Magnesium in PDB 1z0k: Structure of Gtp-Bound RAB4Q67L Gtpase in Complex with the Central Rab Binding Domain of Rabenosyn-5

The structure of Structure of Gtp-Bound RAB4Q67L Gtpase in Complex with the Central Rab Binding Domain of Rabenosyn-5, PDB code: 1z0k 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 / 1.92
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	81.440, 81.440, 137.639, 90.00, 90.00, 120.00
R / Rfree (%)	22.4 / 25.9

The binding sites of Magnesium atom in the Structure of Gtp-Bound RAB4Q67L Gtpase in Complex with the Central Rab Binding Domain of Rabenosyn-5 (pdb code 1z0k). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Structure of Gtp-Bound RAB4Q67L Gtpase in Complex with the Central Rab Binding Domain of Rabenosyn-5, PDB code: 1z0k:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Structure of Gtp-Bound RAB4Q67L Gtpase in Complex with the Central Rab Binding Domain of Rabenosyn-5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Gtp-Bound RAB4Q67L Gtpase in Complex with the Central Rab Binding Domain of Rabenosyn-5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1201 b:44.5 occ:1.00 O2B A:GTP1200 1.8 25.1 1.0 O A:HOH1207 1.9 28.3 1.0 O2G A:GTP1200 2.1 27.0 1.0 OG A:SER22 2.2 25.5 1.0 OG1 A:THR40 2.3 47.6 1.0 O A:HOH1212 2.4 31.1 1.0 CB A:THR40 3.0 47.4 1.0 PB A:GTP1200 3.0 25.0 1.0 PG A:GTP1200 3.0 28.0 1.0 O3B A:GTP1200 3.3 26.2 1.0 CB A:SER22 3.4 22.8 1.0 O3G A:GTP1200 3.5 28.6 1.0 N A:THR40 3.8 47.9 1.0 N A:SER22 3.8 22.3 1.0 OD2 A:ASP63 3.9 30.0 1.0 CA A:THR40 3.9 47.4 1.0 O1B A:GTP1200 4.0 22.8 1.0 CA A:SER22 4.1 22.9 1.0 O2A A:GTP1200 4.1 23.3 1.0 O3A A:GTP1200 4.1 23.2 1.0 OD1 A:ASP63 4.2 29.0 1.0 CG2 A:THR40 4.2 47.3 1.0 O1G A:GTP1200 4.4 26.0 1.0 O A:THR64 4.4 29.1 1.0 CG A:ASP63 4.4 28.9 1.0 PA A:GTP1200 4.5 24.6 1.0 O1A A:GTP1200 4.5 23.9 1.0 CB A:LYS21 4.6 21.8 1.0 C A:LYS21 4.8 22.2 1.0 OE1 A:GLU44 4.8 38.2 1.0 NZ A:LYS21 4.8 24.9 1.0 C A:HIS39 4.9 48.5 1.0 O A:ASN38 4.9 49.6 1.0 CE A:LYS21 5.0 22.8 1.0

Magnesium binding site 2 out of 2 in the Structure of Gtp-Bound RAB4Q67L Gtpase in Complex with the Central Rab Binding Domain of Rabenosyn-5


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Gtp-Bound RAB4Q67L Gtpase in Complex with the Central Rab Binding Domain of Rabenosyn-5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg2201 b:35.2 occ:1.00 O2B C:GTP2200 2.0 30.2 1.0 O C:HOH2208 2.0 30.1 1.0 OG C:SER22 2.1 26.5 1.0 O C:HOH2222 2.1 30.1 1.0 O2G C:GTP2200 2.2 32.2 1.0 OG1 C:THR40 2.3 35.1 1.0 PB C:GTP2200 3.1 28.4 1.0 PG C:GTP2200 3.2 29.3 1.0 CB C:SER22 3.2 25.6 1.0 O3B C:GTP2200 3.3 29.2 1.0 CB C:THR40 3.4 35.5 1.0 O3G C:GTP2200 3.8 30.6 1.0 N C:SER22 3.8 25.4 1.0 N C:THR40 3.8 36.7 1.0 CA C:SER22 4.1 25.6 1.0 OD2 C:ASP63 4.1 25.3 1.0 OD1 C:ASP63 4.1 24.5 1.0 O2A C:GTP2200 4.1 30.4 1.0 CA C:THR40 4.2 35.6 1.0 O3A C:GTP2200 4.2 29.0 1.0 O1B C:GTP2200 4.2 27.1 1.0 O1G C:GTP2200 4.5 32.0 1.0 PA C:GTP2200 4.5 30.0 1.0 CG C:ASP63 4.5 25.4 1.0 O1A C:GTP2200 4.5 29.2 1.0 CG2 C:THR40 4.5 35.3 1.0 O C:ASN38 4.5 39.8 1.0 O C:THR64 4.7 26.8 1.0 CB C:LYS21 4.8 25.2 1.0 C C:HIS39 4.8 37.8 1.0 C C:LYS21 4.8 25.2 1.0 CA C:HIS39 5.0 38.6 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