiquinone Synthesis Protein also contains other interesting chemical elements:

Terbium

(Tb)

2 atoms

The binding sites of Calcium atom in the Ubij-SCP2 Ubiquinone Synthesis Protein (pdb code 6h6n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Ubij-SCP2 Ubiquinone Synthesis Protein, PDB code: 6h6n:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in the Ubij-SCP2 Ubiquinone Synthesis Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca202 b:27.1 occ:1.00 O A:HOH304 2.2 23.9 1.0 O A:HOH335 2.3 29.5 1.0 OD1 A:ASP79 2.4 29.0 1.0 OD2 A:ASP79 2.5 26.1 1.0 CG A:ASP79 2.7 28.8 1.0 O A:GLY45 4.1 28.5 1.0 CB A:ASP79 4.3 23.4 1.0 O A:HOH327 4.5 41.1 1.0 OD2 A:ASP77 4.6 66.8 1.0 CG2 A:VAL47 4.8 26.0 1.0 N A:VAL47 5.0 24.3 1.0 O A:ASP77 5.0 40.4 1.0

Calcium binding site 2 out of 6 in the Ubij-SCP2 Ubiquinone Synthesis Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca203 b:78.9 occ:1.00 O A:HOH327 2.3 41.1 1.0 OD1 A:ASP77 2.5 63.9 1.0 OD2 A:ASP77 2.7 66.8 1.0 CG A:ASP77 2.9 61.7 1.0 O A:ALA78 3.1 31.5 1.0 C A:ALA78 4.1 31.1 1.0 CA A:ASP79 4.3 23.3 1.0 CB A:ASP77 4.4 43.9 1.0 OD1 A:ASP79 4.5 29.0 1.0 N A:ASP79 4.6 24.4 1.0 N A:ALA78 4.8 31.3 1.0 O A:HOH344 4.9 46.2 1.0 O A:ASP79 5.0 29.4 1.0 C A:ASP79 5.0 29.5 1.0

Calcium binding site 3 out of 6 in the Ubij-SCP2 Ubiquinone Synthesis Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca204 b:33.3 occ:1.00 O A:ALA126 2.3 33.8 1.0 O A:ASP129 2.3 37.1 1.0 O A:HOH320 2.4 32.8 1.0 O A:HOH311 2.4 31.0 1.0 O A:ALA131 2.5 42.9 1.0 C A:ASP129 3.5 39.2 1.0 C A:ALA126 3.5 33.6 1.0 C A:ALA131 3.5 84.1 1.0 N A:ALA131 4.0 43.8 1.0 O A:HOH316 4.0 52.1 1.0 C A:PRO130 4.1 48.4 1.0 CB A:ASP129 4.2 32.8 1.0 CA A:ALA126 4.3 27.6 1.0 O A:PRO130 4.3 50.7 1.0 CA A:ASP129 4.3 33.5 1.0 CA A:ALA131 4.4 62.6 1.0 N A:PRO130 4.4 39.5 1.0 CA A:PRO130 4.4 41.0 1.0 OD2 A:ASP129 4.5 48.2 1.0 CG A:ASP129 4.5 38.0 1.0 N A:GLU127 4.5 33.3 1.0 N A:ASP129 4.7 33.8 1.0 CA A:GLU127 4.8 36.1 1.0 O A:PHE29 4.8 32.7 1.0 CB A:ALA126 4.9 26.4 1.0 C A:GLU127 4.9 40.2 1.0 O A:GLU127 5.0 42.3 1.0

Calcium binding site 4 out of 6 in the Ubij-SCP2 Ubiquinone Synthesis Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca205 b:56.1 occ:1.00 O A:HOH333 2.2 40.7 1.0 O A:HOH319 2.3 39.8 1.0 OE2 A:GLU23 2.5 54.9 1.0 OE1 A:GLU23 2.6 32.1 1.0 OD1 A:ASP69 2.6 53.0 1.0 CD A:GLU23 2.8 44.2 1.0 CG A:ASP69 3.7 48.9 1.0 CB A:ASP69 4.1 27.3 1.0 O A:HOH348 4.2 48.8 1.0 CG A:GLU23 4.3 30.7 1.0 CA A:ASP69 4.4 24.8 1.0 NE2 A:GLN67 4.5 63.3 1.0 N A:VAL70 4.7 23.0 1.0 OD2 A:ASP69 4.8 56.9 1.0 O A:VAL70 4.8 28.9 1.0 O A:HOH338 4.8 50.5 1.0

Calcium binding site 5 out of 6 in the Ubij-SCP2 Ubiquinone Synthesis Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca206 b:88.5 occ:1.00 OE1 A:GLU127 2.6 80.0 1.0 OD1 A:ASP124 2.6 48.7 1.0 O A:ARG93 3.3 71.0 1.0 O A:HOH308 3.3 47.4 1.0 OD1 A:ASP94 3.4 79.3 1.0 CD A:GLU127 3.5 86.8 1.0 CG A:ASP124 3.5 47.3 1.0 C A:ARG93 3.8 71.3 1.0 CB A:ARG93 3.8 69.7 1.0 CA A:ASP124 4.0 27.1 1.0 CA A:ARG93 4.0 68.1 1.0 OE2 A:GLU127 4.1 87.1 1.0 CB A:ASP124 4.1 30.5 1.0 OD2 A:ASP124 4.3 57.5 1.0 CB A:GLU127 4.4 38.6 1.0 O A:ASP124 4.4 33.6 1.0 CG A:GLU127 4.5 55.4 1.0 CG A:ASP94 4.6 80.3 1.0 C A:ASP124 4.7 32.1 1.0 N A:ASP94 4.7 66.9 1.0

Calcium binding site 6 out of 6 in the Ubij-SCP2 Ubiquinone Synthesis Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:40.0 occ:1.00 O B:HOH314 2.2 40.4 1.0 O B:ASP124 2.3 28.2 1.0 O B:GLU127 2.4 34.0 1.0 OD1 B:ASP124 2.4 39.9 1.0 OD1 B:ASP129 2.5 72.4 1.0 O B:HOH310 2.5 34.5 1.0 C B:ASP124 3.2 28.4 1.0 C B:GLU127 3.5 34.2 1.0 CG B:ASP124 3.5 39.0 1.0 CG B:ASP129 3.6 74.9 1.0 CA B:ASP124 3.6 26.3 1.0 OD2 B:ASP129 4.1 81.8 1.0 CB B:ASP124 4.1 28.6 1.0 O B:HOH320 4.2 38.0 1.0 O B:ARG93 4.2 52.1 1.0 CA B:GLU127 4.3 31.3 1.0 N B:GLU127 4.3 30.7 1.0 N B:LEU125 4.4 24.9 1.0 CB B:GLU127 4.4 32.4 1.0 N B:ASP129 4.5 35.2 1.0 OD2 B:ASP124 4.5 51.0 1.0 N B:PHE128 4.5 32.3 1.0 OE2 B:GLU127 4.6 47.3 1.0 C B:PHE128 4.6 38.3 1.0 CG B:GLU127 4.7 44.0 1.0 CB B:ASP129 4.8 70.9 1.0 CA B:PHE128 4.8 34.0 1.0 O B:ALA123 4.8 26.7 1.0 N B:ASP124 4.9 25.4 1.0 CA B:LEU125 4.9 24.9 1.0 CA B:ASP129 4.9 68.8 1.0

M.Hajj Chehade, L.Pelosi, C.D.Fyfe, L.Loiseau, B.Rascalou, S.Brugiere, K.Kazemzadeh, C.D.Vo, L.Ciccone, L.Aussel, Y.Coute, M.Fontecave, F.Barras, M.Lombard, F.Pierrel. A Soluble Metabolon Synthesizes the Isoprenoid Lipid Ubiquinone. Cell Chem Biol V. 26 482 2019.
ISSN: ESSN 2451-9456
PubMed: 30686758
DOI: 10.1016/J.CHEMBIOL.2018.12.001