Magnesium in PDB 6d71: Crystal Structure of the Human MIRO1 N-Terminal Gtpase Bound to Gtp

The structure of Crystal Structure of the Human MIRO1 N-Terminal Gtpase Bound to Gtp, PDB code: 6d71 was solved by K.P.Smith, P.J.Focia, S.E.Rice, D.M.Freymann, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.07 / 1.72
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	41.350, 78.270, 99.780, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22

The binding sites of Magnesium atom in the Crystal Structure of the Human MIRO1 N-Terminal Gtpase Bound to Gtp (pdb code 6d71). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Human MIRO1 N-Terminal Gtpase Bound to Gtp, PDB code: 6d71:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of the Human MIRO1 N-Terminal Gtpase Bound to Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of the Human MIRO1 N-Terminal Gtpase Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg202 b:14.8 occ:1.00 O1G A:GTP201 2.0 15.8 1.0 O A:HOH366 2.1 14.1 1.0 OG1 A:THR18 2.1 13.6 1.0 O A:PRO35 2.1 19.0 1.0 O2B A:GTP201 2.1 14.3 1.0 O A:HOH354 2.2 12.4 1.0 CB A:THR18 3.2 13.7 1.0 C A:PRO35 3.2 21.8 1.0 PG A:GTP201 3.3 21.4 1.0 PB A:GTP201 3.3 14.4 1.0 O3B A:GTP201 3.6 16.6 1.0 OD2 A:ASP57 4.0 16.5 1.0 N A:THR18 4.0 13.3 1.0 CA A:PRO35 4.0 19.4 1.0 O A:PRO34 4.1 22.1 1.0 N A:ARG36 4.1 20.6 1.0 O2A A:GTP201 4.1 16.3 1.0 CA A:THR18 4.2 12.1 1.0 CG2 A:THR18 4.2 13.6 1.0 O2G A:GTP201 4.2 22.0 1.0 CA A:ARG36 4.3 19.2 1.0 O1B A:GTP201 4.3 16.4 1.0 O3G A:GTP201 4.4 23.5 1.0 O3A A:GTP201 4.4 12.3 1.0 OD1 A:ASP57 4.5 17.1 1.0 OG A:SER59 4.5 35.2 1.0 CB A:SER59 4.5 24.3 1.0 PA A:GTP201 4.6 15.7 1.0 CG A:ASP57 4.6 17.0 1.0 O1A A:GTP201 4.7 13.6 1.0 O A:TYR58 4.7 17.1 1.0 O A:HOH357 4.8 29.3 1.0 CB A:LYS17 5.0 11.6 1.0 C A:PRO34 5.0 24.5 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of the Human MIRO1 N-Terminal Gtpase Bound to Gtp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of the Human MIRO1 N-Terminal Gtpase Bound to Gtp within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg202 b:12.4 occ:1.00 O1B B:GTP201 2.1 10.1 1.0 O3G B:GTP201 2.1 13.3 1.0 OG1 B:THR18 2.1 10.6 1.0 O B:HOH355 2.1 10.5 1.0 O B:HOH357 2.1 9.5 1.0 O B:PRO35 2.1 12.8 1.0 CB B:THR18 3.2 9.8 1.0 C B:PRO35 3.2 16.6 1.0 PG B:GTP201 3.3 16.2 1.0 PB B:GTP201 3.3 12.3 1.0 O3B B:GTP201 3.5 14.9 1.0 N B:THR18 3.9 9.5 1.0 CA B:PRO35 3.9 15.0 1.0 O B:PRO34 4.0 13.2 1.0 OD2 B:ASP57 4.1 10.2 1.0 CA B:THR18 4.1 11.2 1.0 O2G B:GTP201 4.1 17.4 1.0 O1A B:GTP201 4.2 11.0 1.0 CG2 B:THR18 4.2 11.7 1.0 N B:ARG36 4.2 11.8 1.0 O2B B:GTP201 4.3 10.1 1.0 O B:HOH303 4.4 28.2 1.0 O3A B:GTP201 4.4 12.0 1.0 O1G B:GTP201 4.4 19.7 1.0 OD1 B:ASP57 4.4 12.5 1.0 CA B:ARG36 4.5 13.4 1.0 CB B:SER59 4.6 23.7 1.0 PA B:GTP201 4.6 10.1 1.0 O B:TYR58 4.6 10.5 1.0 CG B:ASP57 4.6 14.4 1.0 O2A B:GTP201 4.7 10.1 1.0 O B:HOH464 4.7 32.0 1.0 OG B:SER59 4.9 27.4 1.0 CB B:LYS17 4.9 9.6 1.0 C B:PRO34 4.9 16.4 1.0 O B:HOH404 5.0 27.5 1.0 N B:PRO35 5.0 12.4 1.0

K.P.Smith, P.J.Focia, S.Chakravarthy, E.C.Landahl, J.L.Klosowiak, S.E.Rice, D.M.Freymann. Structural Assembly of the Human MIRO1/2 Gtpases Based on the Crystal Structure of the N-Terminal Gtpase Domain Biorxiv 2019.
DOI: 10.1101/729251