Magnesium in PDB 5tu6: Pagf Prenyltransferase with Cyclic[Inpylyp] and Dmspp

The structure of Pagf Prenyltransferase with Cyclic[Inpylyp] and Dmspp, PDB code: 5tu6 was solved by Y.Hao, S.K.Nair, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	25.00 / 2.22
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	116.490, 116.490, 43.580, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 23.9

The binding sites of Magnesium atom in the Pagf Prenyltransferase with Cyclic[Inpylyp] and Dmspp (pdb code 5tu6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Pagf Prenyltransferase with Cyclic[Inpylyp] and Dmspp, PDB code: 5tu6:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Pagf Prenyltransferase with Cyclic[Inpylyp] and Dmspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pagf Prenyltransferase with Cyclic[Inpylyp] and Dmspp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:32.2 occ:1.00 O A:HOH543 2.0 32.9 1.0 O A:HOH528 2.0 22.6 1.0 O5 A:DST404 2.0 40.0 1.0 O7 A:DST404 2.1 37.1 1.0 OE1 A:GLU184 2.1 35.6 1.0 O A:HOH501 2.2 29.2 1.0 CD A:GLU184 3.2 35.9 1.0 P1 A:DST404 3.3 42.4 1.0 P3 A:DST404 3.3 38.3 1.0 OE2 A:GLU184 3.5 37.7 1.0 O2 A:DST404 3.7 40.8 1.0 OH A:TYR235 3.8 31.0 1.0 OH A:TYR186 3.8 28.9 1.0 O A:HOH562 3.9 36.8 1.0 O A:HOH529 4.1 25.1 1.0 O A:HOH579 4.2 28.2 1.0 OD1 A:ASN229 4.2 37.8 1.0 O6 A:DST404 4.2 44.3 1.0 O8 A:DST404 4.2 40.0 1.0 O4 A:DST404 4.3 46.8 1.0 NH2 A:ARG288 4.4 32.5 1.0 OD2 A:ASP174 4.5 26.0 1.0 CG A:GLU184 4.5 34.0 1.0 NZ A:LYS136 4.6 23.2 1.0 CZ A:TYR186 4.8 30.2 1.0 S9 A:DST404 4.8 46.0 1.0 CB A:GLU184 4.9 31.7 1.0 CE2 A:TYR186 4.9 30.9 1.0

Magnesium binding site 2 out of 2 in the Pagf Prenyltransferase with Cyclic[Inpylyp] and Dmspp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pagf Prenyltransferase with Cyclic[Inpylyp] and Dmspp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:38.6 occ:1.00 OD1 A:ASP125 2.1 28.6 1.0 O A:HOH511 2.2 30.0 1.0 O A:HOH523 2.3 31.3 1.0 O A:HOH512 2.3 26.6 1.0 O A:HOH562 2.4 36.8 1.0 O6 A:DST404 2.5 44.3 1.0 CG A:ASP125 3.3 29.4 1.0 NH2 A:ARG65 3.4 34.7 1.0 CB A:ASP125 3.8 27.6 1.0 O A:HOH506 3.8 25.1 1.0 P1 A:DST404 3.9 42.4 1.0 OG A:SER134 4.2 22.9 1.0 OH A:TYR176 4.2 25.5 1.0 O5 A:DST404 4.3 40.0 1.0 NZ A:LYS136 4.3 23.2 1.0 OD2 A:ASP174 4.3 26.0 1.0 OD2 A:ASP125 4.3 30.6 1.0 NH2 A:ARG127 4.5 35.0 1.0 O A:HOH608 4.5 43.5 1.0 CD A:LYS136 4.5 23.6 1.0 O4 A:DST404 4.5 46.8 1.0 CZ A:ARG65 4.6 30.5 1.0 CE A:LYS136 4.8 23.1 1.0 O2 A:DST404 4.9 40.8 1.0 CG A:ASP174 4.9 25.5 1.0

Y.Hao, E.Pierce, D.Roe, M.Morita, J.A.Mcintosh, V.Agarwal, T.E.Cheatham, E.W.Schmidt, S.K.Nair. Molecular Basis For the Broad Substrate Selectivity of A Peptide Prenyltransferase. Proc. Natl. Acad. Sci. V. 113 14037 2016U.S.A..
ISSN: ESSN 1091-6490
PubMed: 27872314
DOI: 10.1073/PNAS.1609869113