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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

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