Magnesium in PDB 1yzl: Gppnhp-Bound RAB9 Gtpase

The structure of Gppnhp-Bound RAB9 Gtpase, PDB code: 1yzl 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)	4.80 / 1.85
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.325, 68.325, 83.229, 90.00, 90.00, 120.00
R / Rfree (%)	19.2 / 22.1

The binding sites of Magnesium atom in the Gppnhp-Bound RAB9 Gtpase (pdb code 1yzl). 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 RAB9 Gtpase, PDB code: 1yzl:

Magnesium binding site 1 out of 1 in the Gppnhp-Bound RAB9 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 RAB9 Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:19.8 occ:1.00 O2G A:GNP400 2.0 19.6 1.0 OG A:SER21 2.0 20.8 1.0 O2B A:GNP400 2.1 18.6 1.0 O A:HOH426 2.1 18.3 1.0 OG1 A:THR39 2.1 22.8 1.0 O A:HOH419 2.1 18.1 1.0 PG A:GNP400 3.1 19.7 1.0 CB A:THR39 3.2 24.4 1.0 CB A:SER21 3.2 20.3 1.0 PB A:GNP400 3.2 19.6 1.0 N3B A:GNP400 3.4 19.5 1.0 N A:THR39 3.7 25.8 1.0 O3G A:GNP400 3.8 20.2 1.0 N A:SER21 3.9 19.6 1.0 OD2 A:ASP62 4.0 17.4 1.0 CA A:THR39 4.0 24.8 1.0 O2A A:GNP400 4.1 19.2 1.0 CA A:SER21 4.1 20.1 1.0 O A:HOH445 4.1 25.5 1.0 OD1 A:ASP62 4.2 18.7 1.0 O3A A:GNP400 4.3 19.2 1.0 O1B A:GNP400 4.3 18.4 1.0 CG2 A:THR39 4.3 24.6 1.0 O1G A:GNP400 4.4 20.2 1.0 O A:HOH429 4.5 24.1 1.0 O A:THR63 4.5 18.2 1.0 CG A:ASP62 4.5 17.7 1.0 PA A:GNP400 4.5 20.0 1.0 O A:PHE37 4.6 32.0 1.0 O1A A:GNP400 4.7 18.9 1.0 C A:HIS38 4.7 27.8 1.0 O A:HOH431 4.8 29.3 1.0 CB A:LYS20 5.0 19.3 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