Calcium in PDB 6h6p: Ubij-SCP2 Ubiquinone Synthesis Protein

The structure of Ubij-SCP2 Ubiquinone Synthesis Protein, PDB code: 6h6p 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)	47.28 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	47.690, 94.550, 115.660, 90.00, 90.00, 90.00
R / Rfree (%)	23.3 / 28.9

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Calcium atom in the Ubij-SCP2 Ubiquinone Synthesis Protein (pdb code 6h6p). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 16 binding sites of Calcium where determined in the Ubij-SCP2 Ubiquinone Synthesis Protein, PDB code: 6h6p:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Calcium binding site 1 out of 16 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:0.1 occ:1.00 OD1 A:ASP124 2.9 0.4 1.0 O A:ASP124 3.0 99.5 1.0 O A:HOH311 3.2 71.9 1.0 O A:HOH321 3.4 81.2 1.0 O A:GLU127 3.5 77.0 1.0 C A:GLU127 3.6 0.9 1.0 C A:ASP124 4.1 96.2 1.0 CG A:ASP124 4.1 0.9 1.0 CA A:ASP124 4.4 89.5 1.0 CB A:ASP124 4.8 92.7 1.0 CA A:GLU127 4.9 0.3 1.0 OD2 A:ASP124 5.0 0.5 1.0

Calcium binding site 2 out of 16 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:0.1 occ:1.00 O C:HOH312 2.5 70.1 1.0 O A:GLY45 2.5 73.8 1.0 O C:GLY45 3.0 76.7 1.0 OD1 A:ASP79 3.2 78.7 1.0 O A:HOH308 3.5 74.3 1.0 OD1 C:ASP79 3.5 83.5 1.0 C A:GLY45 3.8 73.1 1.0 OD2 A:ASP79 3.9 89.5 1.0 O A:HOH306 4.0 70.3 1.0 CG A:ASP79 4.0 80.1 1.0 OD2 C:ASP79 4.0 94.5 1.0 CG C:ASP79 4.2 84.3 1.0 C C:GLY45 4.2 76.5 1.0 CA A:LYS46 4.6 65.8 1.0 N A:LYS46 4.6 68.0 1.0 CA A:GLY45 4.7 69.9 1.0 CG2 A:VAL47 4.9 65.0 1.0

Calcium binding site 3 out of 16 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:0.6 occ:1.00 OE2 A:GLU73 2.8 83.5 0.5 OG A:SER58 3.1 79.5 1.0 N A:SER58 3.7 73.5 1.0 CD A:GLU73 3.9 90.5 0.5 O A:GLY72 4.0 77.9 1.0 O A:HOH310 4.1 70.5 1.0 OG1 A:THR57 4.1 78.5 1.0 CB A:SER58 4.3 72.7 1.0 NH2 A:ARG49 4.3 86.4 1.0 CA A:THR57 4.3 78.2 1.0 O A:HOH305 4.3 67.0 1.0 NZ A:LYS15 4.4 74.4 1.0 C A:THR57 4.4 78.2 1.0 CA A:SER58 4.5 71.0 1.0 OE1 A:GLU73 4.6 60.8 0.5 O A:SER58 4.7 74.2 1.0 CG A:GLU73 4.8 85.4 0.5 CB A:THR57 4.9 77.9 1.0

Calcium binding site 4 out of 16 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:0.4 occ:1.00 OE1 A:GLU51 2.8 84.5 1.0 O A:THR57 3.8 76.8 1.0 C A:SER56 3.8 88.8 1.0 CD A:GLU51 3.8 93.6 1.0 N A:THR57 3.9 80.5 1.0 O A:HOH324 3.9 69.0 1.0 C A:THR57 4.0 78.2 1.0 O A:SER56 4.1 90.5 1.0 CA A:SER56 4.2 88.7 1.0 CB A:GLU51 4.2 70.1 1.0 CA A:THR57 4.3 78.2 1.0 CG A:GLU51 4.5 80.4 1.0 CA A:GLU51 4.6 66.0 1.0 O A:VAL52 4.6 82.4 1.0 N A:SER58 4.6 73.5 1.0 OE2 A:GLU51 4.8 92.8 1.0 O A:HOH313 4.8 62.5 1.0 CB A:SER56 4.8 95.3 1.0 CB A:SER58 4.9 72.7 1.0 N A:VAL52 4.9 68.3 1.0 C A:GLU51 5.0 71.8 1.0

Calcium binding site 5 out of 16 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:79.0 occ:1.00 OG A:SER87 2.8 92.1 1.0 N A:SER87 3.7 75.3 1.0 CB A:TYR85 3.7 76.8 1.0 CB A:SER87 3.8 83.5 1.0 CD2 A:TYR85 3.9 79.8 1.0 N A:ALA86 3.9 72.3 1.0 CG A:TYR85 4.2 79.2 1.0 C A:TYR85 4.3 76.8 1.0 CB A:ALA86 4.3 70.2 1.0 CA A:SER87 4.4 76.8 1.0 CA A:ALA86 4.4 69.7 1.0 CA A:TYR85 4.5 74.4 1.0 C A:ALA86 4.6 75.3 1.0 CE2 A:TYR85 5.0 83.3 1.0

Calcium binding site 6 out of 16 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 A:Ca207 b:0.3 occ:1.00 O A:ALA75 3.3 0.3 1.0 OD1 A:ASP77 3.4 0.8 1.0 O A:GLY76 3.5 93.1 1.0 C A:GLY76 3.9 93.4 1.0 C A:ALA75 4.2 96.1 1.0 CG A:ASP77 4.4 0.2 1.0 CA A:GLY76 4.4 89.2 1.0 N A:ASP77 4.4 90.8 1.0 N A:GLY76 4.7 89.2 1.0 CA A:ASP77 4.8 90.8 1.0

Calcium binding site 7 out of 16 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 7 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca208 b:0.6 occ:1.00 O A:HOH321 3.0 81.2 1.0 O A:HOH309 3.6 78.8 1.0 OD2 A:ASP94 3.7 0.1 1.0 CG A:ASP94 3.9 0.8 1.0 NE2 A:GLN96 4.0 0.5 1.0 OD2 A:ASP124 4.0 0.5 1.0 CB A:ASP94 4.1 98.3 1.0 CG A:GLN96 4.2 0.6 1.0 CD A:GLN96 4.4 0.8 1.0 OD1 A:ASP124 4.4 0.4 1.0 OD1 A:ASP94 4.5 0.5 1.0 CG A:ASP124 4.6 0.9 1.0 CB A:GLN96 4.7 0.6 1.0

Calcium binding site 8 out of 16 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 8 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca201 b:0.1 occ:1.00 OE1 B:GLU23 2.6 78.1 1.0 OE2 B:GLU23 2.8 83.7 1.0 OE2 D:GLU65 3.0 0.6 1.0 CD B:GLU23 3.1 74.5 1.0 NH1 D:ARG66 3.7 0.5 1.0 CD D:GLU65 4.0 0.7 1.0 OE1 D:GLU65 4.1 0.9 1.0 O B:VAL70 4.1 58.1 1.0 CD D:ARG66 4.2 0.1 1.0 O D:HOH311 4.3 67.0 1.0 CG B:GLU23 4.6 61.5 1.0 CZ D:ARG66 4.8 0.7 1.0 N B:VAL70 4.9 56.7 1.0 NE D:ARG66 5.0 0.2 1.0

Calcium binding site 9 out of 16 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 9 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca202 b:0.8 occ:1.00 O D:GLY45 2.8 77.3 1.0 O B:HOH308 3.0 67.2 1.0 O B:GLY45 3.0 82.7 1.0 OD2 B:ASP79 3.6 74.2 1.0 C D:GLY45 3.7 74.0 1.0 OD1 D:ASP79 4.0 78.4 1.0 OD1 B:ASP79 4.2 72.7 1.0 C B:GLY45 4.3 79.4 1.0 CG B:ASP79 4.3 70.3 1.0 OD2 D:ASP79 4.3 73.7 1.0 CA D:GLY45 4.4 69.7 1.0 NZ D:LYS46 4.5 79.9 1.0 CG D:ASP79 4.6 75.9 1.0 N D:LYS46 4.7 66.0 1.0 CG2 B:VAL47 4.8 63.3 1.0 CD D:LYS46 4.8 54.5 1.0 CE D:LYS46 4.8 66.9 1.0 CA D:LYS46 4.9 62.6 1.0

Calcium binding site 10 out of 16 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 10 of Ubij-SCP2 Ubiquinone Synthesis Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca203 b:1.0 occ:1.00 O B:VAL52 3.6 66.1 1.0 O B:PHE55 3.6 81.6 1.0 CA B:SER56 3.7 83.0 1.0 OG B:SER56 4.0 99.3 1.0 CB B:SER56 4.2 89.2 1.0 O B:LYS53 4.2 79.2 1.0 C B:SER56 4.3 85.3 1.0 CA B:LYS53 4.4 66.7 1.0 N B:THR57 4.4 77.3 1.0 C B:PHE55 4.5 82.5 1.0 C B:VAL52 4.5 66.8 1.0 C B:LYS53 4.6 75.8 1.0 N B:SER56 4.6 82.3 1.0 N B:LYS53 4.8 65.4 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