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

Protein crystallography data

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

Magnesium Binding Sites:

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 6s6d

Go back to Magnesium Binding Sites List in 6s6d
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 6s6d

Go back to Magnesium Binding Sites List in 6s6d
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

Reference:

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
Page generated: Tue Oct 1 17:46:46 2024

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