Atomistry » Calcium » PDB 4dg4-4dtj » 4dk8
Atomistry »
  Calcium »
    PDB 4dg4-4dtj »
      4dk8 »

Calcium in PDB 4dk8: Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5

Enzymatic activity of Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5

All present enzymatic activity of Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5:
2.3.1.48;

Protein crystallography data

The structure of Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5, PDB code: 4dk8 was solved by D.E.Piper, D.J.Kopecky, H.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.73 / 2.75
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 88.145, 88.145, 198.450, 90.00, 90.00, 90.00
R / Rfree (%) 24.5 / 27.8

Other elements in 4dk8:

The structure of Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5 also contains other interesting chemical elements:

Fluorine (F) 6 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5 (pdb code 4dk8). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5, PDB code: 4dk8:
Jump to Calcium binding site number: 1; 2; 3; 4; 5; 6;

Calcium binding site 1 out of 6 in 4dk8

Go back to Calcium Binding Sites List in 4dk8
Calcium binding site 1 out of 6 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5


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 Partial Agonist 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca503

b:0.1
occ:1.00
 OE1 A:GLN235 3.1 90.6 1.0
OE2 A:GLU281 3.4 78.6 1.0
OE1 A:GLU315 3.6 85.1 1.0
CD A:GLU315 3.7 82.3 1.0
CG A:GLU315 3.8 77.8 1.0
CD A:GLU281 4.1 78.5 1.0
CD A:GLN235 4.2 88.8 1.0
OE2 A:GLU315 4.2 83.7 1.0
CG A:GLU281 4.4 74.2 1.0
O A:HOH603 4.6 86.6 1.0
CG1 A:ILE282 4.6 65.1 1.0
O A:GLU281 4.6 66.1 1.0
CG2 A:ILE311 4.7 48.7 1.0
CG A:GLN235 4.7 84.5 1.0
CB A:PHE285 4.7 63.6 1.0
CG A:PHE285 4.9 60.7 1.0
CD1 A:ILE374 4.9 63.0 1.0
C A:GLU281 4.9 68.1 1.0
CB A:GLU281 5.0 70.0 1.0

Calcium binding site 2 out of 6 in 4dk8

Go back to Calcium Binding Sites List in 4dk8
Calcium binding site 2 out of 6 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5


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 Partial Agonist 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca504

b:0.1
occ:1.00
 OD2 A:ASP339 2.9 74.6 1.0
O A:THR334 3.5 98.6 1.0
CG A:ASP339 3.8 76.1 1.0
OD1 A:ASP339 4.0 76.3 1.0
OG A:SER336 4.3 89.0 1.0
N A:SER336 4.6 90.0 1.0
C A:THR334 4.7 99.2 1.0
OG1 A:THR334 4.9 99.0 1.0
CB A:SER336 4.9 88.2 1.0

Calcium binding site 3 out of 6 in 4dk8

Go back to Calcium Binding Sites List in 4dk8
Calcium binding site 3 out of 6 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5


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 Partial Agonist 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca505

b:73.6
occ:0.50
 OE1 A:GLU325 2.6 68.2 1.0
OE2 A:GLU325 2.7 68.6 1.0
CD A:GLU325 3.0 67.9 1.0
O A:ACT502 3.0 99.7 1.0
OXT A:ACT502 3.1 99.9 1.0
C A:ACT502 3.4 0.6 1.0
CG A:GLU325 4.5 68.1 1.0
NZ A:LYS337 4.7 72.3 1.0
CH3 A:ACT502 4.9 0.7 1.0

Calcium binding site 4 out of 6 in 4dk8

Go back to Calcium Binding Sites List in 4dk8
Calcium binding site 4 out of 6 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5


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 Partial Agonist 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca506

b:1.0
occ:0.50
 CG A:LYS337 3.8 79.7 1.0
O A:GLU325 3.9 66.8 1.0
CB A:GLU325 3.9 63.9 1.0
O A:THR324 4.0 67.1 1.0
CD A:LYS337 4.4 77.8 1.0
CD A:GLU325 4.6 67.9 1.0
CB A:SER336 4.7 88.2 1.0
N A:LYS337 4.7 83.4 1.0
CG A:GLU325 4.7 68.1 1.0
C A:GLU325 4.7 65.6 1.0
OE2 A:GLU325 4.8 68.6 1.0
OE1 A:GLU325 4.9 68.2 1.0
CA A:GLU325 5.0 64.4 1.0

Calcium binding site 5 out of 6 in 4dk8

Go back to Calcium Binding Sites List in 4dk8
Calcium binding site 5 out of 6 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5


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 Partial Agonist 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca502

b:0.6
occ:1.00
 ND2 C:ASN239 3.2 0.5 1.0
OE1 C:GLU315 3.6 83.5 1.0
OE1 C:GLN235 3.8 0.5 1.0
CD C:GLU315 4.0 84.1 1.0
CG C:GLU315 4.1 82.5 1.0
CG C:ASN239 4.1 0.7 1.0
OD1 C:ASN239 4.2 0.1 1.0
NE2 C:GLN235 4.2 0.9 1.0
CD C:GLN235 4.2 0.2 1.0
CD2 C:PHE285 4.5 75.4 1.0
CB C:PHE285 4.5 73.4 1.0
CG C:PHE285 4.6 74.8 1.0
CG1 C:ILE282 4.7 67.0 1.0
CG2 C:ILE311 4.7 61.0 1.0
CD1 C:ILE374 4.7 67.7 1.0
OE2 C:GLU315 4.8 87.0 1.0
CA C:ILE282 4.9 69.8 1.0
O C:GLU281 4.9 77.1 1.0
CB C:GLU281 5.0 80.8 1.0
C C:GLU281 5.0 76.4 1.0
N C:ILE282 5.0 73.3 1.0

Calcium binding site 6 out of 6 in 4dk8

Go back to Calcium Binding Sites List in 4dk8
Calcium binding site 6 out of 6 in the Crystal Structure of Lxr Ligand Binding Domain in Complex with Partial Agonist 5


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 Partial Agonist 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca503

b:0.7
occ:1.00
 O C:THR334 2.9 0.7 1.0
OG1 C:THR334 2.9 0.3 1.0
C C:THR334 3.8 0.2 1.0
CB C:THR334 3.9 0.3 1.0
CA C:THR334 4.2 0.5 1.0
N C:THR334 4.3 0.1 1.0
OD1 C:ASP339 4.8 0.3 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: Sat Jul 13 23:28:37 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy