Magnesium in PDB 6fd4: Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization

All present enzymatic activity of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization:
2.4.2.7;

The structure of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization, PDB code: 6fd4 was solved by P.Nioche, J.Huyet, M.Ozeir, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.64 / 1.50
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.380, 47.540, 47.670, 69.86, 77.20, 61.76
R / Rfree (%)	16.6 / 17.8

The binding sites of Magnesium atom in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization (pdb code 6fd4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization, PDB code: 6fd4:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg200 b:11.5 occ:1.00 O B:HOH325 2.0 13.9 1.0 O1B B:PRP201 2.0 11.2 1.0 O B:HOH306 2.2 8.7 1.0 O3 B:PRP201 2.2 8.4 1.0 O2 B:PRP201 2.2 9.1 1.0 O1 B:PRP201 2.3 7.7 1.0 C2 B:PRP201 2.9 8.7 1.0 C3 B:PRP201 3.1 7.1 1.0 C1 B:PRP201 3.2 7.9 1.0 PB B:PRP201 3.2 11.0 1.0 O3A B:PRP201 3.3 12.5 1.0 PA B:PRP201 3.4 9.9 1.0 O B:ASP65 3.7 9.2 1.0 N B:SER66 3.9 8.1 1.0 C4 B:PRP201 4.0 8.5 1.0 O3B B:PRP201 4.0 13.8 1.0 O1A B:PRP201 4.0 11.9 1.0 OD1 B:ASP127 4.0 9.5 1.0 O4 B:PRP201 4.1 9.7 1.0 N B:ARG67 4.1 8.2 1.0 OD2 B:ASP127 4.1 8.5 1.0 O B:HOH328 4.2 14.7 1.0 C B:ASP65 4.2 8.8 1.0 OD1 B:ASP128 4.3 11.9 1.0 O2B B:PRP201 4.4 13.9 1.0 CG B:ASP127 4.5 10.1 1.0 CB B:ARG67 4.5 9.4 1.0 O2A B:PRP201 4.6 12.6 1.0 NE B:ARG67 4.8 21.7 1.0 O B:LEU64 4.8 8.7 1.0 CA B:ARG67 4.9 8.9 1.0 NZ B:LYS88 4.9 27.5 1.0 CA B:SER66 5.0 7.0 0.2 CA B:SER66 5.0 7.9 0.2 CA B:SER66 5.0 8.9 0.5 C B:SER66 5.0 7.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Aprt-TYR105PHE Variant in Complex with Adenine, Prpp and MG2+, 14 Hours Post Crystallization within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg200 b:10.7 occ:1.00 O3B A:PRP201 2.0 10.3 1.0 O A:HOH312 2.1 12.2 1.0 O A:HOH307 2.1 9.6 1.0 O3 A:PRP201 2.2 7.6 1.0 O2 A:PRP201 2.3 8.3 1.0 O1 A:PRP201 2.3 8.5 1.0 C2 A:PRP201 2.9 8.3 1.0 C3 A:PRP201 3.1 7.9 1.0 C1 A:PRP201 3.1 7.9 1.0 PB A:PRP201 3.2 9.8 1.0 O3A A:PRP201 3.3 10.6 1.0 PA A:PRP201 3.4 9.4 1.0 O A:ASP65 3.7 10.2 1.0 N A:SER66 3.8 7.7 1.0 C4 A:PRP201 4.0 7.9 1.0 OD1 A:ASP127 4.0 9.6 1.0 O1B A:PRP201 4.0 11.8 1.0 O4 A:PRP201 4.0 8.4 1.0 O2A A:PRP201 4.0 12.8 1.0 OD2 A:ASP127 4.1 8.8 1.0 N A:ARG67 4.2 7.6 1.0 C A:ASP65 4.2 9.2 1.0 O A:HOH335 4.3 14.3 1.0 OD1 A:ASP128 4.3 12.3 1.0 O2B A:PRP201 4.4 13.4 1.0 CG A:ASP127 4.5 8.8 1.0 O1A A:PRP201 4.6 13.4 1.0 CB A:ARG67 4.6 8.4 0.5 CB A:ARG67 4.6 8.8 0.5 CG A:ARG67 4.6 9.6 0.5 NE A:ARG67 4.7 11.0 0.5 O A:LEU64 4.9 9.9 1.0 CA A:SER66 4.9 7.0 0.5 NH2 A:ARG67 4.9 12.3 0.5 CA A:ARG67 4.9 8.2 0.5 CA A:ARG67 4.9 8.0 0.5 CA A:SER66 4.9 8.0 0.5 NZ A:LYS88 4.9 17.6 0.7 C A:SER66 5.0 7.5 1.0

J.Huyet, M.Ozeir, M.C.Burgevin, B.Pinson, F.Chesney, J.M.Remy, A.R.Siddiqi, R.Lupoli, G.Pinon, C.Saint-Marc, J.F.Gibert, R.Morales, I.Ceballos-Picot, R.Barouki, B.Daignan-Fornier, A.Olivier-Bandini, F.Auge, P.Nioche. Structural Insights Into the Forward and Reverse Enzymatic Reactions in Human Adenine Phosphoribosyltransferase. Cell Chem Biol V. 25 666 2018.
ISSN: ESSN 2451-9448
PubMed: 29576532
DOI: 10.1016/J.CHEMBIOL.2018.02.011