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Calcium in PDB 6h6o: Ubij-SCP2 Ubiquinone Synthesis Protein

Protein crystallography data

The structure of Ubij-SCP2 Ubiquinone Synthesis Protein, PDB code: 6h6o 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) 39.55 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 48.660, 67.870, 74.607, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 22.2

Calcium Binding Sites:

The binding sites of Calcium atom in the Ubij-SCP2 Ubiquinone Synthesis Protein (pdb code 6h6o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Ubij-SCP2 Ubiquinone Synthesis Protein, PDB code: 6h6o:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 6h6o

Go back to Calcium Binding Sites List in 6h6o
Calcium binding site 1 out of 7 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:Ca204

b:17.7
occ:1.00
 O A:HOH306 2.3 14.3 1.0
O A:HOH342 2.3 22.9 1.0
OD1 A:ASP79 2.4 18.4 1.0
OD2 A:ASP79 2.6 16.4 1.0
CG A:ASP79 2.8 19.9 1.0
HO2 A:LMR203 4.1 49.2 1.0
O A:GLY45 4.1 19.8 1.0
CB A:ASP79 4.4 16.6 1.0
O2 A:LMR203 4.4 49.1 1.0
CG2 A:VAL47 4.7 16.8 1.0
OD2 A:ASP77 4.7 46.7 0.5
N A:VAL47 4.9 13.4 1.0

Calcium binding site 2 out of 7 in 6h6o

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Calcium binding site 2 out of 7 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:Ca205

b:21.9
occ:1.00
 O A:ALA126 2.2 24.9 1.0
O A:HOH384 2.3 38.7 1.0
O A:ASP129 2.3 21.0 1.0
O A:HOH326 2.3 20.1 1.0
O A:HOH313 2.4 18.9 1.0
O A:ALA131 2.6 40.7 1.0
C A:ALA126 3.4 24.6 1.0
C A:ASP129 3.5 23.3 1.0
C A:ALA131 3.8 76.2 1.0
N A:ALA131 4.1 28.6 1.0
CA A:ALA126 4.2 19.6 1.0
C A:PRO130 4.2 32.9 1.0
CB A:ASP129 4.4 19.6 1.0
O A:HOH365 4.4 42.0 1.0
CA A:ASP129 4.4 18.8 1.0
OD2 A:ASP129 4.4 24.0 1.0
N A:PRO130 4.5 25.1 1.0
N A:GLU127 4.5 22.9 1.0
CA A:PRO130 4.5 26.1 1.0
CA A:ALA131 4.5 44.6 0.8
CG A:ASP129 4.6 24.1 1.0
O A:HOH350 4.6 23.4 1.0
O A:PRO130 4.6 34.6 1.0
N A:ASP129 4.7 19.8 1.0
CA A:GLU127 4.7 24.4 1.0
O A:PHE29 4.7 21.1 1.0
CB A:ALA126 4.7 19.6 1.0
O A:GLU127 4.8 25.9 1.0
C A:GLU127 4.8 26.8 1.0
O A:HOH404 4.9 51.4 1.0

Calcium binding site 3 out of 7 in 6h6o

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Calcium binding site 3 out of 7 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:Ca206

b:58.3
occ:1.00
 O A:ARG93 2.5 43.2 1.0
O A:HOH355 2.6 61.9 1.0
O A:HOH362 2.6 47.7 1.0
OD1 A:ASP124 2.7 38.2 1.0
OE1 A:GLU127 2.9 59.6 1.0
C A:ARG93 3.5 43.7 1.0
CG A:ASP124 3.5 39.0 1.0
CA A:ARG93 3.8 41.5 1.0
O A:HOH318 3.9 40.5 1.0
CB A:ARG93 4.0 43.5 1.0
CD A:GLU127 4.1 69.8 1.0
CA A:ASP124 4.1 21.5 1.0
CB A:ASP124 4.2 24.7 1.0
OD2 A:ASP124 4.3 48.5 1.0
N A:ASP94 4.7 38.7 1.0
O A:HOH330 4.7 40.3 1.0
O A:HOH320 4.7 55.9 1.0
O A:ASP124 4.7 21.1 1.0
CG A:ARG93 4.8 57.2 1.0
OE2 A:GLU127 4.8 70.1 1.0
CB A:GLU127 4.9 27.1 1.0
C A:ASP124 4.9 22.5 1.0

Calcium binding site 4 out of 7 in 6h6o

Go back to Calcium Binding Sites List in 6h6o
Calcium binding site 4 out of 7 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:Ca207

b:17.8
occ:0.50
 O A:HOH314 2.2 43.0 1.0
O A:HOH373 2.2 35.3 1.0
OE1 A:GLU23 2.3 18.5 1.0
O A:HOH392 2.4 48.6 1.0
OE2 A:GLU23 2.4 31.4 1.0
O A:HOH349 2.4 30.6 1.0
OD1 A:ASP69 2.5 30.8 1.0
CD A:GLU23 2.7 30.0 1.0
CG A:ASP69 3.6 29.9 1.0
CB A:ASP69 4.0 18.6 1.0
CG A:GLU23 4.2 19.8 1.0
CA A:ASP69 4.3 16.4 1.0
O A:HOH352 4.3 30.0 1.0
N A:VAL70 4.5 18.0 1.0
OE1 A:GLN67 4.6 49.5 1.0
O A:VAL70 4.7 20.1 1.0
OD2 A:ASP69 4.7 32.0 1.0
C A:ASP69 4.9 21.5 1.0

Calcium binding site 5 out of 7 in 6h6o

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Calcium binding site 5 out of 7 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:Ca208

b:85.5
occ:1.00
 OD1 A:ASP77 2.3 33.9 0.5
OD2 A:ASP77 2.6 39.0 0.5
CG A:ASP77 2.8 35.0 0.5
O A:HOH396 3.2 59.2 1.0
O A:HOH387 3.3 51.9 1.0
O A:HOH382 3.4 63.4 1.0
O A:HOH311 3.7 73.3 1.0
CB A:ASP77 4.3 28.5 0.5
CB A:ASP77 4.5 29.7 0.5
OD1 A:ASP77 4.6 44.0 0.5
CG A:ASP77 4.9 42.0 0.5

Calcium binding site 6 out of 7 in 6h6o

Go back to Calcium Binding Sites List in 6h6o
Calcium binding site 6 out of 7 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:Ca203

b:23.8
occ:1.00
 O B:ASP124 2.3 20.0 1.0
O B:GLU127 2.3 22.0 1.0
O B:HOH315 2.3 23.6 1.0
OD1 B:ASP124 2.4 23.9 1.0
OD1 B:ASP129 2.5 47.2 1.0
C B:ASP124 3.2 21.4 1.0
C B:GLU127 3.5 23.3 1.0
CG B:ASP124 3.6 27.1 1.0
CA B:ASP124 3.6 18.6 1.0
CG B:ASP129 3.7 50.6 1.0
CB B:ASP124 4.1 20.6 1.0
CA B:GLU127 4.2 21.0 1.0
CB B:GLU127 4.2 22.4 1.0
O B:ARG93 4.3 34.9 1.0
N B:GLU127 4.3 19.8 1.0
OD2 B:ASP129 4.4 53.0 1.0
N B:ASP129 4.4 30.2 1.0
N B:LEU125 4.5 18.2 1.0
N B:PHE128 4.6 21.6 1.0
OD2 B:ASP124 4.6 30.8 1.0
C B:PHE128 4.6 31.4 1.0
CG B:GLU127 4.7 32.5 1.0
OE2 B:GLU127 4.7 32.2 1.0
O B:HOH371 4.8 44.7 1.0
O B:ALA123 4.8 19.8 1.0
CA B:PHE128 4.8 24.7 1.0
CB B:ASP129 4.8 48.0 1.0
CA B:ASP129 4.9 46.1 1.0
N B:ASP124 4.9 18.7 1.0

Calcium binding site 7 out of 7 in 6h6o

Go back to Calcium Binding Sites List in 6h6o
Calcium binding site 7 out of 7 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
B:Ca204

b:94.5
occ:1.00
 O B:HOH337 2.5 47.7 1.0
O B:HOH374 2.7 68.5 1.0
O B:HOH338 2.9 45.0 1.0
O B:ARG42 3.0 23.6 1.0
C B:ARG42 3.9 22.5 1.0
CA B:ARG42 4.1 19.8 1.0
NE B:ARG42 4.1 43.7 1.0
O B:HOH328 4.3 25.5 1.0
O B:HOH351 4.6 38.5 1.0
CE B:LYS46 4.6 36.0 1.0
CB B:ARG42 4.8 19.7 1.0
CD B:ARG42 4.8 31.0 1.0
O B:SER41 4.8 21.0 1.0
NH1 B:ARG42 4.9 49.8 1.0

Reference:

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
Page generated: Wed Jul 9 14:30:40 2025

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