Magnesium in PDB 5lef: RAB6A:KIF20A Complex

The structure of RAB6A:KIF20A Complex, PDB code: 5lef was solved by G.Bressanelli, O.Pylypenko, A.Houdusse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.79 / 2.09
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	125.250, 128.190, 36.030, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 20.4

The binding sites of Magnesium atom in the RAB6A:KIF20A Complex (pdb code 5lef). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the RAB6A:KIF20A Complex, PDB code: 5lef:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the RAB6A:KIF20A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of RAB6A:KIF20A Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:30.9 occ:1.00 O1G A:GTP201 2.0 31.0 1.0 O A:HOH306 2.0 27.0 1.0 OG1 A:THR45 2.0 36.1 1.0 OG1 A:THR27 2.0 29.1 1.0 O1B A:GTP201 2.1 28.4 1.0 O A:HOH328 2.1 32.8 1.0 HB A:THR45 3.1 44.2 1.0 CB A:THR45 3.1 36.8 1.0 H A:THR45 3.2 46.9 1.0 CB A:THR27 3.2 31.2 1.0 HB A:THR27 3.2 37.4 1.0 PG A:GTP201 3.2 33.1 1.0 PB A:GTP201 3.2 30.2 1.0 H A:THR27 3.3 36.8 1.0 O3B A:GTP201 3.5 33.8 1.0 N A:THR45 3.8 39.1 1.0 HB2 A:LYS26 3.8 36.5 1.0 OD2 A:ASP68 3.8 39.0 1.0 HE2 A:LYS26 3.8 38.2 1.0 N A:THR27 3.9 30.7 1.0 CA A:THR45 4.0 38.4 1.0 OD1 A:ASP68 4.0 39.0 1.0 CA A:THR27 4.1 29.8 1.0 O3G A:GTP201 4.1 31.7 1.0 HG21 A:THR27 4.1 40.5 1.0 HG21 A:THR45 4.1 43.1 1.0 O A:HOH317 4.2 48.0 1.0 O2A A:GTP201 4.2 31.6 1.0 O2B A:GTP201 4.2 29.6 1.0 CG2 A:THR45 4.2 35.9 1.0 CG2 A:THR27 4.3 33.7 1.0 O2G A:GTP201 4.3 34.2 1.0 CG A:ASP68 4.3 38.5 1.0 HA A:THR45 4.3 46.1 1.0 HA A:THR27 4.4 35.8 1.0 O3A A:GTP201 4.4 33.1 1.0 O A:THR69 4.4 33.2 1.0 HA A:ALA70 4.5 45.6 1.0 HG23 A:THR27 4.6 40.5 1.0 HG23 A:THR45 4.6 43.1 1.0 HA A:ALA44 4.6 46.6 1.0 HZ1 A:LYS26 4.6 38.3 1.0 PA A:GTP201 4.7 32.2 1.0 O A:GLN43 4.7 42.0 1.0 CE A:LYS26 4.7 31.9 1.0 CB A:LYS26 4.8 30.4 1.0 O1A A:GTP201 4.8 31.1 1.0 O A:HOH393 4.8 54.6 1.0 HZ3 A:LYS26 4.8 38.3 1.0 C A:ALA44 4.8 39.1 1.0 HE1 A:TYR42 4.9 44.5 1.0 NZ A:LYS26 4.9 31.9 1.0 C A:LYS26 5.0 29.9 1.0 HG22 A:THR45 5.0 43.1 1.0

Magnesium binding site 2 out of 2 in the RAB6A:KIF20A Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of RAB6A:KIF20A Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:31.8 occ:1.00 O B:HOH314 2.0 34.0 1.0 OG1 B:THR45 2.0 45.7 1.0 O3G B:GTP201 2.0 34.4 1.0 OG1 B:THR27 2.1 37.2 1.0 O B:HOH319 2.1 31.3 1.0 O2B B:GTP201 2.2 31.6 1.0 HB B:THR45 3.0 54.5 1.0 CB B:THR45 3.1 45.4 1.0 H B:THR45 3.1 55.2 1.0 HB B:THR27 3.2 44.5 1.0 CB B:THR27 3.2 37.1 1.0 PG B:GTP201 3.3 35.6 1.0 H B:THR27 3.3 42.0 1.0 PB B:GTP201 3.3 33.6 1.0 O3B B:GTP201 3.5 42.4 1.0 N B:THR45 3.7 46.0 1.0 HB2 B:LYS26 3.9 44.4 1.0 CA B:THR45 3.9 47.5 1.0 N B:THR27 3.9 35.0 1.0 OD2 B:ASP68 4.0 45.9 1.0 HE2 B:LYS26 4.0 49.5 1.0 O1A B:GTP201 4.1 33.7 1.0 CA B:THR27 4.1 36.8 1.0 O B:HOH317 4.1 52.3 1.0 HG21 B:THR27 4.1 47.6 1.0 O1G B:GTP201 4.2 37.4 1.0 OD1 B:ASP68 4.2 48.2 1.0 HG21 B:THR45 4.2 56.8 1.0 HA B:THR45 4.2 57.0 1.0 CG2 B:THR45 4.2 47.3 1.0 CG2 B:THR27 4.2 39.7 1.0 O1B B:GTP201 4.3 35.4 1.0 O2G B:GTP201 4.3 36.3 1.0 HA B:THR27 4.4 44.2 1.0 O3A B:GTP201 4.5 42.0 1.0 CG B:ASP68 4.5 47.7 1.0 HA B:ALA44 4.5 59.5 1.0 O B:THR69 4.5 47.8 1.0 HG23 B:THR27 4.6 47.6 1.0 O B:GLN43 4.6 51.7 1.0 HG23 B:THR45 4.6 56.8 1.0 PA B:GTP201 4.6 33.3 1.0 O2A B:GTP201 4.7 30.3 1.0 HA B:ALA70 4.7 63.7 1.0 H31 B:IPA205 4.7 64.6 1.0 HZ1 B:LYS26 4.7 49.6 1.0 C B:ALA44 4.8 48.9 1.0 HE1 B:TYR42 4.8 62.2 1.0 CB B:LYS26 4.8 37.0 1.0 HZ3 B:LYS26 4.8 49.6 1.0 CE B:LYS26 4.9 41.3 1.0 O B:HOH353 5.0 69.5 1.0 HG22 B:THR45 5.0 56.8 1.0

S.Miserey-Lenkei, H.Bousquet, O.Pylypenko, S.Bardin, A.Dimitrov, G.Bressanelli, R.Bonifay, V.Fraisier, C.Guillou, C.Bougeret, A.Houdusse, A.Echard, B.Goud. Coupling Fission and Exit of RAB6 Vesicles at Golgi Hotspots Through Kinesin-Myosin Interactions. Nat Commun V. 8 1254 2017.
ISSN: ESSN 2041-1723
PubMed: 29093437
DOI: 10.1038/S41467-017-01266-0