Magnesium in PDB 1zn7: Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P

All present enzymatic activity of Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P:
2.4.2.7;

The structure of Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P, PDB code: 1zn7 was solved by J.Iulek, M.Silva, C.H.T.P.Tomich, O.H.Thiemann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.75 / 1.83
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	47.019, 47.267, 47.522, 76.59, 69.26, 61.89
R / Rfree (%)	14.6 / 19

The binding sites of Magnesium atom in the Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P (pdb code 1zn7). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P, PDB code: 1zn7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg500 b:25.9 occ:1.00 O4 A:PO4504 1.9 27.6 0.5 O A:HOH662 2.0 20.6 1.0 O3B A:PRP502 2.1 17.4 0.5 O A:HOH663 2.2 16.1 1.0 O3 A:PRP502 2.2 12.3 0.5 O1 A:PRP502 2.2 13.9 0.5 O3' A:HSX506 2.3 23.2 0.5 O2 A:PRP502 2.3 12.1 0.5 C2 A:PRP502 2.8 15.6 0.5 C1 A:PRP502 2.9 15.3 0.5 C3 A:PRP502 2.9 12.8 0.5 P A:PO4504 3.0 29.7 0.5 O1 A:HSX506 3.1 28.9 0.5 O3 A:PO4504 3.1 27.9 0.5 PB A:PRP502 3.2 20.4 0.5 O2' A:HSX506 3.3 23.1 0.5 O3A A:PRP502 3.3 20.3 0.5 PA A:PRP502 3.4 20.2 0.5 C3' A:HSX506 3.5 22.4 0.5 O A:ASP65 3.7 16.1 1.0 C4 A:PRP502 3.8 13.1 0.5 O4 A:PRP502 3.9 14.9 0.5 C2' A:HSX506 3.9 24.6 0.5 OD1 A:ASP127 3.9 16.0 1.0 N A:SER66 3.9 17.4 1.0 O1B A:PRP502 3.9 22.5 0.5 O1 A:PO4504 3.9 30.0 0.5 OD2 A:ASP127 4.0 16.1 1.0 C1' A:HSX506 4.0 24.4 0.5 O2 A:PO4504 4.1 28.0 0.5 C A:ASP65 4.1 16.8 1.0 O1A A:PRP502 4.2 18.0 0.5 N A:ARG67 4.3 17.1 1.0 O A:HOH729 4.3 23.3 1.0 C4' A:HSX506 4.4 21.7 0.5 CG A:ASP127 4.4 16.8 1.0 OD2 A:ASP128 4.5 19.2 1.0 O2B A:PRP502 4.5 18.3 0.5 O2A A:PRP502 4.5 21.3 0.5 CB A:ARG67 4.7 16.1 1.0 O1' A:HSX506 4.7 23.2 0.5 O A:LEU64 4.8 14.7 1.0 NE A:ARG67 4.9 26.7 1.0 CA A:SER66 5.0 19.0 1.0 CG2 A:THR135 5.0 17.2 1.0

Magnesium binding site 2 out of 2 in the Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Human Adenine Phosphoribosyltransferase Complexed with Prpp, Ade and R5P within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg501 b:25.7 occ:1.00 O3B B:PRP503 1.9 22.2 0.5 O4 A:PO4505 1.9 23.3 0.5 O2 B:PRP503 2.1 14.0 0.5 O B:HOH664 2.1 18.4 1.0 O B:HOH663 2.1 18.1 1.0 O3 B:PRP503 2.1 12.9 0.5 O1 B:PRP503 2.1 20.7 0.5 O1 B:HSX507 2.4 26.2 0.5 O3' B:HSX507 2.6 23.7 0.5 C2 B:PRP503 2.6 16.9 0.5 C3 B:PRP503 2.9 14.5 0.5 O2' B:HSX507 2.9 24.5 0.5 C1 B:PRP503 2.9 17.6 0.5 PB B:PRP503 3.0 24.6 0.5 P A:PO4505 3.2 24.7 0.5 O3A B:PRP503 3.3 24.9 0.5 PA B:PRP503 3.4 25.2 0.5 O3 A:PO4505 3.4 23.8 0.5 C1' B:HSX507 3.6 26.1 0.5 C2' B:HSX507 3.6 25.6 0.5 C3' B:HSX507 3.6 25.1 0.5 O B:ASP65 3.7 18.4 1.0 O1B B:PRP503 3.8 23.5 0.5 OD1 B:ASP127 3.9 16.7 1.0 C4 B:PRP503 3.9 14.0 0.5 N B:SER66 3.9 17.8 1.0 O4 B:PRP503 3.9 16.6 0.5 OD2 B:ASP127 4.0 16.8 1.0 O2 A:PO4505 4.1 21.3 0.5 O1A B:PRP503 4.2 20.6 0.5 C B:ASP65 4.2 17.2 1.0 N B:ARG67 4.3 15.8 1.0 O1 A:PO4505 4.3 26.3 0.5 O2B B:PRP503 4.3 25.7 0.5 O B:HOH794 4.3 20.9 1.0 C4' B:HSX507 4.4 24.4 0.5 OD2 B:ASP128 4.4 21.5 1.0 CG B:ASP127 4.4 16.9 1.0 O2A B:PRP503 4.5 22.3 0.5 O1' B:HSX507 4.5 25.5 0.5 CB B:ARG67 4.6 15.2 1.0 NE B:ARG67 4.8 24.1 1.0 NH2 B:ARG67 4.8 28.1 1.0 O B:LEU64 4.8 15.3 1.0 CA B:SER66 5.0 17.8 1.0 CA B:ARG67 5.0 16.5 1.0 CZ B:ARG67 5.0 28.3 1.0

C.H.Silva, M.Silva, J.Iulek, O.H.Thiemann. Structural Complexes of Human Adenine Phosphoribosyltransferase Reveal Novel Features of the Aprt Catalytic Mechanism J.Biomol.Struct.Dyn. V. 25 589 2008.
ISSN: ISSN 0739-1102
PubMed: 18399692