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Magnesium in PDB 6s6a: Crystal Structure of Raga-Q66L/Ragc-T90N Gtpase Heterodimer Complex

Protein crystallography data

The structure of Crystal Structure of Raga-Q66L/Ragc-T90N Gtpase Heterodimer Complex, PDB code: 6s6a 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) 46.62 / 2.63
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.103, 81.856, 244.076, 90.00, 90.00, 90.00
R / Rfree (%) 19.5 / 27.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Raga-Q66L/Ragc-T90N Gtpase Heterodimer Complex (pdb code 6s6a). 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/Ragc-T90N Gtpase Heterodimer Complex, PDB code: 6s6a:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 6s6a

Go back to Magnesium Binding Sites List in 6s6a
Magnesium binding site 1 out of 2 in the Crystal Structure of Raga-Q66L/Ragc-T90N 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/Ragc-T90N Gtpase Heterodimer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:70.4
occ:1.00
O A:HOH501 1.5 62.9 1.0
O A:HOH504 1.7 57.6 1.0
O1B A:GTP401 1.8 54.1 1.0
OG1 A:THR21 2.2 55.0 1.0
O1G A:GTP401 2.2 52.7 1.0
OG1 A:THR42 2.2 59.2 1.0
PB A:GTP401 3.0 60.4 1.0
PG A:GTP401 3.1 66.0 1.0
CB A:THR42 3.2 59.8 1.0
CB A:THR21 3.2 54.9 1.0
O3B A:GTP401 3.2 69.3 1.0
O3G A:GTP401 3.7 56.9 1.0
N A:THR21 3.9 54.8 1.0
O1A A:GTP401 3.9 68.0 1.0
N A:THR42 3.9 60.6 1.0
O3A A:GTP401 4.0 60.1 1.0
OD2 A:ASP62 4.1 59.0 1.0
CA A:THR21 4.1 54.9 1.0
CA A:THR42 4.2 60.8 1.0
O2B A:GTP401 4.2 65.6 1.0
OD1 A:ASP62 4.2 58.9 1.0
CG2 A:THR21 4.2 55.3 1.0
CG2 A:THR42 4.3 59.8 1.0
PA A:GTP401 4.4 59.2 1.0
O2G A:GTP401 4.5 67.9 1.0
CG A:ASP62 4.5 59.4 1.0
O A:HOH512 4.6 68.6 1.0
CB A:LYS20 4.8 55.1 1.0
O A:GLY40 4.8 61.9 1.0
O2A A:GTP401 4.8 61.3 1.0
C A:ALA41 4.9 61.3 1.0
NZ A:LYS20 4.9 56.0 1.0
CE A:LYS20 5.0 55.6 1.0
C A:LYS20 5.0 55.0 1.0

Magnesium binding site 2 out of 2 in 6s6a

Go back to Magnesium Binding Sites List in 6s6a
Magnesium binding site 2 out of 2 in the Crystal Structure of Raga-Q66L/Ragc-T90N 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/Ragc-T90N Gtpase Heterodimer Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:0.5
occ:1.00
O B:HOH503 1.8 94.3 1.0
OG1 B:THR21 1.9 79.2 1.0
O1B B:GTP401 1.9 86.1 1.0
O1G B:GTP401 2.0 0.1 1.0
OG1 B:THR42 2.1 93.6 1.0
O B:HOH501 2.2 74.4 1.0
CB B:THR21 2.9 79.3 1.0
CB B:THR42 3.2 94.7 1.0
PB B:GTP401 3.2 87.6 1.0
PG B:GTP401 3.2 89.5 1.0
O3B B:GTP401 3.4 84.7 1.0
N B:THR21 3.7 75.4 1.0
N B:THR42 3.8 97.5 1.0
OD2 B:ASP62 3.8 85.8 1.0
CA B:THR21 3.9 76.6 1.0
O3G B:GTP401 4.0 94.6 1.0
CG2 B:THR21 4.0 81.3 1.0
O2A B:GTP401 4.0 99.3 1.0
OD1 B:ASP62 4.1 82.0 1.0
O1A B:GTP401 4.1 82.3 1.0
CA B:THR42 4.1 97.1 1.0
O3A B:GTP401 4.1 86.8 1.0
CG2 B:THR42 4.3 95.6 1.0
PA B:GTP401 4.3 86.8 1.0
CG B:ASP62 4.3 84.3 1.0
O2B B:GTP401 4.4 94.3 1.0
O2G B:GTP401 4.4 0.9 1.0
O B:GLY40 4.8 0.6 1.0
C B:LYS20 4.8 75.3 1.0
NZ B:LYS20 4.8 84.1 1.0
C B:ALA41 4.8 99.2 1.0
CB B:LYS20 4.8 77.1 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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