Aluminium 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
Magnesium	(Mg)	4 atoms
Sodium	(Na)	4 atoms

The binding sites of Aluminium 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 Aluminium atom.
In total 4 binding sites of Aluminium where determined in the VPS1 Gtpase-Bse Fusion Complexed with Gdp.ALF4-, PDB code: 6djq:
Jump to Aluminium binding site number: 1; 2; 3; 4;

Aluminium 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 Aluminium with other atoms in the Al 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:Al1002 b:27.5 occ:1.00 AL A:ALF1002 0.0 27.5 1.0 F3 A:ALF1002 1.8 29.4 1.0 F4 A:ALF1002 1.8 26.7 1.0 F1 A:ALF1002 1.8 33.2 1.0 F2 A:ALF1002 1.8 29.2 1.0 O3B A:GDP1001 1.8 24.9 1.0 O A:HOH1106 2.0 31.3 1.0 PB A:GDP1001 3.0 21.7 1.0 H A:SER53 3.1 27.5 1.0 H A:THR77 3.2 25.4 1.0 H A:VAL76 3.3 27.5 1.0 NA A:NA1004 3.3 31.8 1.0 H A:GLY173 3.4 68.5 1.0 O1B A:GDP1001 3.4 23.6 1.0 MG A:MG1003 3.5 27.6 1.0 O2B A:GDP1001 3.5 20.6 1.0 HB A:THR77 3.5 27.0 1.0 HZ1 A:LYS56 3.6 42.2 1.0 O A:HOH1101 3.9 2.1 1.0 HG3 A:GLN52 3.9 39.0 1.0 HA A:PRO172 3.9 39.2 1.0 HA A:ILE75 3.9 32.0 1.0 N A:THR77 4.0 21.4 1.0 O A:HOH1105 4.0 33.8 1.0 N A:SER53 4.0 23.1 1.0 HA A:SER53 4.0 24.8 1.0 N A:GLY173 4.1 57.2 1.0 N A:VAL76 4.1 23.1 1.0 HB A:VAL76 4.1 26.5 1.0 HA A:GLN52 4.2 43.2 1.0 OG1 A:THR77 4.2 25.1 1.0 CB A:THR77 4.2 22.6 1.0 HZ3 A:LYS56 4.2 42.2 1.0 O A:HOH1104 4.3 28.5 1.0 O3A A:GDP1001 4.3 21.0 1.0 HG13 A:ILE75 4.3 24.0 1.0 HA3 A:GLY173 4.3 73.2 1.0 NZ A:LYS56 4.3 35.3 1.0 O A:THR77 4.3 23.5 1.0 HG23 A:VAL76 4.5 26.0 1.0 O A:GLY74 4.5 29.2 1.0 CA A:SER53 4.6 20.8 1.0 CA A:THR77 4.6 21.4 1.0 HE2 A:LYS56 4.6 42.4 1.0 HG2 A:GLN52 4.7 39.0 1.0 CG A:GLN52 4.7 32.7 1.0 CA A:PRO172 4.8 32.9 1.0 CA A:GLY173 4.8 61.1 1.0 CA A:VAL76 4.8 23.2 1.0 CA A:ILE75 4.8 26.8 1.0 CB A:VAL76 4.8 22.3 1.0 C A:VAL76 4.9 22.1 1.0 C A:PRO172 4.9 41.0 1.0 CA A:GLN52 4.9 36.2 1.0 C A:THR77 5.0 20.7 1.0 C A:GLN52 5.0 38.5 1.0 C A:ILE75 5.0 26.3 1.0

Aluminium 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 Aluminium with other atoms in the Al 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:Al1002 b:25.7 occ:1.00 AL B:ALF1002 0.0 25.7 1.0 O B:HOH1104 1.8 28.6 1.0 F3 B:ALF1002 1.8 29.8 1.0 F4 B:ALF1002 1.8 34.5 1.0 F1 B:ALF1002 1.8 37.0 1.0 F2 B:ALF1002 1.8 27.6 1.0 O1B B:GDP1001 1.8 26.8 1.0 PB B:GDP1001 3.0 35.2 1.0 H B:SER53 3.1 34.1 1.0 NA B:NA1004 3.3 25.1 1.0 O3B B:GDP1001 3.4 37.7 1.0 H B:THR77 3.4 55.7 1.0 H B:VAL76 3.4 71.5 1.0 MG B:MG1003 3.5 27.8 1.0 H B:GLY173 3.5 93.7 1.0 HB B:THR77 3.6 40.0 1.0 O2B B:GDP1001 3.6 29.6 1.0 HZ1 B:LYS56 3.6 66.2 1.0 HG3 B:GLN52 3.7 58.3 1.0 N B:SER53 3.9 28.6 1.0 HA B:ILE75 3.9 39.5 1.0 O B:HOH1102 4.0 18.0 1.0 HA B:SER53 4.0 31.5 1.0 HA B:GLN52 4.0 49.9 1.0 HA B:PRO172 4.1 65.0 1.0 N B:THR77 4.1 46.6 1.0 HZ3 B:LYS56 4.2 66.2 1.0 N B:GLY173 4.2 78.3 1.0 CB B:THR77 4.3 33.5 1.0 N B:VAL76 4.3 59.7 1.0 HG13 B:ILE75 4.3 39.2 1.0 O3A B:GDP1001 4.3 38.2 1.0 OG1 B:THR77 4.3 32.2 1.0 O B:THR77 4.3 51.0 1.0 NZ B:LYS56 4.3 55.3 1.0 HA3 B:GLY173 4.4 95.8 1.0 HB B:VAL76 4.4 72.9 1.0 O B:GLY74 4.5 32.5 1.0 CA B:SER53 4.5 26.4 1.0 HG2 B:GLN52 4.5 58.3 1.0 CG B:GLN52 4.6 48.7 1.0 CA B:THR77 4.7 43.5 1.0 HG23 B:VAL76 4.8 74.1 1.0 HE2 B:LYS56 4.8 59.6 1.0 CA B:GLN52 4.8 41.8 1.0 CA B:ILE75 4.9 33.1 1.0 CA B:GLY173 4.9 80.0 1.0 C B:GLN52 4.9 38.6 1.0 CA B:PRO172 4.9 54.4 1.0 HZ2 B:LYS56 4.9 66.2 1.0 O1A B:GDP1001 5.0 39.2 1.0

Aluminium 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 Aluminium with other atoms in the Al 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:Al1002 b:50.9 occ:1.00 AL C:ALF1002 0.0 50.9 1.0 O C:HOH1102 1.8 49.1 1.0 F3 C:ALF1002 1.8 53.6 1.0 F4 C:ALF1002 1.8 49.2 1.0 F1 C:ALF1002 1.8 58.2 1.0 F2 C:ALF1002 1.8 48.6 1.0 O3B C:GDP1001 1.9 48.0 1.0 H C:SER53 3.2 61.4 1.0 H C:VAL76 3.2 56.2 1.0 PB C:GDP1001 3.2 45.5 1.0 H C:THR77 3.2 65.4 1.0 NA C:NA1004 3.3 41.9 1.0 MG C:MG1003 3.5 48.5 1.0 HZ2 C:LYS56 3.5 73.6 1.0 O1B C:GDP1001 3.6 50.4 1.0 H C:GLY173 3.7 81.5 1.0 HG3 C:GLN52 3.7 42.3 1.0 HB C:THR77 3.7 50.0 1.0 O2B C:GDP1001 3.9 45.3 1.0 HA C:ILE75 3.9 88.4 1.0 N C:SER53 4.0 51.3 1.0 N C:THR77 4.0 54.6 1.0 HA C:SER53 4.0 66.1 1.0 N C:VAL76 4.0 47.0 1.0 HB C:VAL76 4.1 40.7 1.0 O C:GLY74 4.1 65.6 1.0 O C:HOH1101 4.1 14.8 1.0 HA C:PRO172 4.2 56.7 1.0 HA C:GLN52 4.2 35.9 1.0 HZ1 C:LYS56 4.2 73.6 1.0 NZ C:LYS56 4.3 61.5 1.0 HG23 C:VAL76 4.3 40.8 1.0 O3A C:GDP1001 4.4 43.1 1.0 CB C:THR77 4.4 41.9 1.0 N C:GLY173 4.4 68.1 1.0 OG1 C:THR77 4.4 35.7 1.0 HG2 C:GLN52 4.5 42.3 1.0 O C:THR77 4.5 33.5 1.0 HG C:SER53 4.5 79.6 1.0 CG C:GLN52 4.5 35.4 1.0 CA C:SER53 4.6 55.3 1.0 HG13 C:ILE75 4.7 92.8 1.0 HA3 C:GLY173 4.7 83.9 1.0 CA C:THR77 4.7 50.7 1.0 CB C:VAL76 4.7 34.1 1.0 CA C:ILE75 4.8 73.9 1.0 CA C:VAL76 4.8 37.2 1.0 HZ3 C:LYS56 4.8 73.6 1.0 HE2 C:LYS56 4.9 71.9 1.0 C C:VAL76 4.9 34.7 1.0 O2A C:GDP1001 4.9 41.2 1.0 HD13 C:ILE75 4.9 91.5 1.0 C C:ILE75 4.9 79.0 1.0 CA C:GLN52 4.9 30.1 1.0 C C:GLN52 5.0 38.0 1.0

Aluminium 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 Aluminium with other atoms in the Al 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:Al1002 b:19.8 occ:1.00 AL D:ALF1002 0.0 19.8 1.0 O D:HOH1105 1.7 17.2 1.0 F3 D:ALF1002 1.8 20.3 1.0 F4 D:ALF1002 1.8 25.1 1.0 F1 D:ALF1002 1.8 18.2 1.0 F2 D:ALF1002 1.8 25.6 1.0 O1B D:GDP1001 1.9 19.9 1.0 PB D:GDP1001 3.0 23.9 1.0 H D:SER53 3.1 34.2 1.0 H D:THR77 3.2 50.1 1.0 NA D:NA1004 3.3 69.3 1.0 O3B D:GDP1001 3.4 27.3 1.0 H D:VAL76 3.4 61.4 1.0 HB D:THR77 3.4 44.4 1.0 MG D:MG1003 3.5 24.3 1.0 H D:GLY173 3.5 49.4 1.0 HZ2 D:LYS56 3.5 54.3 1.0 O2B D:GDP1001 3.5 22.8 1.0 HG3 D:GLN52 3.7 30.1 1.0 O D:HOH1104 3.8 16.1 1.0 HZ1 D:LYS56 3.9 54.3 1.0 HA D:PRO172 3.9 47.1 1.0 N D:SER53 3.9 28.7 1.0 N D:THR77 4.0 41.9 1.0 HA D:SER53 4.0 39.8 1.0 HA D:GLN52 4.1 35.0 1.0 HA D:ILE75 4.1 53.3 1.0 NZ D:LYS56 4.1 45.4 1.0 OG1 D:THR77 4.1 39.1 1.0 CB D:THR77 4.1 37.1 1.0 N D:GLY173 4.2 41.4 1.0 O D:HOH1103 4.2 23.0 1.0 HG13 D:ILE75 4.3 52.7 1.0 N D:VAL76 4.3 51.4 1.0 O3A D:GDP1001 4.3 25.7 1.0 HB D:VAL76 4.3 65.5 1.0 O D:THR77 4.4 32.0 1.0 HE2 D:LYS56 4.4 52.1 1.0 HA3 D:GLY173 4.4 51.8 1.0 HG2 D:GLN52 4.5 30.1 1.0 CG D:GLN52 4.6 25.2 1.0 CA D:SER53 4.6 33.4 1.0 CA D:THR77 4.6 36.2 1.0 O D:GLY74 4.7 46.1 1.0 CA D:PRO172 4.8 39.4 1.0 HZ3 D:LYS56 4.8 54.3 1.0 CE D:LYS56 4.8 43.6 1.0 HG23 D:VAL76 4.8 69.2 1.0 CA D:GLN52 4.8 29.3 1.0 CA D:GLY173 4.9 43.3 1.0 C D:GLN52 4.9 33.0 1.0 C D:PRO172 4.9 39.4 1.0 O D:LEU171 4.9 26.8 1.0 O1A D:GDP1001 4.9 24.4 1.0 CA D:ILE75 5.0 44.6 1.0 C D:VAL76 5.0 46.8 1.0 CA D:VAL76 5.0 51.5 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