Magnesium in PDB 3rwo: Crystal Structure of YPT32 in Complex with Gdp

The structure of Crystal Structure of YPT32 in Complex with Gdp, PDB code: 3rwo was solved by A.Sultana, Y.Jin, C.Dregger, E.Franklin, L.S.Weisman, A.R.Khan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	68.75 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	130.000, 45.200, 73.400, 90.00, 110.50, 90.00
R / Rfree (%)	16.7 / 20.3

The binding sites of Magnesium atom in the Crystal Structure of YPT32 in Complex with Gdp (pdb code 3rwo). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of YPT32 in Complex with Gdp, PDB code: 3rwo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of YPT32 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of YPT32 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1176 b:13.5 occ:1.00 O3B B:GDP4032 2.0 10.3 1.0 O B:HOH465 2.1 6.5 1.0 O B:HOH466 2.1 2.0 1.0 OG B:SER27 2.1 8.4 1.0 O B:HOH464 2.2 11.9 1.0 O B:HOH209 2.2 9.4 1.0 PB B:GDP4032 3.2 10.6 1.0 CB B:SER27 3.3 8.4 1.0 O1B B:GDP4032 3.4 11.8 1.0 N B:SER27 3.9 8.9 1.0 OG B:SER44 4.0 25.6 1.0 OD2 B:ASP68 4.0 10.5 1.0 O2A B:GDP4032 4.0 11.2 1.0 O B:HOH288 4.1 20.2 1.0 CA B:SER27 4.2 8.2 1.0 OD1 B:ASP68 4.2 10.6 1.0 O B:HOH546 4.2 37.0 1.0 O2B B:GDP4032 4.3 10.8 1.0 O3A B:GDP4032 4.3 10.0 1.0 O B:HOH203 4.4 11.6 1.0 CB B:ALA70 4.5 12.3 1.0 CG B:ASP68 4.5 9.6 1.0 O B:THR69 4.6 11.6 1.0 PA B:GDP4032 4.6 11.3 1.0 O B:HOH205 4.8 34.4 1.0 CB B:SER44 4.8 31.0 1.0 O1A B:GDP4032 4.9 10.6 1.0 NZ B:LYS26 4.9 9.4 1.0 CB B:LYS26 5.0 8.0 1.0 O B:HOH561 5.0 18.4 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of YPT32 in Complex with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of YPT32 in Complex with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1175 b:12.1 occ:1.00 O3B A:GDP4032 2.0 7.8 1.0 OG A:SER27 2.1 8.2 1.0 O A:HOH461 2.1 8.6 1.0 O A:HOH462 2.1 6.7 1.0 O A:HOH194 2.2 7.7 1.0 O A:HOH463 2.2 2.0 1.0 CB A:SER27 3.2 8.6 1.0 PB A:GDP4032 3.3 8.8 1.0 O1B A:GDP4032 3.5 11.6 1.0 N A:SER27 3.9 8.6 1.0 OD2 A:ASP68 4.0 9.4 1.0 O2A A:GDP4032 4.1 10.7 1.0 CA A:SER27 4.1 8.6 1.0 O A:HOH297 4.2 17.9 1.0 OD1 A:ASP68 4.2 9.1 1.0 O A:HOH189 4.2 14.4 1.0 O A:HOH413 4.2 32.0 1.0 O A:HOH244 4.3 13.8 1.0 O2B A:GDP4032 4.3 9.5 1.0 O3A A:GDP4032 4.3 8.6 1.0 O A:HOH562 4.4 14.4 1.0 CG A:ASP68 4.5 8.5 1.0 CB A:ALA70 4.6 11.0 1.0 O A:THR69 4.6 10.8 1.0 PA A:GDP4032 4.6 10.1 1.0 O1A A:GDP4032 4.8 12.0 1.0 O A:HOH197 4.8 28.7 1.0 NZ A:LYS26 5.0 9.8 1.0

A.Sultana, Y.Jin, C.Dregger, E.Franklin, L.S.Weisman, A.R.Khan. The Activation Cycle of Rab Gtpase YPT32 Reveals Structural Determinants of Effector Recruitment and Gdi Binding. Febs Lett. V. 585 3520 2011.
ISSN: ISSN 0014-5793
PubMed: 22024479
DOI: 10.1016/J.FEBSLET.2011.10.013