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

Protein crystallography data

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

Other elements in 6h6n:

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

Terbium (Tb) 2 atoms

Calcium Binding Sites:

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 6h6n

Go back to Calcium Binding Sites List in 6h6n
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 6h6n

Go back to Calcium Binding Sites List in 6h6n
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 6h6n

Go back to Calcium Binding Sites List in 6h6n
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 6h6n

Go back to Calcium Binding Sites List in 6h6n
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 6h6n

Go back to Calcium Binding Sites List in 6h6n
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 6h6n

Go back to Calcium Binding Sites List in 6h6n
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

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: Sat Dec 12 06:08:58 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy