Magnesium in PDB 6def: VPS1 Gtpase-Bse Fusion Complexed with Gmppcp

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

Resolution Low / High (Å)	40.79 / 2.26
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	82.659, 118.740, 84.140, 90.00, 99.30, 90.00
R / Rfree (%)	19.3 / 22.5

The binding sites of Magnesium atom in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp (pdb code 6def). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp, PDB code: 6def:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp


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 Gmppcp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1002 b:28.3 occ:1.00 HOB2 A:GCP1001 1.0 33.0 1.0 O2B A:GCP1001 2.0 27.5 1.0 OG A:SER57 2.1 38.0 1.0 OG1 A:THR77 2.1 45.7 1.0 O A:HOH1111 2.1 27.7 1.0 O1G A:GCP1001 2.1 36.6 1.0 O A:HOH1130 2.2 28.8 1.0 HB A:THR77 2.9 49.7 1.0 CB A:THR77 3.0 41.4 1.0 H A:SER57 3.1 36.6 1.0 HB2 A:SER57 3.2 40.3 1.0 CB A:SER57 3.2 33.6 1.0 PG A:GCP1001 3.3 35.3 1.0 PB A:GCP1001 3.3 29.6 1.0 H A:THR77 3.3 45.1 1.0 HOA2 A:GCP1001 3.4 38.8 1.0 C3B A:GCP1001 3.5 30.9 1.0 H3B2 A:GCP1001 3.6 37.0 1.0 N A:SER57 3.7 30.5 1.0 HG21 A:THR77 3.8 51.9 1.0 HB2 A:LYS56 3.9 41.9 1.0 HB3 A:SER57 3.9 40.3 1.0 HB A:VAL76 4.0 45.1 1.0 OD2 A:ASP170 4.0 34.6 1.0 N A:THR77 4.0 37.6 1.0 CA A:SER57 4.0 29.9 1.0 CG2 A:THR77 4.0 43.2 1.0 OD1 A:ASP170 4.1 33.8 1.0 CA A:THR77 4.1 37.8 1.0 O1B A:GCP1001 4.1 33.9 1.0 HE2 A:LYS56 4.2 38.7 1.0 O A:HOH1113 4.2 31.5 1.0 O2G A:GCP1001 4.2 34.8 1.0 O2A A:GCP1001 4.3 32.3 1.0 HA A:SER57 4.3 35.9 1.0 O3A A:GCP1001 4.4 30.6 1.0 HZ2 A:LYS56 4.4 40.0 1.0 O3G A:GCP1001 4.4 38.5 1.0 CG A:ASP170 4.5 33.6 1.0 O A:LEU171 4.5 27.9 1.0 HG23 A:THR77 4.5 51.9 1.0 HOG2 A:GCP1001 4.6 41.7 1.0 H3B1 A:GCP1001 4.6 37.0 1.0 HG12 A:VAL76 4.6 45.7 1.0 HA A:THR77 4.6 45.4 1.0 O A:PRO70 4.6 33.9 1.0 HZ3 A:LYS56 4.7 40.0 1.0 HG22 A:THR77 4.7 51.9 1.0 H A:LYS56 4.8 38.0 1.0 CB A:LYS56 4.8 34.9 1.0 PA A:GCP1001 4.8 31.4 1.0 C A:LYS56 4.8 32.8 1.0 NZ A:LYS56 4.9 33.3 1.0 CB A:VAL76 4.9 37.6 1.0 CE A:LYS56 5.0 32.2 1.0 HA A:PRO172 5.0 36.6 1.0

Magnesium binding site 2 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of VPS1 Gtpase-Bse Fusion Complexed with Gmppcp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1002 b:21.1 occ:1.00 HOB2 B:GCP1001 1.1 31.9 1.0 O1G B:GCP1001 2.0 25.9 1.0 OG1 B:THR77 2.0 36.8 1.0 OG B:SER57 2.0 35.7 1.0 O B:HOH1112 2.1 20.7 1.0 O2B B:GCP1001 2.1 26.6 1.0 O B:HOH1167 2.2 21.6 1.0 HB B:THR77 2.9 39.0 1.0 CB B:THR77 3.0 32.5 1.0 H B:SER57 3.1 37.0 1.0 CB B:SER57 3.2 30.6 1.0 HB2 B:SER57 3.2 36.7 1.0 PG B:GCP1001 3.2 29.1 1.0 H B:THR77 3.4 39.1 1.0 PB B:GCP1001 3.4 27.5 1.0 C3B B:GCP1001 3.6 29.8 1.0 H3B2 B:GCP1001 3.7 35.7 1.0 N B:SER57 3.7 30.9 1.0 HG21 B:THR77 3.8 41.5 1.0 OD2 B:ASP170 3.8 31.1 1.0 HB2 B:LYS56 3.8 32.6 1.0 HB3 B:SER57 3.9 36.7 1.0 O B:HOH1105 3.9 31.5 1.0 OD1 B:ASP170 3.9 31.4 1.0 HB B:VAL76 4.0 42.9 1.0 CA B:SER57 4.0 30.4 1.0 CG2 B:THR77 4.0 34.6 1.0 N B:THR77 4.0 32.6 1.0 HE2 B:LYS56 4.1 31.9 1.0 CA B:THR77 4.1 32.6 1.0 O2G B:GCP1001 4.2 24.6 1.0 O1B B:GCP1001 4.2 25.1 1.0 HA B:SER57 4.2 36.4 1.0 CG B:ASP170 4.3 30.9 1.0 O2A B:GCP1001 4.3 34.9 1.0 O3G B:GCP1001 4.3 37.6 1.0 O B:LEU171 4.4 34.0 1.0 HG23 B:THR77 4.5 41.5 1.0 O3A B:GCP1001 4.5 29.5 1.0 HZ3 B:LYS56 4.6 34.9 1.0 HA B:THR77 4.6 39.1 1.0 HOG2 B:GCP1001 4.6 29.5 1.0 O B:PRO70 4.6 28.0 1.0 HG12 B:VAL76 4.6 42.3 1.0 H3B1 B:GCP1001 4.7 35.7 1.0 HZ1 B:LYS56 4.7 34.9 1.0 HOA2 B:GCP1001 4.7 41.9 1.0 HG22 B:THR77 4.7 41.5 1.0 CB B:LYS56 4.7 27.1 1.0 H B:LYS56 4.8 35.2 1.0 C B:LYS56 4.8 29.9 1.0 CB B:VAL76 4.9 35.8 1.0 PA B:GCP1001 4.9 30.0 1.0 CE B:LYS56 4.9 26.6 1.0 NZ B:LYS56 4.9 29.1 1.0

Magnesium binding site 3 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of VPS1 Gtpase-Bse Fusion Complexed with Gmppcp within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1002 b:25.5 occ:1.00 HOB2 C:GCP1001 1.1 41.2 1.0 O1G C:GCP1001 2.0 31.4 1.0 O2B C:GCP1001 2.0 34.3 1.0 OG1 C:THR77 2.1 45.0 1.0 O C:HOH1135 2.1 28.2 1.0 OG C:SER57 2.1 42.2 1.0 O C:HOH1126 2.2 29.7 1.0 HB C:THR77 2.9 47.3 1.0 CB C:THR77 3.0 39.4 1.0 PG C:GCP1001 3.2 31.0 1.0 H C:SER57 3.2 36.9 1.0 CB C:SER57 3.2 35.4 1.0 HB2 C:SER57 3.2 42.5 1.0 H C:THR77 3.3 44.2 1.0 PB C:GCP1001 3.3 33.0 1.0 C3B C:GCP1001 3.4 32.3 1.0 H3B2 C:GCP1001 3.5 38.8 1.0 HOA2 C:GCP1001 3.5 44.0 1.0 HB C:VAL76 3.8 50.3 1.0 N C:SER57 3.9 30.7 1.0 N C:THR77 3.9 36.9 1.0 HG21 C:THR77 3.9 46.9 1.0 HB3 C:SER57 3.9 42.5 1.0 OD2 C:ASP170 3.9 39.6 1.0 HB2 C:LYS56 4.0 44.8 1.0 CA C:THR77 4.1 36.9 1.0 CG2 C:THR77 4.1 39.1 1.0 CA C:SER57 4.1 30.6 1.0 O1B C:GCP1001 4.1 32.7 1.0 OD1 C:ASP170 4.2 39.3 1.0 O2G C:GCP1001 4.2 26.5 1.0 O C:HOH1152 4.2 35.2 1.0 O2A C:GCP1001 4.2 36.7 1.0 O3G C:GCP1001 4.2 34.4 1.0 HE2 C:LYS56 4.3 47.9 1.0 HA C:SER57 4.3 36.8 1.0 O3A C:GCP1001 4.4 32.8 1.0 HOG2 C:GCP1001 4.4 31.8 1.0 CG C:ASP170 4.5 38.9 1.0 HG12 C:VAL76 4.5 49.8 1.0 HZ3 C:LYS56 4.5 50.0 1.0 O C:LEU171 4.5 33.0 1.0 H3B1 C:GCP1001 4.5 38.8 1.0 HA C:THR77 4.5 44.3 1.0 HG23 C:THR77 4.6 46.9 1.0 O C:PRO70 4.6 32.6 1.0 HZ1 C:LYS56 4.7 50.0 1.0 CB C:VAL76 4.7 41.9 1.0 HG22 C:THR77 4.8 46.9 1.0 PA C:GCP1001 4.8 32.9 1.0 H C:LYS56 4.9 42.0 1.0 NZ C:LYS56 4.9 41.6 1.0 CB C:LYS56 4.9 37.3 1.0 HA C:PRO172 4.9 45.5 1.0 CG1 C:VAL76 5.0 41.5 1.0 C C:LYS56 5.0 35.1 1.0 HG11 C:VAL76 5.0 49.8 1.0

Magnesium binding site 4 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gmppcp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of VPS1 Gtpase-Bse Fusion Complexed with Gmppcp within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1002 b:22.4 occ:1.00 HOB2 D:GCP1001 1.1 32.6 1.0 O1G D:GCP1001 1.9 30.3 1.0 O D:HOH1117 2.0 26.3 1.0 OG1 D:THR77 2.1 33.0 1.0 OG D:SER57 2.1 30.1 1.0 O2B D:GCP1001 2.1 27.1 1.0 O D:HOH1129 2.2 23.7 1.0 HB D:THR77 2.9 33.7 1.0 CB D:THR77 3.1 28.1 1.0 PG D:GCP1001 3.1 29.9 1.0 H D:SER57 3.2 30.9 1.0 CB D:SER57 3.2 24.4 1.0 HB2 D:SER57 3.2 29.3 1.0 H D:THR77 3.3 33.4 1.0 PB D:GCP1001 3.3 29.6 1.0 C3B D:GCP1001 3.5 30.4 1.0 H3B2 D:GCP1001 3.6 36.5 1.0 N D:SER57 3.8 25.8 1.0 HB D:VAL76 3.9 42.2 1.0 HG21 D:THR77 3.9 37.4 1.0 OD2 D:ASP170 3.9 32.2 1.0 HB3 D:SER57 3.9 29.3 1.0 HB2 D:LYS56 3.9 36.2 1.0 N D:THR77 4.0 27.9 1.0 CA D:SER57 4.0 23.1 1.0 OD1 D:ASP170 4.0 30.6 1.0 CG2 D:THR77 4.1 31.2 1.0 CA D:THR77 4.1 26.1 1.0 O D:HOH1146 4.1 32.9 1.0 O2G D:GCP1001 4.1 28.5 1.0 HE2 D:LYS56 4.1 39.3 1.0 O3G D:GCP1001 4.2 31.8 1.0 O1B D:GCP1001 4.2 32.3 1.0 HA D:SER57 4.3 27.7 1.0 O2A D:GCP1001 4.3 25.8 1.0 HZ3 D:LYS56 4.4 38.7 1.0 CG D:ASP170 4.4 32.6 1.0 HG12 D:VAL76 4.5 42.3 1.0 O3A D:GCP1001 4.5 29.1 1.0 O D:LEU171 4.5 30.4 1.0 HOA2 D:GCP1001 4.5 30.9 1.0 HOG2 D:GCP1001 4.5 34.2 1.0 HG23 D:THR77 4.5 37.4 1.0 O D:PRO70 4.5 28.9 1.0 HZ1 D:LYS56 4.6 38.7 1.0 H3B1 D:GCP1001 4.6 36.5 1.0 HA D:THR77 4.6 31.3 1.0 CB D:VAL76 4.8 35.2 1.0 NZ D:LYS56 4.8 32.2 1.0 HG22 D:THR77 4.8 37.4 1.0 CB D:LYS56 4.8 30.2 1.0 H D:LYS56 4.9 35.8 1.0 PA D:GCP1001 4.9 27.3 1.0 C D:LYS56 4.9 28.8 1.0 HA D:PRO172 4.9 34.6 1.0 CE D:LYS56 4.9 32.7 1.0 CG1 D:VAL76 5.0 35.3 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