Magnesium in PDB 6djq: VPS1 Gtpase-Bse Fusion Complexed with Gdp.ALF4-

The structure of VPS1 Gtpase-Bse Fusion Complexed with Gdp.ALF4-, PDB code: 6djq was solved by N.V.Varlakhanova, T.M.Brady, B.A.Tornabene, C.J.Hosford, J.S.Chappie, M.G.J.Ford, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.60 / 3.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	69.060, 121.220, 104.560, 90.00, 90.60, 90.00
R / Rfree (%)	22.2 / 27.9

The structure of VPS1 Gtpase-Bse Fusion Complexed with Gdp.ALF4- also contains other interesting chemical elements:

Fluorine	(F)	16 atoms
Aluminium	(Al)	4 atoms
Sodium	(Na)	4 atoms

The binding sites of Magnesium atom in the VPS1 Gtpase-Bse Fusion Complexed with Gdp.ALF4- (pdb code 6djq). 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 Gdp.ALF4-, PDB code: 6djq:
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 Gdp.ALF4-


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.ALF4- within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg1003 b:27.6 occ:1.00 O1B A:GDP1001 1.9 23.6 1.0 F4 A:ALF1002 1.9 26.7 1.0 O A:HOH1105 2.0 33.8 1.0 OG A:SER57 2.1 32.5 1.0 OG1 A:THR77 2.1 25.1 1.0 O A:HOH1101 2.4 2.1 1.0 HB2 A:SER57 3.1 38.0 1.0 PB A:GDP1001 3.1 21.7 1.0 CB A:SER57 3.1 31.8 1.0 HB A:THR77 3.1 27.0 1.0 CB A:THR77 3.2 22.6 1.0 H A:SER57 3.2 42.9 1.0 H A:THR77 3.4 25.4 1.0 O3B A:GDP1001 3.5 24.9 1.0 AL A:ALF1002 3.5 27.5 1.0 OD2 A:ASP170 3.6 32.0 1.0 F1 A:ALF1002 3.7 33.2 1.0 HB3 A:SER57 3.8 38.0 1.0 N A:SER57 3.9 36.0 1.0 HG21 A:THR77 4.0 26.0 1.0 N A:THR77 4.1 21.4 1.0 HB A:VAL76 4.1 26.5 1.0 CA A:SER57 4.1 34.6 1.0 O2B A:GDP1001 4.1 20.6 1.0 CG2 A:THR77 4.2 21.9 1.0 OD1 A:ASP170 4.2 28.6 1.0 O2A A:GDP1001 4.2 19.1 1.0 HB2 A:LYS56 4.2 48.9 1.0 O A:PRO70 4.2 35.7 1.0 F2 A:ALF1002 4.2 29.2 1.0 O3A A:GDP1001 4.2 21.0 1.0 CA A:THR77 4.3 21.4 1.0 CG A:ASP170 4.3 33.7 1.0 HA A:SER57 4.4 41.4 1.0 HE2 A:LYS56 4.5 42.4 1.0 HG23 A:THR77 4.5 26.0 1.0 O A:LEU171 4.6 15.1 1.0 HA A:ARG71 4.6 58.3 1.0 O A:HOH1106 4.6 31.3 1.0 PA A:GDP1001 4.6 23.4 1.0 HA A:THR77 4.7 25.5 1.0 H A:LYS56 4.8 51.2 1.0 HG2 A:ARG71 4.9 62.1 1.0 O1A A:GDP1001 4.9 22.1 1.0 HA A:PRO172 4.9 39.2 1.0 HG22 A:THR77 5.0 26.0 1.0

Magnesium binding site 2 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gdp.ALF4-


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 Gdp.ALF4- within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg1003 b:27.8 occ:1.00 O3B B:GDP1001 1.8 37.7 1.0 F4 B:ALF1002 1.9 34.5 1.0 OG B:SER57 2.1 37.2 1.0 O B:HOH1102 2.2 18.0 1.0 OG1 B:THR77 2.2 32.2 1.0 HB B:THR77 3.0 40.0 1.0 PB B:GDP1001 3.1 35.2 1.0 HB2 B:SER57 3.2 42.3 1.0 H B:SER57 3.2 41.7 1.0 CB B:THR77 3.2 33.5 1.0 CB B:SER57 3.2 35.5 1.0 AL B:ALF1002 3.5 25.7 1.0 O1B B:GDP1001 3.5 26.8 1.0 H B:THR77 3.5 55.7 1.0 F1 B:ALF1002 3.7 37.0 1.0 HG21 B:THR77 3.9 37.9 1.0 N B:SER57 3.9 34.9 1.0 HB3 B:SER57 3.9 42.3 1.0 OD2 B:ASP170 3.9 44.0 1.0 O2B B:GDP1001 4.1 29.6 1.0 HB2 B:LYS56 4.1 58.2 1.0 CG2 B:THR77 4.1 31.8 1.0 OD1 B:ASP170 4.1 43.4 1.0 CA B:SER57 4.1 34.6 1.0 N B:THR77 4.2 46.6 1.0 F2 B:ALF1002 4.2 27.6 1.0 O1A B:GDP1001 4.3 39.2 1.0 O3A B:GDP1001 4.3 38.2 1.0 CA B:THR77 4.3 43.5 1.0 HB B:VAL76 4.4 72.9 1.0 CG B:ASP170 4.4 43.8 1.0 O B:LEU171 4.4 51.0 1.0 HA B:SER57 4.5 41.3 1.0 HE2 B:LYS56 4.5 59.6 1.0 O B:PRO70 4.5 46.6 1.0 HG23 B:THR77 4.6 37.9 1.0 O B:HOH1104 4.6 28.6 1.0 H B:LYS56 4.7 52.8 1.0 PA B:GDP1001 4.7 39.2 1.0 HZ3 B:LYS56 4.8 66.2 1.0 HA B:THR77 4.8 52.0 1.0 HG22 B:THR77 4.9 37.9 1.0 HA B:ARG71 4.9 54.1 1.0 HZ1 B:LYS56 5.0 66.2 1.0 O2A B:GDP1001 5.0 33.6 1.0 C B:LYS56 5.0 49.8 1.0

Magnesium binding site 3 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gdp.ALF4-


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 Gdp.ALF4- within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg1003 b:48.5 occ:1.00 F4 C:ALF1002 1.9 49.2 1.0 O1B C:GDP1001 1.9 50.4 1.0 O C:HOH1101 2.2 14.8 1.0 OG1 C:THR77 2.2 35.7 1.0 OG C:SER57 2.4 57.7 1.0 HG C:SER57 2.9 69.1 1.0 HB C:THR77 3.1 50.0 1.0 PB C:GDP1001 3.1 45.5 1.0 CB C:THR77 3.2 41.9 1.0 H C:SER57 3.3 61.3 1.0 HB2 C:SER57 3.3 67.7 1.0 O3B C:GDP1001 3.4 48.0 1.0 H C:THR77 3.4 65.4 1.0 CB C:SER57 3.4 56.6 1.0 AL C:ALF1002 3.5 50.9 1.0 F1 C:ALF1002 3.7 58.2 1.0 O2A C:GDP1001 3.9 41.2 1.0 N C:SER57 4.0 51.2 1.0 HG21 C:THR77 4.0 44.5 1.0 N C:THR77 4.0 54.6 1.0 HB C:VAL76 4.0 40.7 1.0 HB2 C:LYS56 4.1 74.7 1.0 OD2 C:ASP170 4.1 53.6 1.0 HB3 C:SER57 4.1 67.7 1.0 O3A C:GDP1001 4.1 43.1 1.0 O2B C:GDP1001 4.2 45.3 1.0 CG2 C:THR77 4.2 37.2 1.0 F2 C:ALF1002 4.2 48.6 1.0 CA C:THR77 4.2 50.7 1.0 CA C:SER57 4.3 52.9 1.0 OD1 C:ASP170 4.3 53.1 1.0 HE2 C:LYS56 4.3 71.9 1.0 O C:HOH1102 4.4 49.1 1.0 O C:PRO70 4.5 48.7 1.0 PA C:GDP1001 4.5 44.2 1.0 O C:LEU171 4.5 39.0 1.0 CG C:ASP170 4.6 54.5 1.0 HA C:SER57 4.6 63.3 1.0 HZ2 C:LYS56 4.6 73.6 1.0 HG23 C:THR77 4.7 44.5 1.0 H C:LYS56 4.7 75.8 1.0 HZ1 C:LYS56 4.7 73.6 1.0 HA C:THR77 4.7 60.6 1.0 HA C:PRO172 4.8 56.7 1.0 HA C:ARG71 4.8 62.1 1.0 O1A C:GDP1001 4.8 43.0 1.0 HG22 C:THR77 4.9 44.5 1.0 CB C:LYS56 5.0 62.4 1.0 CB C:VAL76 5.0 34.1 1.0

Magnesium binding site 4 out of 4 in the VPS1 Gtpase-Bse Fusion Complexed with Gdp.ALF4-


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 Gdp.ALF4- within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg1003 b:24.3 occ:1.00 F4 D:ALF1002 1.9 25.1 1.0 O3B D:GDP1001 2.0 27.3 1.0 O D:HOH1104 2.1 16.1 1.0 OG D:SER57 2.1 36.6 1.0 OG1 D:THR77 2.1 39.1 1.0 O D:HOH1103 2.2 23.0 1.0 H D:SER57 3.1 53.5 1.0 HB D:THR77 3.1 44.4 1.0 CB D:THR77 3.2 37.1 1.0 HB2 D:SER57 3.2 43.4 1.0 CB D:SER57 3.2 36.4 1.0 PB D:GDP1001 3.2 23.9 1.0 AL D:ALF1002 3.5 19.8 1.0 O1B D:GDP1001 3.5 19.9 1.0 H D:THR77 3.5 50.1 1.0 OD2 D:ASP170 3.6 42.4 1.0 F1 D:ALF1002 3.7 18.2 1.0 N D:SER57 3.7 44.7 1.0 HG21 D:THR77 3.9 42.0 1.0 HB3 D:SER57 3.9 43.4 1.0 HB2 D:LYS56 3.9 68.5 1.0 OD1 D:ASP170 4.0 42.7 1.0 CA D:SER57 4.0 37.8 1.0 CG2 D:THR77 4.1 35.2 1.0 N D:THR77 4.2 41.9 1.0 O2B D:GDP1001 4.2 22.8 1.0 F2 D:ALF1002 4.2 25.6 1.0 O1A D:GDP1001 4.2 24.4 1.0 CG D:ASP170 4.2 42.8 1.0 HB D:VAL76 4.3 65.5 1.0 CA D:THR77 4.3 36.2 1.0 O D:PRO70 4.3 29.5 1.0 HA D:SER57 4.3 45.2 1.0 O3A D:GDP1001 4.3 25.7 1.0 HE2 D:LYS56 4.4 52.1 1.0 HG23 D:THR77 4.5 42.0 1.0 O D:LEU171 4.5 26.8 1.0 O D:HOH1105 4.7 17.2 1.0 H D:LYS56 4.7 86.0 1.0 PA D:GDP1001 4.7 28.4 1.0 HA D:THR77 4.7 43.2 1.0 HA D:ARG71 4.8 41.0 1.0 HZ1 D:LYS56 4.8 54.3 1.0 CB D:LYS56 4.9 57.3 1.0 C D:LYS56 4.9 58.6 1.0 HG22 D:THR77 4.9 42.0 1.0 O2A D:GDP1001 4.9 27.2 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