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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

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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

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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

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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

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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: Sat Jul 13 23:28:32 2024

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