Sodium 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
Aluminium	(Al)	4 atoms

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

Sodium 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 Sodium with other atoms in the Na 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:Na1004 b:31.8 occ:1.00 O A:GLY74 2.0 29.2 1.0 OG A:SER53 2.3 21.4 1.0 F3 A:ALF1002 2.5 29.4 1.0 O3B A:GDP1001 2.7 24.9 1.0 F1 A:ALF1002 2.7 33.2 1.0 O A:GLY72 2.7 41.2 1.0 HG23 A:VAL76 2.7 26.0 1.0 HA A:SER53 2.8 24.8 1.0 C A:GLY74 3.3 20.8 1.0 H A:SER53 3.3 27.5 1.0 AL A:ALF1002 3.3 27.5 1.0 H A:VAL76 3.3 27.5 1.0 CB A:SER53 3.3 24.0 1.0 CA A:SER53 3.3 20.8 1.0 H5'' A:GDP1001 3.4 26.9 1.0 HA A:ILE75 3.5 32.0 1.0 N A:SER53 3.6 23.1 1.0 CG2 A:VAL76 3.7 21.8 1.0 HG2 A:GLN52 3.7 39.0 1.0 HA A:GLN73 3.8 56.2 1.0 H5' A:GDP1001 3.8 26.9 1.0 C A:GLN73 3.8 46.0 1.0 HB3 A:SER53 3.9 28.5 1.0 C A:GLY72 3.9 45.1 1.0 N A:VAL76 3.9 23.1 1.0 O A:GLN73 4.0 51.2 1.0 N A:GLY74 4.0 25.3 1.0 HB2 A:SER53 4.0 28.5 1.0 HG3 A:GLN52 4.0 39.0 1.0 PB A:GDP1001 4.1 21.7 1.0 C5' A:GDP1001 4.1 22.6 1.0 HG21 A:VAL76 4.1 26.0 1.0 HB A:VAL76 4.1 26.5 1.0 N A:ILE75 4.2 27.5 1.0 HG22 A:VAL76 4.2 26.0 1.0 CA A:ILE75 4.2 26.8 1.0 CA A:GLN73 4.2 47.0 1.0 O3A A:GDP1001 4.2 21.0 1.0 CA A:GLY74 4.2 20.1 1.0 O2A A:GDP1001 4.3 19.1 1.0 H A:GLY74 4.3 30.2 1.0 CG A:GLN52 4.4 32.7 1.0 CB A:VAL76 4.4 22.3 1.0 C A:ILE75 4.5 26.3 1.0 H A:GLY72 4.5 61.3 1.0 N A:GLN73 4.6 50.5 1.0 OD2 B:ASP214 4.6 22.5 1.0 O A:HOH1106 4.6 31.3 1.0 F2 A:ALF1002 4.6 29.2 1.0 F4 A:ALF1002 4.7 26.7 1.0 HE21 A:GLN52 4.7 36.4 1.0 HA2 A:GLY74 4.7 23.9 1.0 C A:SER53 4.7 15.7 1.0 C A:GLN52 4.8 38.5 1.0 PA A:GDP1001 4.8 23.4 1.0 CA A:VAL76 4.8 23.2 1.0 H A:THR77 4.9 25.4 1.0 O2B A:GDP1001 4.9 20.6 1.0 O5' A:GDP1001 4.9 26.7 1.0 HA3 A:GLY74 5.0 23.9 1.0 O A:HOH1105 5.0 33.8 1.0 H A:ILE75 5.0 32.8 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1004 b:25.1 occ:1.00 O B:GLY74 1.9 32.5 1.0 F3 B:ALF1002 2.5 29.8 1.0 OG B:SER53 2.5 29.4 1.0 F1 B:ALF1002 2.7 37.0 1.0 O1B B:GDP1001 2.7 26.8 1.0 O B:GLY72 2.8 43.5 1.0 HA B:SER53 2.9 31.5 1.0 HG23 B:VAL76 2.9 74.1 1.0 C B:GLY74 3.1 33.0 1.0 H B:VAL76 3.3 71.5 1.0 AL B:ALF1002 3.3 25.7 1.0 H5'' B:GDP1001 3.4 40.5 1.0 H B:SER53 3.4 34.1 1.0 HA B:ILE75 3.5 39.5 1.0 CB B:SER53 3.5 28.4 1.0 CA B:SER53 3.5 26.4 1.0 HA B:GLN73 3.6 52.6 1.0 C B:GLN73 3.7 37.9 1.0 N B:SER53 3.8 28.6 1.0 N B:GLY74 3.8 33.0 1.0 H5' B:GDP1001 3.8 40.5 1.0 CG2 B:VAL76 3.9 62.0 1.0 HG2 B:GLN52 3.9 58.3 1.0 N B:VAL76 3.9 59.7 1.0 C B:GLY72 3.9 51.7 1.0 O B:GLN73 4.0 39.7 1.0 HB3 B:SER53 4.0 33.8 1.0 N B:ILE75 4.0 33.3 1.0 PB B:GDP1001 4.0 35.2 1.0 CA B:GLN73 4.1 44.0 1.0 CA B:ILE75 4.1 33.1 1.0 H B:GLY74 4.1 39.4 1.0 CA B:GLY74 4.1 33.2 1.0 C5' B:GDP1001 4.1 34.0 1.0 O1A B:GDP1001 4.1 39.2 1.0 HB2 B:SER53 4.2 33.8 1.0 O3A B:GDP1001 4.2 38.2 1.0 HG21 B:VAL76 4.2 74.1 1.0 HG3 B:GLN52 4.2 58.3 1.0 HB B:VAL76 4.2 72.9 1.0 OD2 A:ASP214 4.3 39.3 1.0 HG22 B:VAL76 4.4 74.1 1.0 C B:ILE75 4.4 39.2 1.0 O B:HOH1104 4.5 28.6 1.0 N B:GLN73 4.5 49.5 1.0 CG B:GLN52 4.5 48.7 1.0 CB B:VAL76 4.5 60.9 1.0 HA2 B:GLY74 4.6 39.7 1.0 F2 B:ALF1002 4.6 27.6 1.0 H B:GLY72 4.6 63.1 1.0 F4 B:ALF1002 4.7 34.5 1.0 PA B:GDP1001 4.7 39.2 1.0 HA3 B:GLY74 4.8 39.7 1.0 H B:THR77 4.8 55.7 1.0 CA B:VAL76 4.9 60.3 1.0 H B:ILE75 4.9 39.7 1.0 C B:SER53 4.9 26.4 1.0 O5' B:GDP1001 4.9 35.2 1.0 C B:GLN52 4.9 38.6 1.0 O3B B:GDP1001 4.9 37.7 1.0 HE21 B:GLN52 4.9 61.5 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1004 b:41.9 occ:1.00 O C:GLY74 2.0 65.6 1.0 O C:GLY72 2.4 47.0 1.0 F3 C:ALF1002 2.5 53.6 1.0 HG C:SER53 2.5 79.6 1.0 OG C:SER53 2.7 66.5 1.0 F1 C:ALF1002 2.7 58.2 1.0 HG23 C:VAL76 2.7 40.8 1.0 O3B C:GDP1001 3.1 48.0 1.0 HA C:SER53 3.1 66.1 1.0 HA C:GLN73 3.2 68.6 1.0 C C:GLY74 3.2 66.2 1.0 AL C:ALF1002 3.3 50.9 1.0 H5'' C:GDP1001 3.4 51.8 1.0 C C:GLN73 3.4 59.2 1.0 C C:GLY72 3.5 52.5 1.0 H C:VAL76 3.5 56.2 1.0 N C:GLY74 3.6 58.4 1.0 CG2 C:VAL76 3.7 34.2 1.0 CA C:GLN73 3.7 57.4 1.0 H C:SER53 3.7 61.4 1.0 CB C:SER53 3.7 60.3 1.0 O C:GLN73 3.7 66.5 1.0 CA C:SER53 3.8 55.3 1.0 H5' C:GDP1001 3.8 51.8 1.0 HA C:ILE75 3.9 88.4 1.0 HG21 C:VAL76 3.9 40.8 1.0 H C:GLY74 3.9 69.8 1.0 CA C:GLY74 4.0 62.4 1.0 N C:GLN73 4.1 56.2 1.0 N C:SER53 4.1 51.3 1.0 N C:VAL76 4.1 47.0 1.0 C5' C:GDP1001 4.1 43.3 1.0 HG2 C:GLN52 4.1 42.3 1.0 HB C:VAL76 4.2 40.7 1.0 N C:ILE75 4.2 64.8 1.0 OD2 D:ASP214 4.2 48.5 1.0 HG22 C:VAL76 4.2 40.8 1.0 HB3 C:SER53 4.2 72.1 1.0 O2A C:GDP1001 4.4 41.2 1.0 H C:GLY72 4.4 61.1 1.0 CA C:ILE75 4.4 73.9 1.0 PB C:GDP1001 4.4 45.5 1.0 HG3 C:GLN52 4.4 42.3 1.0 HB2 C:SER53 4.4 72.1 1.0 CB C:VAL76 4.5 34.1 1.0 O3A C:GDP1001 4.5 43.1 1.0 HA2 C:GLY74 4.6 74.7 1.0 C C:ILE75 4.6 79.0 1.0 F2 C:ALF1002 4.6 48.6 1.0 F4 C:ALF1002 4.7 49.2 1.0 O C:HOH1102 4.7 49.1 1.0 HA3 C:GLY74 4.7 74.7 1.0 CG C:GLN52 4.7 35.4 1.0 CA C:GLY72 4.8 54.1 1.0 N C:GLY72 4.9 51.1 1.0 H C:GLN73 4.9 67.3 1.0 H4' C:GDP1001 4.9 50.1 1.0 CA C:VAL76 4.9 37.2 1.0 PA C:GDP1001 5.0 44.2 1.0 HE21 C:GLN52 5.0 51.0 1.0 H C:ILE75 5.0 77.6 1.0

Sodium 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 Sodium with other atoms in the Na 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:Na1004 b:69.3 occ:1.00 O D:GLY74 2.1 46.1 1.0 OG D:SER53 2.5 31.0 1.0 F3 D:ALF1002 2.5 20.3 1.0 O1B D:GDP1001 2.6 19.9 1.0 F1 D:ALF1002 2.7 18.2 1.0 HA D:SER53 2.7 39.8 1.0 O D:GLY72 2.9 73.2 1.0 HG23 D:VAL76 3.0 69.2 1.0 H D:SER53 3.2 34.2 1.0 H D:VAL76 3.3 61.4 1.0 AL D:ALF1002 3.3 19.8 1.0 CA D:SER53 3.3 33.4 1.0 H5'' D:GDP1001 3.4 39.4 1.0 C D:GLY74 3.4 40.4 1.0 CB D:SER53 3.4 33.8 1.0 HA D:ILE75 3.5 53.3 1.0 N D:SER53 3.6 28.7 1.0 HG2 D:GLN52 3.7 30.1 1.0 H5' D:GDP1001 3.8 39.4 1.0 HA D:GLN73 3.8 44.9 1.0 CG2 D:VAL76 3.9 57.9 1.0 HB3 D:SER53 4.0 40.3 1.0 N D:VAL76 4.0 51.4 1.0 PB D:GDP1001 4.0 23.9 1.0 C D:GLN73 4.0 36.7 1.0 C D:GLY72 4.0 72.4 1.0 O1A D:GDP1001 4.1 24.4 1.0 HG3 D:GLN52 4.1 30.1 1.0 C5' D:GDP1001 4.1 33.0 1.0 HB2 D:SER53 4.1 40.3 1.0 O3A D:GDP1001 4.1 25.7 1.0 N D:GLY74 4.1 41.0 1.0 O D:HOH1105 4.2 17.2 1.0 CA D:ILE75 4.2 44.6 1.0 HB D:VAL76 4.2 65.5 1.0 HG21 D:VAL76 4.2 69.2 1.0 N D:ILE75 4.2 47.5 1.0 O D:GLN73 4.2 36.1 1.0 CA D:GLN73 4.3 37.6 1.0 CG D:GLN52 4.3 25.2 1.0 CA D:GLY74 4.4 38.7 1.0 OD2 C:ASP214 4.4 35.9 1.0 H D:GLY74 4.4 49.0 1.0 C D:ILE75 4.5 46.5 1.0 HG22 D:VAL76 4.5 69.2 1.0 CB D:VAL76 4.5 54.7 1.0 H D:GLY72 4.6 82.0 1.0 F2 D:ALF1002 4.6 25.6 1.0 HE21 D:GLN52 4.6 30.5 1.0 F4 D:ALF1002 4.7 25.1 1.0 N D:GLN73 4.7 47.8 1.0 PA D:GDP1001 4.7 28.4 1.0 C D:SER53 4.7 38.9 1.0 C D:GLN52 4.8 33.0 1.0 H D:THR77 4.8 50.1 1.0 HA2 D:GLY74 4.9 46.3 1.0 O2B D:GDP1001 4.9 22.8 1.0 O5' D:GDP1001 4.9 31.0 1.0 CA D:VAL76 4.9 51.5 1.0 O3B D:GDP1001 4.9 27.3 1.0 O D:HOH1103 5.0 23.0 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