Magnesium in PDB 6hgq: Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+

All present enzymatic activity of Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+:
2.4.2.7;

The structure of Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+, PDB code: 6hgq 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)	71.69 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.060, 49.800, 71.810, 90.08, 93.22, 102.31
R / Rfree (%)	17.5 / 21.4

The binding sites of Magnesium atom in the Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+ (pdb code 6hgq). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+, PDB code: 6hgq:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+


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 Wild Type in Complex with Hypoxanthine, Prpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:9.6 occ:1.00 O3B A:PRP203 2.0 12.0 1.0 O A:HOH320 2.1 10.7 1.0 O2 A:PRP203 2.1 8.2 1.0 O A:HOH308 2.1 11.1 1.0 O3 A:PRP203 2.2 8.5 1.0 O1 A:PRP203 2.2 11.0 1.0 C2 A:PRP203 2.8 8.6 1.0 C3 A:PRP203 3.0 8.5 1.0 C1 A:PRP203 3.0 8.9 1.0 PB A:PRP203 3.2 11.4 1.0 O3A A:PRP203 3.3 12.8 1.0 PA A:PRP203 3.3 13.9 1.0 O A:ASP65 3.9 12.9 1.0 O4 A:PRP203 3.9 8.2 1.0 N A:SER66 4.0 14.3 1.0 C4 A:PRP203 4.0 8.8 1.0 O2B A:PRP203 4.0 11.0 1.0 O1A A:PRP203 4.0 15.9 1.0 OD1 A:ASP127 4.1 11.2 1.0 OD2 A:ASP127 4.1 12.1 1.0 O A:HOH326 4.1 12.1 1.0 N A:ARG67 4.2 12.3 1.0 OD1 A:ASP128 4.3 15.8 1.0 C A:ASP65 4.3 13.9 1.0 O1B A:PRP203 4.3 15.3 1.0 O2A A:PRP203 4.4 14.5 1.0 CB A:ARG67 4.5 13.8 1.0 CG A:ASP127 4.5 11.8 1.0 NH2 A:ARG67 4.5 21.6 1.0 NE A:ARG67 4.5 16.7 1.0 O A:LEU64 4.8 11.2 1.0 CZ A:ARG67 4.8 20.3 1.0 CA A:ARG67 4.9 13.6 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+


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 Wild Type in Complex with Hypoxanthine, Prpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg200 b:11.6 occ:1.00 O3B C:PRP201 2.0 11.1 1.0 O1 C:PRP201 2.1 11.9 1.0 O2 C:PRP201 2.1 9.6 1.0 O3 C:PRP201 2.1 8.5 1.0 O C:HOH307 2.1 11.3 1.0 O C:HOH303 2.2 17.1 1.0 C2 C:PRP201 2.7 10.2 1.0 C1 C:PRP201 2.9 10.2 1.0 C3 C:PRP201 2.9 8.7 1.0 PB C:PRP201 3.2 12.1 1.0 PA C:PRP201 3.3 17.6 1.0 O3A C:PRP201 3.3 13.7 1.0 O4 C:PRP201 3.8 9.9 1.0 C4 C:PRP201 3.8 9.4 1.0 O C:ASP65 4.0 15.6 1.0 OD1 C:ASP127 4.0 14.1 1.0 O2B C:PRP201 4.0 11.5 1.0 OD2 C:ASP127 4.0 14.2 1.0 O1A C:PRP201 4.1 15.6 1.0 OD1 C:ASP128 4.1 17.4 1.0 N C:SER66 4.2 13.6 1.0 O C:HOH342 4.2 16.4 1.0 N C:ARG67 4.3 12.5 1.0 O2A C:PRP201 4.4 13.4 1.0 O1B C:PRP201 4.4 13.2 1.0 NH2 C:ARG67 4.4 19.9 1.0 C C:ASP65 4.5 14.4 1.0 CG C:ASP127 4.5 13.9 1.0 CB C:ARG67 4.5 16.1 1.0 NE C:ARG67 4.5 16.7 1.0 CZ C:ARG67 4.6 17.7 1.0 O C:LEU64 4.9 13.7 1.0 CA C:ARG67 4.9 13.4 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg200 b:10.8 occ:1.00 O D:HOH321 2.0 17.3 1.0 O1 D:PRP201 2.1 13.1 1.0 O3B D:PRP201 2.1 13.4 1.0 O D:HOH311 2.1 15.2 1.0 O2 D:PRP201 2.1 10.9 1.0 O3 D:PRP201 2.2 10.7 1.0 C2 D:PRP201 2.8 12.9 1.0 C1 D:PRP201 3.0 13.2 1.0 C3 D:PRP201 3.0 12.2 1.0 PB D:PRP201 3.2 15.9 1.0 PA D:PRP201 3.2 19.0 1.0 O3A D:PRP201 3.3 14.6 1.0 O4 D:PRP201 3.9 12.6 1.0 O D:ASP65 4.0 14.1 1.0 O2B D:PRP201 4.0 12.8 1.0 C4 D:PRP201 4.0 12.7 1.0 O2A D:PRP201 4.0 15.5 1.0 N D:SER66 4.0 14.0 1.0 OD1 D:ASP127 4.1 18.2 1.0 O D:HOH330 4.1 18.2 1.0 OD2 D:ASP127 4.2 16.6 1.0 N D:ARG67 4.2 12.1 1.0 OD1 D:ASP128 4.3 19.3 1.0 O1A D:PRP201 4.3 15.7 1.0 C D:ASP65 4.4 14.6 1.0 CB D:ARG67 4.4 12.6 1.0 O1B D:PRP201 4.4 15.7 1.0 CG D:ASP127 4.6 16.6 1.0 NE D:ARG67 4.7 17.1 1.0 NH2 D:ARG67 4.7 17.4 1.0 CZ D:ARG67 4.8 18.1 1.0 CA D:ARG67 4.9 12.2 1.0 O D:LEU64 4.9 12.1 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Human Aprt Wild Type in Complex with Hypoxanthine, Prpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg200 b:14.4 occ:1.00 O3B B:PRP201 2.0 14.0 1.0 O B:HOH308 2.1 17.9 1.0 O B:HOH314 2.1 13.5 1.0 O1 B:PRP201 2.2 14.8 1.0 O2 B:PRP201 2.2 11.7 1.0 O3 B:PRP201 2.2 12.4 1.0 C2 B:PRP201 2.8 14.4 1.0 C3 B:PRP201 3.0 12.8 1.0 C1 B:PRP201 3.0 15.0 1.0 PB B:PRP201 3.2 16.4 1.0 O3A B:PRP201 3.3 15.9 1.0 PA B:PRP201 3.3 19.4 1.0 O B:ASP65 3.8 11.6 1.0 C4 B:PRP201 3.9 13.5 1.0 O4 B:PRP201 4.0 14.5 1.0 O B:HOH309 4.0 22.3 1.0 O2B B:PRP201 4.0 15.7 1.0 N B:SER66 4.0 13.3 1.0 O2A B:PRP201 4.0 14.8 1.0 OD1 B:ASP127 4.0 17.1 1.0 OD2 B:ASP127 4.1 14.5 1.0 N B:ARG67 4.2 12.3 1.0 C B:ASP65 4.3 12.8 1.0 OD1 B:ASP128 4.3 17.8 1.0 O1B B:PRP201 4.4 15.1 1.0 O1A B:PRP201 4.4 16.3 1.0 CB B:ARG67 4.5 14.6 1.0 CG B:ASP127 4.5 15.1 1.0 NH2 B:ARG67 4.7 20.4 1.0 NE B:ARG67 4.7 19.8 1.0 O B:LEU64 4.9 11.7 1.0 CA B:ARG67 4.9 12.5 1.0 CZ B:ARG67 4.9 23.3 1.0

M.Ozeir, J.Huyet, 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 Basis For Substrate Selectivity and Nucleophilic Substitution Mechanisms in Human Adenine Phosphoribosyltransferase Catalyzed Reaction. J.Biol.Chem. V. 294 11980 2019.
ISSN: ESSN 1083-351X
PubMed: 31160323
DOI: 10.1074/JBC.RA119.009087