Magnesium in PDB 4z8y: Crystal Structure of Rab Gtpase SEC4P Mutant - S29V

The structure of Crystal Structure of Rab Gtpase SEC4P Mutant - S29V, PDB code: 4z8y was solved by F.C.Rinadi, R.N.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.30 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	31.720, 75.450, 66.230, 90.00, 91.58, 90.00
R / Rfree (%)	23.6 / 29.8

The structure of Crystal Structure of Rab Gtpase SEC4P Mutant - S29V also contains other interesting chemical elements:

Zinc

(Zn)

3 atoms

The binding sites of Magnesium atom in the Crystal Structure of Rab Gtpase SEC4P Mutant - S29V (pdb code 4z8y). 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 Rab Gtpase SEC4P Mutant - S29V, PDB code: 4z8y:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Rab Gtpase SEC4P Mutant - S29V


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 Rab Gtpase SEC4P Mutant - S29V within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:2.8 occ:1.00 O A:HOH314 1.8 20.1 1.0 O A:HOH380 1.8 15.0 1.0 OG A:SER34 1.9 15.8 1.0 O A:HOH318 2.0 19.3 1.0 O3B A:GDP201 2.0 14.4 1.0 O A:HOH422 2.3 30.4 1.0 PB A:GDP201 3.2 14.2 1.0 CB A:SER34 3.3 13.8 1.0 O2B A:GDP201 3.5 14.8 1.0 OD2 A:ASP75 3.8 22.3 1.0 N A:SER34 3.9 13.7 1.0 O2A A:GDP201 4.1 16.4 1.0 CA A:SER34 4.2 14.2 1.0 O1B A:GDP201 4.2 14.3 1.0 O3A A:GDP201 4.3 14.5 1.0 OD1 A:ASP75 4.3 20.7 1.0 O A:THR76 4.3 30.0 1.0 O A:HOH333 4.5 21.4 1.0 O A:HOH435 4.5 30.5 1.0 PA A:GDP201 4.5 17.6 1.0 CG A:ASP75 4.5 21.5 1.0 O1A A:GDP201 4.6 14.9 1.0 CA A:ALA77 4.8 36.3 1.0 O A:HOH374 4.8 15.6 1.0 CB A:LYS33 4.9 12.7 1.0 NZ A:LYS33 4.9 11.6 1.0 C A:THR76 5.0 32.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Rab Gtpase SEC4P Mutant - S29V


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 Rab Gtpase SEC4P Mutant - S29V within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:2.8 occ:1.00 O B:HOH323 1.8 13.8 1.0 O B:HOH382 1.9 21.7 1.0 O2B B:GDP201 2.0 13.8 1.0 O B:HOH356 2.0 13.9 1.0 OG B:SER34 2.0 14.7 1.0 O B:HOH391 2.1 22.4 1.0 CB B:SER34 3.1 13.3 1.0 PB B:GDP201 3.2 13.5 1.0 O3B B:GDP201 3.6 14.6 1.0 N B:SER34 3.9 13.0 1.0 O1A B:GDP201 4.0 17.0 1.0 OD2 B:ASP75 4.0 17.7 1.0 CA B:SER34 4.1 13.1 1.0 OD1 B:ASP75 4.1 17.1 1.0 O3A B:GDP201 4.2 15.7 1.0 O1B B:GDP201 4.3 13.8 1.0 PA B:GDP201 4.4 16.8 1.0 O B:HOH308 4.4 17.7 1.0 CG B:ASP75 4.5 17.1 1.0 O B:HOH310 4.5 22.0 1.0 O B:HOH329 4.7 25.8 1.0 O2A B:GDP201 4.7 16.1 1.0 CB B:THR52 4.9 26.1 1.0

F.C.Rinaldi, M.Packer, R.Collins. New Insights Into the Molecular Mechanism of the Rab Gtpase SEC4P Activation. Bmc Struct.Biol. V. 15 14 2015.
ISSN: ESSN 1472-6807
PubMed: 26263895
DOI: 10.1186/S12900-015-0041-5