Magnesium in PDB 1yzn: Gppnhp-Bound YPT1P Gtpase

The structure of Gppnhp-Bound YPT1P Gtpase, PDB code: 1yzn was solved by S.Eathiraj, X.Pan, C.Ritacco, D.G.Lambright, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.00 / 2.06
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	39.011, 56.930, 74.720, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.5

The binding sites of Magnesium atom in the Gppnhp-Bound YPT1P Gtpase (pdb code 1yzn). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Gppnhp-Bound YPT1P Gtpase, PDB code: 1yzn:

Magnesium binding site 1 out of 1 in the Gppnhp-Bound YPT1P Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Gppnhp-Bound YPT1P Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg301 b:17.2 occ:1.00 O2G A:GNP300 1.9 13.0 1.0 OG A:SER22 2.0 15.2 1.0 O2B A:GNP300 2.1 15.1 1.0 OG1 A:THR40 2.1 18.4 1.0 O A:HOH306 2.1 14.3 1.0 O A:HOH307 2.2 14.2 1.0 CB A:SER22 3.1 15.9 1.0 PG A:GNP300 3.1 15.1 1.0 CB A:THR40 3.2 20.4 1.0 PB A:GNP300 3.2 15.5 1.0 N3B A:GNP300 3.4 13.9 1.0 N A:THR40 3.7 21.6 1.0 N A:SER22 3.9 15.2 1.0 O3G A:GNP300 3.9 15.2 1.0 O2A A:GNP300 4.0 16.7 1.0 OD2 A:ASP63 4.0 19.5 1.0 CA A:THR40 4.1 20.2 1.0 CA A:SER22 4.1 15.7 1.0 O A:HOH381 4.2 28.3 1.0 OD1 A:ASP63 4.2 17.6 1.0 O3A A:GNP300 4.2 16.3 1.0 O1B A:GNP300 4.3 15.6 1.0 CG2 A:THR40 4.3 18.9 1.0 O A:ILE38 4.3 23.6 1.0 O1G A:GNP300 4.4 12.9 1.0 PA A:GNP300 4.4 16.9 1.0 O A:THR64 4.5 17.3 1.0 CG A:ASP63 4.5 18.3 1.0 O1A A:GNP300 4.6 15.9 1.0 C A:SER39 4.7 22.4 1.0 CA A:SER39 4.9 22.7 1.0 NZ A:LYS21 5.0 16.8 1.0

S.Eathiraj, X.Pan, C.Ritacco, D.G.Lambright. Structural Basis of Family-Wide Rab Gtpase Recognition By Rabenosyn-5. Nature V. 436 415 2005.
ISSN: ISSN 0028-0836
PubMed: 16034420
DOI: 10.1038/NATURE03798