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

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

The structure of Crystal Structure of Human Aprt Wild Type in Complex with Adenine, Prpp and MG2+, PDB code: 6fci 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)	71.35 / 1.94
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	49.710, 49.790, 71.490, 90.05, 93.48, 101.91
R / Rfree (%)	19.6 / 23.7

The binding sites of Magnesium atom in the Crystal Structure of Human Aprt Wild Type in Complex with Adenine, Prpp and MG2+ (pdb code 6fci). 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 Adenine, Prpp and MG2+, PDB code: 6fci:
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 Adenine, 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 Adenine, Prpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg200 b:7.1 occ:1.00 O3B A:PRP201 2.0 5.8 1.0 O A:HOH315 2.1 5.8 1.0 O2 A:PRP201 2.1 5.7 1.0 O A:HOH307 2.1 7.3 1.0 O1 A:PRP201 2.2 6.0 1.0 O3 A:PRP201 2.3 5.8 1.0 C2 A:PRP201 2.8 5.7 1.0 C3 A:PRP201 3.1 5.6 1.0 C1 A:PRP201 3.1 6.0 1.0 PB A:PRP201 3.2 6.0 1.0 O3A A:PRP201 3.3 6.3 1.0 PA A:PRP201 3.4 6.5 1.0 O A:ASP65 3.8 8.8 1.0 O2B A:PRP201 4.0 5.6 1.0 O4 A:PRP201 4.0 5.6 1.0 N A:SER66 4.0 8.4 1.0 C4 A:PRP201 4.0 5.7 1.0 OD1 A:ASP127 4.0 9.0 1.0 OD2 A:ASP127 4.0 8.2 1.0 OD1 A:ASP128 4.1 10.1 1.0 O1A A:PRP201 4.2 7.2 1.0 O A:HOH326 4.2 7.8 1.0 N A:ARG67 4.2 7.4 1.0 C A:ASP65 4.3 8.6 1.0 CB A:ARG67 4.3 8.8 1.0 NZ A:LYS88 4.3 20.4 1.0 O1B A:PRP201 4.4 5.7 1.0 O2A A:PRP201 4.4 6.6 1.0 CG A:ASP127 4.5 8.3 1.0 NE A:ARG67 4.6 11.9 1.0 O A:LEU64 4.7 7.0 1.0 NH2 A:ARG67 4.8 13.0 1.0 CA A:ARG67 4.8 8.2 1.0 CZ A:ARG67 4.8 11.9 1.0 CG A:ARG67 4.9 9.4 1.0 N A:GLY68 4.9 6.7 1.0

Magnesium binding site 2 out of 4 in the Crystal Structure of Human Aprt Wild Type in Complex with Adenine, 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 Adenine, Prpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg200 b:7.5 occ:1.00 O3B B:PRP201 2.0 6.8 1.0 O2 B:PRP201 2.1 7.1 1.0 O B:HOH307 2.1 12.4 1.0 O B:HOH304 2.2 6.6 1.0 O3 B:PRP201 2.2 6.5 1.0 O1 B:PRP201 2.3 6.7 1.0 C2 B:PRP201 2.8 6.9 1.0 C3 B:PRP201 3.0 6.8 1.0 C1 B:PRP201 3.1 6.8 1.0 PB B:PRP201 3.2 7.2 1.0 O3A B:PRP201 3.4 6.6 1.0 PA B:PRP201 3.4 7.3 1.0 N B:SER66 3.8 7.9 1.0 O B:ASP65 3.8 7.0 1.0 O2B B:PRP201 3.9 5.8 1.0 OD1 B:ASP127 3.9 9.3 1.0 C4 B:PRP201 4.0 6.4 1.0 O4 B:PRP201 4.0 6.7 1.0 N B:ARG67 4.1 7.2 1.0 OD2 B:ASP127 4.1 9.6 1.0 OD1 B:ASP128 4.1 16.2 1.0 C B:ASP65 4.2 7.8 1.0 O2A B:PRP201 4.2 6.1 1.0 O B:HOH308 4.3 13.1 1.0 CB B:ARG67 4.3 8.2 1.0 O1B B:PRP201 4.4 6.5 1.0 CG B:ASP127 4.4 9.8 1.0 O1A B:PRP201 4.5 6.5 1.0 O B:LEU64 4.7 7.7 1.0 NE B:ARG67 4.7 10.1 1.0 NH2 B:ARG67 4.7 12.3 1.0 CA B:ARG67 4.7 7.4 1.0 CZ B:ARG67 4.8 11.0 1.0 N B:GLY68 4.9 6.7 1.0 CA B:SER66 4.9 7.4 0.5 CA B:SER66 4.9 7.7 0.5 C B:SER66 4.9 7.1 1.0

Magnesium binding site 3 out of 4 in the Crystal Structure of Human Aprt Wild Type in Complex with Adenine, 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 Adenine, Prpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg200 b:6.4 occ:1.00 O2 C:PRP201 2.0 4.3 1.0 O3B C:PRP201 2.0 5.8 1.0 O C:HOH310 2.1 6.9 1.0 O1 C:PRP201 2.1 5.0 1.0 O3 C:PRP201 2.2 4.4 1.0 O C:HOH304 2.2 7.7 1.0 C2 C:PRP201 2.7 4.6 1.0 C3 C:PRP201 2.9 4.4 1.0 C1 C:PRP201 3.0 4.7 1.0 PB C:PRP201 3.2 5.5 1.0 O3A C:PRP201 3.3 5.5 1.0 PA C:PRP201 3.3 5.4 1.0 O4 C:PRP201 3.9 4.5 1.0 C4 C:PRP201 3.9 4.5 1.0 O2B C:PRP201 3.9 5.2 1.0 O C:ASP65 4.0 9.3 1.0 N C:SER66 4.0 9.8 1.0 OD2 C:ASP127 4.0 8.9 1.0 OD1 C:ASP127 4.0 8.2 1.0 O C:HOH321 4.1 10.4 1.0 O1A C:PRP201 4.1 5.3 1.0 OD1 C:ASP128 4.1 11.5 1.0 N C:ARG67 4.2 8.5 1.0 CB C:ARG67 4.4 9.5 1.0 C C:ASP65 4.4 9.8 1.0 O1B C:PRP201 4.4 5.5 1.0 O2A C:PRP201 4.4 5.3 1.0 CG C:ASP127 4.5 8.2 1.0 NZ C:LYS88 4.5 20.8 1.0 NE C:ARG67 4.6 11.2 1.0 NH2 C:ARG67 4.7 11.9 1.0 CZ C:ARG67 4.8 11.6 1.0 O C:LEU64 4.8 9.2 1.0 CA C:ARG67 4.8 9.0 1.0

Magnesium binding site 4 out of 4 in the Crystal Structure of Human Aprt Wild Type in Complex with Adenine, 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 Adenine, Prpp and MG2+ within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg200 b:4.7 occ:1.00 O2 D:PRP201 2.0 7.8 1.0 O D:HOH339 2.0 8.7 1.0 O D:HOH311 2.0 7.9 1.0 O3B D:PRP201 2.0 7.2 1.0 O1 D:PRP201 2.2 8.3 1.0 O3 D:PRP201 2.2 7.0 1.0 C2 D:PRP201 2.7 7.9 1.0 C3 D:PRP201 3.0 7.5 1.0 C1 D:PRP201 3.0 8.1 1.0 PB D:PRP201 3.2 7.4 1.0 O3A D:PRP201 3.3 7.6 1.0 PA D:PRP201 3.4 9.0 1.0 O4 D:PRP201 3.9 7.9 1.0 O D:ASP65 3.9 7.7 1.0 C4 D:PRP201 3.9 7.1 1.0 OD1 D:ASP127 4.0 12.0 1.0 O2B D:PRP201 4.0 6.3 1.0 N D:SER66 4.1 8.6 1.0 OD2 D:ASP127 4.1 10.6 1.0 O D:HOH320 4.1 8.6 1.0 O2A D:PRP201 4.1 7.8 1.0 OD1 D:ASP128 4.2 18.0 1.0 N D:ARG67 4.3 7.8 1.0 C D:ASP65 4.4 8.3 1.0 O1B D:PRP201 4.4 6.7 1.0 CB D:ARG67 4.4 8.2 1.0 CG D:ASP127 4.5 11.8 1.0 O1A D:PRP201 4.5 8.1 1.0 NE D:ARG67 4.7 9.7 1.0 NH2 D:ARG67 4.8 11.2 1.0 O D:LEU64 4.8 6.6 1.0 CA D:ARG67 4.9 7.9 1.0 CZ D:ARG67 4.9 10.4 1.0 N D:GLY68 4.9 7.6 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