Atomistry » Calcium » PDB 4dg4-4dtj » 4dk7
Atomistry »
  Calcium »
    PDB 4dg4-4dtj »
      4dk7 »

Calcium in PDB 4dk7: Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1

Enzymatic activity of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1

All present enzymatic activity of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1, PDB code: 4dk7 was solved by D.E.Piper, H.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.45
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 87.261, 87.261, 197.709, 90.00, 90.00, 90.00
R / Rfree (%) 23 / 27

Other elements in 4dk7:

The structure of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 also contains other interesting chemical elements:

Fluorine (F) 12 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 (pdb code 4dk7). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 7 binding sites of Calcium where determined in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1, PDB code: 4dk7:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6; 7;

Calcium binding site 1 out of 7 in 4dk7

Go back to Calcium Binding Sites List in 4dk7
Calcium binding site 1 out of 7 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:92.4
occ:1.00
 OE1 A:GLN235 3.3 70.3 1.0
OE2 A:GLU281 3.7 70.8 1.0
CG A:GLU281 4.1 64.2 1.0
CB A:PHE285 4.2 44.4 1.0
CD A:GLU281 4.3 68.6 1.0
CD A:GLN235 4.3 65.8 1.0
CD A:GLU315 4.4 65.8 1.0
CG A:GLU315 4.5 62.0 1.0
CG A:PHE285 4.5 43.0 1.0
OE2 A:GLU315 4.5 68.2 1.0
O A:GLU281 4.6 51.5 1.0
OE1 A:GLU315 4.7 66.6 1.0
CD2 A:PHE285 4.7 40.0 1.0
CA A:ILE282 4.7 47.3 1.0
CG1 A:ILE282 4.7 43.6 1.0
C A:GLU281 4.8 52.2 1.0
N A:ILE282 4.8 49.5 1.0
CG2 A:ILE311 4.8 37.0 1.0
CG A:GLN235 4.8 61.6 1.0
CB A:GLU281 5.0 56.5 1.0

Calcium binding site 2 out of 7 in 4dk7

Go back to Calcium Binding Sites List in 4dk7
Calcium binding site 2 out of 7 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:0.5
occ:1.00
 O A:THR334 3.5 69.7 1.0
CD1 A:PHE333 4.0 89.6 1.0
CZ A:TYR335 4.2 70.2 1.0
CE2 A:TYR335 4.3 69.1 1.0
CD1 A:TRP252 4.4 69.6 1.0
CE1 A:TYR335 4.4 70.5 1.0
C A:THR334 4.4 69.3 1.0
CG A:TRP252 4.5 71.0 1.0
NE1 A:TRP252 4.5 67.5 1.0
CB A:PHE333 4.5 86.7 1.0
CD2 A:TYR335 4.6 68.4 1.0
OH A:TYR335 4.6 71.7 1.0
N A:THR334 4.6 75.5 1.0
CD2 A:TRP252 4.6 68.2 1.0
CD1 A:TYR335 4.6 69.0 1.0
CE2 A:TRP252 4.6 68.0 1.0
OD2 A:ASP339 4.7 53.1 1.0
CG A:TYR335 4.7 67.2 1.0
CG A:PHE333 4.8 89.1 1.0
CG A:ASP339 4.9 53.0 1.0
CE1 A:PHE333 4.9 90.2 1.0

Calcium binding site 3 out of 7 in 4dk7

Go back to Calcium Binding Sites List in 4dk7
Calcium binding site 3 out of 7 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:70.7
occ:0.50
 OE2 A:GLU325 2.7 50.9 1.0
OE1 A:GLU325 2.8 50.6 1.0
CD A:GLU325 3.1 50.9 1.0
O A:ACT502 3.1 75.5 1.0
OXT A:ACT502 3.1 78.6 1.0
C A:ACT502 3.5 79.9 1.0
NZ A:LYS337 4.2 51.1 1.0
CG A:GLU325 4.6 49.5 1.0
O A:HOH643 4.7 41.4 1.0
O A:HOH607 4.9 47.8 1.0

Calcium binding site 4 out of 7 in 4dk7

Go back to Calcium Binding Sites List in 4dk7
Calcium binding site 4 out of 7 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:0.9
occ:0.50
 OD2 A:ASP339 3.2 53.1 1.0
OD1 A:ASP339 3.5 52.8 1.0
CG A:ASP339 3.7 53.0 1.0
CB A:SER336 4.7 59.1 1.0
OG A:SER336 4.8 60.0 1.0

Calcium binding site 5 out of 7 in 4dk7

Go back to Calcium Binding Sites List in 4dk7
Calcium binding site 5 out of 7 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 5 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca507

b:90.9
occ:0.50
 O A:HOH646 3.4 42.9 1.0
O A:GLU325 3.8 47.1 1.0
CB A:GLU325 4.2 44.6 1.0
O A:THR324 4.2 43.5 1.0
OG A:SER336 4.3 60.0 1.0
CB A:SER336 4.3 59.1 1.0
N A:LYS337 4.4 50.7 1.0
CG A:LYS337 4.6 45.0 1.0
CB A:LYS337 4.7 46.3 1.0
C A:GLU325 4.7 46.8 1.0
CD A:LYS337 4.7 45.3 1.0
OE2 A:GLU325 4.8 50.9 1.0
CD A:GLU325 4.8 50.9 1.0

Calcium binding site 6 out of 7 in 4dk7

Go back to Calcium Binding Sites List in 4dk7
Calcium binding site 6 out of 7 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 6 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:0.4
occ:1.00
 OE1 C:GLU315 3.9 76.5 1.0
CD C:GLU315 4.2 75.9 1.0
CG C:GLU315 4.2 73.2 1.0
CG1 C:ILE282 4.3 47.1 1.0
CG C:GLN235 4.4 85.4 1.0
CB C:PHE285 4.4 54.9 1.0
CG2 C:ILE311 4.4 43.3 1.0
CD2 C:PHE285 4.5 59.7 1.0
CA C:ILE282 4.5 51.7 1.0
CG C:PHE285 4.5 60.5 1.0
OE1 C:GLN235 4.6 88.3 1.0
N C:ILE282 4.7 54.7 1.0
CD1 C:ILE374 4.8 46.8 1.0
O C:GLU281 4.9 55.5 1.0
C C:GLU281 4.9 56.9 1.0
CD C:GLN235 5.0 87.0 1.0

Calcium binding site 7 out of 7 in 4dk7

Go back to Calcium Binding Sites List in 4dk7
Calcium binding site 7 out of 7 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 7 of Crystal Structure of Lxr Ligand Binding Domain in Complex with Full Agonist 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:0.8
occ:1.00
 O C:THR334 3.1 93.0 1.0
OD1 C:ASP339 3.2 97.2 1.0
OG1 C:THR334 3.4 92.5 1.0
C C:THR334 3.8 93.4 1.0
CB C:THR334 4.3 93.4 1.0
CG C:ASP339 4.3 98.0 1.0
N C:TYR335 4.5 93.3 1.0
CA C:TYR335 4.5 93.8 1.0
OD2 C:ASP339 4.6 98.0 1.0
CA C:THR334 4.7 93.7 1.0
N C:SER336 4.8 93.8 1.0
C C:TYR335 5.0 93.4 1.0

Reference:

D.J.Kopecky, X.Y.Jiao, B.Fisher, S.Mckendry, M.Labelle, D.E.Piper, P.Coward, A.K.Shiau, P.Escaron, J.Danao, A.Chai, J.Jaen, F.Kayser. Discovery of A New Binding Mode For A Series of Liver X Receptor Agonists. Bioorg.Med.Chem.Lett. V. 22 2407 2012.
ISSN: ISSN 0960-894X
PubMed: 22406115
DOI: 10.1016/J.BMCL.2012.02.028
Page generated: Tue Jul 8 19:28:10 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy