Magnesium in PDB 1ukv: Structure of Rabgdp-Dissociation Inhibitor in Complex with Prenylated YPT1 Gtpase

The structure of Structure of Rabgdp-Dissociation Inhibitor in Complex with Prenylated YPT1 Gtpase, PDB code: 1ukv was solved by A.Rak, O.Pylypenko, T.Durek, A.Watzke, S.Kushnir, L.Brunsveld, H.Waldmann, R.S.Goody, K.Alexandrov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.49 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.503, 119.577, 60.723, 90.00, 90.61, 90.00
R / Rfree (%)	19.2 / 21.6

The binding sites of Magnesium atom in the Structure of Rabgdp-Dissociation Inhibitor in Complex with Prenylated YPT1 Gtpase (pdb code 1ukv). 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 Structure of Rabgdp-Dissociation Inhibitor in Complex with Prenylated YPT1 Gtpase, PDB code: 1ukv:

Magnesium binding site 1 out of 1 in the Structure of Rabgdp-Dissociation Inhibitor in Complex with Prenylated YPT1 Gtpase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rabgdp-Dissociation Inhibitor in Complex with Prenylated YPT1 Gtpase within 5.0Å range: probe atom residue distance (Å) B Occ Y:Mg1208 b:5.7 occ:1.00 O3B Y:GDP1207 2.0 6.2 1.0 O Y:HOH1366 2.0 6.8 1.0 O Y:HOH1363 2.1 7.0 1.0 O Y:HOH1365 2.1 6.9 1.0 OG Y:SER22 2.1 7.8 1.0 O Y:HOH1364 2.2 9.2 1.0 PB Y:GDP1207 3.2 5.7 1.0 CB Y:SER22 3.3 5.6 1.0 O1B Y:GDP1207 3.5 8.9 1.0 N Y:SER22 3.9 6.0 1.0 OD2 Y:ASP63 4.0 7.6 1.0 O2A Y:GDP1207 4.0 8.1 1.0 O Y:HOH1226 4.2 9.9 1.0 O Y:HOH1428 4.2 27.0 1.0 CA Y:SER22 4.2 4.5 1.0 O Y:HOH1214 4.2 7.6 1.0 O2B Y:GDP1207 4.2 6.7 1.0 O3A Y:GDP1207 4.3 8.9 1.0 OD1 Y:ASP63 4.3 6.5 1.0 OE1 Y:GLU68 4.3 8.5 1.0 OG1 Y:THR64 4.3 5.6 1.0 O Y:HOH1367 4.4 9.6 1.0 PA Y:GDP1207 4.5 7.1 1.0 CG Y:ASP63 4.5 6.3 1.0 O Y:HOH1402 4.6 21.7 1.0 O1A Y:GDP1207 4.7 6.0 1.0 N Y:GLY66 4.9 6.7 1.0 CB Y:LYS21 4.9 6.0 1.0 O Y:HOH1283 5.0 23.2 1.0 NZ Y:LYS21 5.0 5.5 1.0

A.Rak, O.Pylypenko, T.Durek, A.Watzke, S.Kushnir, L.Brunsveld, H.Waldmann, R.S.Goody, K.Alexandrov. Structure of Rab Gdp-Dissociation Inhibitor in Complex with Prenylated YPT1 Gtpase Science V. 302 646 2003.
ISSN: ISSN 0036-8075
PubMed: 14576435
DOI: 10.1126/SCIENCE.1087761