Magnesium in PDB 6vjf: The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse

The structure of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse, PDB code: 6vjf was solved by B.A.Tornabene, N.V.Varlakhanova, 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)	80.38 / 2.47
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.873, 119.032, 84.576, 90.00, 100.95, 90.00
R / Rfree (%)	18.9 / 23.8

The binding sites of Magnesium atom in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse (pdb code 6vjf). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse, PDB code: 6vjf:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:43.0 occ:1.00 OG A:SER57 1.8 28.9 1.0 O2G A:GCP701 2.0 34.7 1.0 O A:HOH804 2.0 37.4 1.0 OG1 A:THR77 2.1 32.1 1.0 O A:HOH801 2.2 43.9 1.0 O2B A:GCP701 2.2 23.4 1.0 CB A:SER57 3.0 30.2 1.0 CB A:THR77 3.3 32.2 1.0 PG A:GCP701 3.3 34.5 1.0 PB A:GCP701 3.4 30.5 1.0 C3B A:GCP701 3.5 33.4 1.0 N A:SER57 3.7 31.5 1.0 OD2 A:ASP170 3.8 49.4 1.0 CA A:SER57 3.9 30.4 1.0 N A:THR77 4.0 33.3 1.0 OD1 A:ASP170 4.1 47.4 1.0 O3G A:GCP701 4.1 35.6 1.0 O2A A:GCP701 4.2 32.0 1.0 CG2 A:THR77 4.2 31.2 1.0 O A:HOH806 4.2 52.8 1.0 CA A:THR77 4.3 31.9 1.0 O1B A:GCP701 4.3 34.5 1.0 CG A:ASP170 4.3 47.7 1.0 O1G A:GCP701 4.4 34.4 1.0 O3A A:GCP701 4.4 31.4 1.0 O A:PRO70 4.4 36.8 1.0 PA A:GCP701 4.7 30.8 1.0 O1A A:GCP701 4.7 32.2 1.0 CB A:VAL76 4.8 36.6 1.0 O A:LEU171 4.8 37.2 1.0 CG1 A:VAL76 4.8 38.0 1.0 C A:ALA56 4.9 32.4 1.0 CB A:ALA56 4.9 33.4 1.0

Magnesium binding site 2 out of 4 in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:38.5 occ:1.00 OG B:SER57 1.8 23.5 1.0 O3G B:GCP701 2.1 26.9 1.0 OG1 B:THR77 2.1 37.6 1.0 O B:HOH804 2.1 36.1 1.0 O2B B:GCP701 2.1 25.6 1.0 O B:HOH805 2.1 41.8 1.0 CB B:SER57 2.9 28.3 1.0 CB B:THR77 3.2 31.6 1.0 PG B:GCP701 3.4 33.2 1.0 PB B:GCP701 3.4 30.2 1.0 C3B B:GCP701 3.5 36.7 1.0 N B:SER57 3.8 27.2 1.0 OD2 B:ASP170 3.8 33.7 1.0 CA B:SER57 3.9 26.7 1.0 N B:THR77 3.9 31.4 1.0 O2A B:GCP701 4.1 29.6 1.0 CA B:THR77 4.1 32.9 1.0 OD1 B:ASP170 4.2 39.7 1.0 CG2 B:THR77 4.2 30.8 1.0 O1G B:GCP701 4.3 29.7 1.0 O1B B:GCP701 4.4 32.2 1.0 O3A B:GCP701 4.4 32.5 1.0 O B:PRO70 4.4 32.6 1.0 CG B:ASP170 4.4 34.0 1.0 O2G B:GCP701 4.6 37.5 1.0 CB B:VAL76 4.7 41.5 1.0 PA B:GCP701 4.7 31.2 1.0 O B:LEU171 4.9 28.7 1.0 C B:VAL76 4.9 33.9 1.0 C B:ALA56 4.9 27.8 1.0

Magnesium binding site 3 out of 4 in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg702 b:41.6 occ:1.00 OG C:SER57 2.0 32.4 1.0 O2G C:GCP701 2.0 34.0 1.0 O C:HOH802 2.1 39.5 1.0 O2B C:GCP701 2.1 29.3 1.0 OG1 C:THR77 2.2 34.0 1.0 O C:HOH805 2.2 44.3 1.0 CB C:SER57 3.0 35.6 1.0 PG C:GCP701 3.2 35.0 1.0 CB C:THR77 3.3 38.0 1.0 C3B C:GCP701 3.3 37.3 1.0 PB C:GCP701 3.3 33.1 1.0 N C:SER57 3.9 38.7 1.0 O3G C:GCP701 3.9 37.5 1.0 OD2 C:ASP170 3.9 48.5 1.0 N C:THR77 3.9 35.9 1.0 CA C:SER57 4.0 36.1 1.0 O2A C:GCP701 4.1 32.7 1.0 CA C:THR77 4.2 36.0 1.0 OD1 C:ASP170 4.3 49.5 1.0 CG2 C:THR77 4.3 37.5 1.0 O3A C:GCP701 4.3 33.4 1.0 O1B C:GCP701 4.4 38.9 1.0 O1G C:GCP701 4.4 39.8 1.0 O C:PRO70 4.4 39.1 1.0 CG C:ASP170 4.5 49.0 1.0 PA C:GCP701 4.6 32.0 1.0 CB C:VAL76 4.6 41.5 1.0 O C:LEU171 4.8 40.6 1.0 CG1 C:VAL76 4.9 42.0 1.0 C C:VAL76 5.0 37.2 1.0 O1A C:GCP701 5.0 34.1 1.0

Magnesium binding site 4 out of 4 in the The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of The P-Loop K to A Mutation of C. Therm VPS1 Gtpase-Bse within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg702 b:45.1 occ:1.00 O2G D:GCP701 1.9 25.8 1.0 OG D:SER57 2.0 28.2 1.0 O D:HOH809 2.0 35.9 1.0 O2B D:GCP701 2.0 26.6 1.0 OG1 D:THR77 2.1 37.0 1.0 O D:HOH804 2.2 43.4 1.0 CB D:SER57 3.1 26.7 1.0 PG D:GCP701 3.2 28.4 1.0 CB D:THR77 3.2 33.2 1.0 PB D:GCP701 3.3 29.1 1.0 C3B D:GCP701 3.4 32.1 1.0 N D:SER57 3.8 25.9 1.0 OD2 D:ASP170 3.9 35.8 1.0 N D:THR77 3.9 33.5 1.0 O3G D:GCP701 4.0 34.1 1.0 CA D:SER57 4.0 25.5 1.0 O2A D:GCP701 4.1 31.5 1.0 OD1 D:ASP170 4.1 40.1 1.0 CA D:THR77 4.2 33.0 1.0 CG2 D:THR77 4.2 33.5 1.0 O1B D:GCP701 4.3 31.9 1.0 O3A D:GCP701 4.3 31.9 1.0 O1G D:GCP701 4.4 32.9 1.0 CG D:ASP170 4.4 36.9 1.0 O D:PRO70 4.5 28.1 1.0 PA D:GCP701 4.6 32.3 1.0 O D:LEU171 4.8 31.9 1.0 CB D:VAL76 4.8 33.6 1.0 CB D:ALA56 4.9 27.3 1.0 C D:ALA56 4.9 30.5 1.0

B.A.Tornabene, N.V.Varlakhanova, C.J.Hosford, J.S.Chappie, M.G.J.Ford. Structural and Functional Characterization of the Dominant Negative P-Loop Lysine Mutation in the Dynamin Superfamily Protein VPS1. Protein Sci. 2020.
ISSN: ESSN 1469-896X
PubMed: 31981262
DOI: 10.1002/PRO.3830