Magnesium in PDB 6s6d: Crystal Structure of Raga-Q66L-Gtp/Ragc-S75N-Gdp Gtpase Heterodimer Complex

The structure of Crystal Structure of Raga-Q66L-Gtp/Ragc-S75N-Gdp Gtpase Heterodimer Complex, PDB code: 6s6d was solved by M.Anandapadamanaban, G.R.Masson, O.Perisic, J.Kaufman, R.L.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.29 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	71.504, 81.439, 246.033, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 28.7

The binding sites of Magnesium atom in the Crystal Structure of Raga-Q66L-Gtp/Ragc-S75N-Gdp Gtpase Heterodimer Complex (pdb code 6s6d). 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 Raga-Q66L-Gtp/Ragc-S75N-Gdp Gtpase Heterodimer Complex, PDB code: 6s6d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Raga-Q66L-Gtp/Ragc-S75N-Gdp Gtpase Heterodimer Complex


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 Raga-Q66L-Gtp/Ragc-S75N-Gdp Gtpase Heterodimer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:43.7 occ:1.00 OG1 A:THR42 2.0 39.1 1.0 OG1 A:THR21 2.0 35.9 1.0 O A:HOH507 2.1 39.6 1.0 O1B A:GTP401 2.1 33.2 1.0 O1G A:GTP401 2.1 41.6 1.0 O A:HOH503 2.3 52.4 1.0 CB A:THR21 2.9 37.2 1.0 CB A:THR42 3.1 40.9 1.0 PG A:GTP401 3.4 42.3 1.0 PB A:GTP401 3.4 41.9 1.0 N A:THR42 3.5 39.8 1.0 O3B A:GTP401 3.6 40.0 1.0 CG2 A:THR21 3.9 34.9 1.0 CA A:THR42 3.9 42.2 1.0 N A:THR21 4.0 40.8 1.0 CA A:THR21 4.0 39.0 1.0 O3G A:GTP401 4.0 41.8 1.0 OD2 A:ASP62 4.1 50.0 1.0 O1A A:GTP401 4.2 42.7 1.0 O3A A:GTP401 4.3 36.2 1.0 CG2 A:THR42 4.3 40.1 1.0 OD1 A:ASP62 4.3 47.2 1.0 O A:GLY40 4.3 57.2 1.0 C A:ALA41 4.5 44.8 1.0 CG A:ASP62 4.5 45.6 1.0 PA A:GTP401 4.6 41.5 1.0 O2B A:GTP401 4.6 36.3 1.0 O2G A:GTP401 4.6 44.9 1.0 O2A A:GTP401 4.6 40.5 1.0 CA A:ALA41 4.8 43.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Raga-Q66L-Gtp/Ragc-S75N-Gdp Gtpase Heterodimer Complex


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 Raga-Q66L-Gtp/Ragc-S75N-Gdp Gtpase Heterodimer Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:58.9 occ:1.00 OG1 B:THR21 2.0 52.3 1.0 O B:HOH502 2.2 56.8 1.0 O1G B:GTP401 2.3 60.2 1.0 O B:HOH501 2.4 53.6 1.0 O1B B:GTP401 2.5 50.5 1.0 CB B:THR42 2.5 76.4 1.0 OG1 B:THR42 2.5 86.9 1.0 CB B:THR21 3.0 62.9 1.0 CG2 B:THR42 3.4 98.0 1.0 N B:THR42 3.6 93.5 1.0 CA B:THR42 3.6 84.9 1.0 PG B:GTP401 3.6 68.7 1.0 PB B:GTP401 3.8 61.9 1.0 CG2 B:THR21 3.8 62.6 1.0 O3B B:GTP401 4.0 58.8 1.0 OD2 B:ASP62 4.1 75.7 1.0 O B:GLY40 4.1 0.5 1.0 OD1 B:ASP62 4.1 62.7 1.0 CA B:THR21 4.2 54.0 1.0 O3G B:GTP401 4.2 66.9 1.0 N B:THR21 4.2 53.4 1.0 CG B:ASP62 4.4 60.6 1.0 O1A B:GTP401 4.5 52.1 1.0 C B:ALA41 4.7 83.5 1.0 O3A B:GTP401 4.8 53.9 1.0 O2A B:GTP401 4.8 56.9 1.0 O2G B:GTP401 4.8 80.2 1.0 O2B B:GTP401 4.8 57.5 1.0 C B:THR42 4.9 82.5 1.0 PA B:GTP401 4.9 59.1 1.0

M.Anandapadamanaban, G.R.Masson, O.Perisic, A.Berndt, J.Kaufman, C.M.Johnson, B.Santhanam, K.B.Rogala, D.M.Sabatini, R.L.Williams. Architecture of Human Rag Gtpase Heterodimers and Their Complex with MTORC1. Science V. 366 203 2019.
ISSN: ESSN 1095-9203
PubMed: 31601764
DOI: 10.1126/SCIENCE.AAX3939