Magnesium in PDB 6di7: VPS1 Gtpase-Bse Fusion Complexed with Gdp

The structure of VPS1 Gtpase-Bse Fusion Complexed with Gdp, PDB code: 6di7 was solved by N.V.Varlakhanova, T.M.Brady, M.G.J.Ford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.90 / 2.30
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	84.979, 84.979, 271.502, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 19.9

The binding sites of Magnesium atom in the VPS1 Gtpase-Bse Fusion Complexed with Gdp (pdb code 6di7). 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 VPS1 Gtpase-Bse Fusion Complexed with Gdp, PDB code: 6di7:

Magnesium binding site 1 out of 1 in the VPS1 Gtpase-Bse Fusion Complexed with Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of VPS1 Gtpase-Bse Fusion Complexed with Gdp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:55.9 occ:1.00 OG1 A:THR77 2.4 39.1 1.0 OG A:SER57 2.5 44.0 1.0 O3B A:GDP1001 2.6 29.7 1.0 O A:HOH1131 2.8 46.6 1.0 HB A:THR77 3.2 49.1 1.0 OD2 A:ASP170 3.3 49.3 1.0 CB A:THR77 3.4 40.9 1.0 H A:SER57 3.4 41.4 1.0 HE2 A:LYS56 3.4 48.7 1.0 HB2 A:LYS56 3.4 41.7 1.0 OD1 A:ASP170 3.6 48.2 1.0 O A:HOH1113 3.6 33.6 1.0 H A:THR77 3.6 50.2 1.0 PB A:GDP1001 3.7 33.5 1.0 CB A:SER57 3.7 37.2 1.0 CG A:ASP170 3.8 48.9 1.0 O1B A:GDP1001 3.8 33.4 1.0 N A:SER57 3.9 34.4 1.0 HB2 A:SER57 3.9 44.7 1.0 HZ1 A:LYS56 3.9 50.1 1.0 HZ3 A:LYS56 4.0 50.1 1.0 HG23 A:THR77 4.0 50.1 1.0 CE A:LYS56 4.2 40.5 1.0 NZ A:LYS56 4.2 41.7 1.0 CA A:SER57 4.3 34.3 1.0 CG2 A:THR77 4.3 41.7 1.0 N A:THR77 4.3 41.8 1.0 HA A:SER57 4.3 41.2 1.0 O2B A:GDP1001 4.4 31.9 1.0 CB A:LYS56 4.4 34.7 1.0 HB3 A:SER57 4.4 44.7 1.0 CA A:THR77 4.5 39.9 1.0 O A:LEU171 4.5 40.3 1.0 HB3 A:LYS56 4.5 41.7 1.0 HE3 A:LYS56 4.7 48.7 1.0 HG22 A:THR77 4.8 50.1 1.0 C A:LYS56 4.8 35.8 1.0 O A:HOH1163 4.9 33.7 1.0 HA A:THR77 4.9 47.9 1.0 HA A:PRO172 5.0 43.0 1.0

N.V.Varlakhanova, F.J.D.Alvarez, T.M.Brady, B.A.Tornabene, C.J.Hosford, J.S.Chappie, P.Zhang, M.G.J.Ford. Structures of the Fungal Dynamin-Related Protein VPS1 Reveal A Unique, Open Helical Architecture. J. Cell Biol. V. 217 3608 2018.
ISSN: ESSN 1540-8140
PubMed: 30087125
DOI: 10.1083/JCB.201712021