Magnesium in PDB 7qpi: Structure of Lamprey Vdr in Complex with 1,25D3

All present enzymatic activity of Structure of Lamprey Vdr in Complex with 1,25D3:
2.3.1.48;

The structure of Structure of Lamprey Vdr in Complex with 1,25D3, PDB code: 7qpi was solved by N.Rochel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.76 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	37.32, 66.17, 105.69, 90, 90, 90
R / Rfree (%)	18.3 / 25.6

The binding sites of Magnesium atom in the Structure of Lamprey Vdr in Complex with 1,25D3 (pdb code 7qpi). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Lamprey Vdr in Complex with 1,25D3, PDB code: 7qpi:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Lamprey Vdr in Complex with 1,25D3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Lamprey Vdr in Complex with 1,25D3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg302 b:22.4 occ:1.00 CA A:HIS226 3.3 27.9 1.0 N A:LEU228 3.3 50.8 1.0 C A:HIS226 3.5 28.6 1.0 CB A:LEU228 3.5 47.6 1.0 CD A:PRO227 3.6 28.6 1.0 N A:PRO227 3.7 32.5 1.0 CB A:HIS226 3.8 22.1 1.0 CA A:LEU228 3.9 57.0 1.0 O A:HIS226 4.0 27.2 1.0 CG A:LEU228 4.0 48.0 1.0 OG A:SER229 4.1 45.3 1.0 N A:SER229 4.2 43.0 1.0 O A:ARG225 4.3 30.4 1.0 C A:LEU228 4.4 49.6 1.0 CD1 A:LEU228 4.4 54.8 1.0 C A:PRO227 4.4 43.9 1.0 N A:HIS226 4.6 27.8 1.0 ND1 A:HIS226 4.6 35.9 1.0 CA A:PRO227 4.6 37.1 1.0 CG A:HIS226 4.7 36.5 1.0 CG A:PRO227 4.9 29.1 1.0 C A:ARG225 4.9 31.6 1.0 CB A:SER229 5.0 38.7 1.0

Magnesium binding site 2 out of 2 in the Structure of Lamprey Vdr in Complex with 1,25D3


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Lamprey Vdr in Complex with 1,25D3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg303 b:16.7 occ:1.00 NZ A:LYS95 3.2 39.5 1.0 N A:ASP23 3.3 20.6 1.0 NH1 A:ARG129 3.5 16.4 1.0 CA A:TYR22 3.7 26.4 1.0 CE1 A:TYR91 3.9 28.9 1.0 O A:THR21 3.9 31.5 1.0 NH2 A:ARG129 4.0 22.5 1.0 C A:TYR22 4.0 24.5 1.0 CG A:LYS95 4.0 18.0 1.0 CD2 A:TYR22 4.1 21.4 1.0 CG A:TYR22 4.2 29.5 1.0 CZ A:ARG129 4.2 26.2 1.0 OH A:TYR91 4.3 43.2 1.0 CB A:ASP23 4.3 26.8 1.0 CA A:ASP23 4.3 29.6 1.0 CB A:TYR22 4.5 29.6 1.0 CE2 A:TYR22 4.5 19.4 1.0 CE A:LYS95 4.5 31.3 1.0 CZ A:TYR91 4.5 40.5 1.0 CB A:LYS95 4.6 19.4 1.0 C2 A:VDX301 4.6 19.4 1.0 N A:TYR22 4.6 26.4 1.0 C A:THR21 4.7 25.5 1.0 CD1 A:TYR22 4.7 29.3 1.0 O A:ASP23 4.7 45.1 1.0 CD A:LYS95 4.8 19.5 1.0 CD1 A:TYR91 4.8 24.9 1.0 C A:ASP23 4.8 38.0 1.0 CZ A:TYR22 5.0 28.2 1.0

R.Sigueiro, L.Bianchetti, C.Peluso-Iltis, S.Chalhoub, A.Dejaegere, J.Osz, N.Rochel. Advances in Vitamin D Receptor Function and Evolution Based on the 3D Structure of the Lamprey Ligand-Binding Domain. J.Med.Chem. V. 65 5821 2022.
ISSN: ISSN 0022-2623
PubMed: 35302785
DOI: 10.1021/ACS.JMEDCHEM.2C00171