Atomistry » Calcium » PDB 6guy-6hhy » 6h6o
Atomistry »
  Calcium »
    PDB 6guy-6hhy »
      6h6o »

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

Go back to Calcium Binding Sites List in 6h6o
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

Go back to Calcium Binding Sites List in 6h6o
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

Go back to Calcium Binding Sites List in 6h6o
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: Tue Jul 16 08:14:27 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy