Magnesium in PDB 5yxh: Structure of Rheb-Gdp

Protein crystallography data

The structure of Structure of Rheb-Gdp, PDB code: 5yxh was solved by S.J.Mahoney, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.80 / 2.04
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.166, 58.963, 64.345, 110.53, 90.03, 108.16
R / Rfree (%) 24.4 / 29.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Structure of Rheb-Gdp (pdb code 5yxh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Structure of Rheb-Gdp, PDB code: 5yxh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 5yxh

Go back to Magnesium Binding Sites List in 5yxh
Magnesium binding site 1 out of 4 in the Structure of Rheb-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of Rheb-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:35.2
occ:1.00
O A:HOH310 2.2 35.6 1.0
O A:HOH301 2.2 36.2 1.0
O A:HOH313 2.2 37.5 1.0
OG A:SER20 2.2 28.5 1.0
O1B A:GDP201 2.2 33.0 1.0
O A:HOH317 2.2 37.0 1.0
CB A:SER20 3.1 28.0 1.0
PB A:GDP201 3.2 31.7 1.0
O3B A:GDP201 3.4 32.9 1.0
O1A A:GDP201 3.7 34.4 1.0
CA A:PRO37 4.0 64.5 1.0
N A:SER20 4.0 27.4 1.0
CA A:SER20 4.1 27.8 1.0
O A:ASP36 4.2 64.4 1.0
O3A A:GDP201 4.3 33.2 1.0
PA A:GDP201 4.3 33.6 1.0
OD2 A:ASP60 4.3 35.1 1.0
O2B A:GDP201 4.3 31.5 1.0
CD2 A:TYR35 4.4 68.3 1.0
O2A A:GDP201 4.5 34.0 1.0
O A:ALA62 4.5 46.0 1.0
OD1 A:ASP60 4.6 35.6 1.0
N A:PRO37 4.7 65.2 1.0
C A:ASP36 4.7 66.8 1.0
CB A:PRO37 4.7 65.3 1.0
C A:PRO37 4.8 62.8 1.0
O A:THR61 4.8 37.3 1.0
CG A:ASP60 4.9 34.5 1.0
CE2 A:TYR35 4.9 68.8 1.0
O A:PRO37 5.0 60.0 1.0

Magnesium binding site 2 out of 4 in 5yxh

Go back to Magnesium Binding Sites List in 5yxh
Magnesium binding site 2 out of 4 in the Structure of Rheb-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of Rheb-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg202

b:37.0
occ:1.00
O B:HOH302 2.2 32.4 1.0
O B:HOH303 2.2 38.9 1.0
OG B:SER20 2.2 31.2 1.0
O B:HOH310 2.2 39.4 1.0
O3B B:GDP201 2.2 33.4 1.0
O B:HOH323 2.2 39.8 1.0
CB B:SER20 3.3 29.4 1.0
PB B:GDP201 3.3 33.9 1.0
O2B B:GDP201 3.4 32.0 1.0
CD2 B:TYR35 4.0 63.4 1.0
O2A B:GDP201 4.0 34.0 1.0
N B:SER20 4.2 28.7 1.0
O B:ASP36 4.2 69.8 1.0
CB B:TYR35 4.2 62.7 1.0
O3A B:GDP201 4.2 33.2 1.0
CA B:SER20 4.3 28.8 1.0
OD2 B:ASP60 4.3 31.6 1.0
O B:ALA62 4.3 40.1 1.0
O1B B:GDP201 4.5 33.4 1.0
CA B:PRO37 4.5 69.1 1.0
PA B:GDP201 4.5 32.6 1.0
CG B:TYR35 4.5 62.5 1.0
OD1 B:ASP60 4.6 32.5 1.0
C B:ASP36 4.7 70.3 1.0
O1A B:GDP201 4.7 33.5 1.0
O B:THR61 4.8 36.0 1.0
N B:PRO37 4.8 70.3 1.0
CG B:ASP60 4.9 31.8 1.0
CE2 B:TYR35 4.9 63.6 1.0
O B:TYR35 4.9 65.3 1.0
C B:TYR35 5.0 66.7 1.0

Magnesium binding site 3 out of 4 in 5yxh

Go back to Magnesium Binding Sites List in 5yxh
Magnesium binding site 3 out of 4 in the Structure of Rheb-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of Rheb-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg202

b:36.7
occ:1.00
O C:HOH308 2.2 35.0 1.0
OG C:SER20 2.2 32.6 1.0
O C:HOH312 2.2 38.3 1.0
O C:HOH303 2.2 36.6 1.0
O1B C:GDP201 2.2 38.1 1.0
O C:HOH322 2.2 38.8 1.0
CB C:SER20 3.2 31.2 1.0
PB C:GDP201 3.3 37.9 1.0
O3B C:GDP201 3.5 38.2 1.0
N C:SER20 4.0 31.9 1.0
CD1 C:TYR35 4.0 79.9 1.0
O1A C:GDP201 4.0 35.2 1.0
OD2 C:ASP60 4.1 34.6 1.0
CA C:PRO37 4.1 78.5 1.0
CA C:SER20 4.1 30.9 1.0
CE1 C:TYR35 4.2 81.7 1.0
O C:ASP36 4.3 77.6 1.0
O3A C:GDP201 4.3 36.6 1.0
OD1 C:ASP60 4.4 34.9 1.0
O2B C:GDP201 4.4 37.3 1.0
PA C:GDP201 4.5 35.3 1.0
O C:ALA62 4.6 48.6 1.0
CG C:ASP60 4.6 34.5 1.0
CB C:PRO37 4.6 79.4 1.0
O2A C:GDP201 4.7 36.4 1.0
O C:THR61 4.8 37.4 1.0
N C:PRO37 4.8 78.7 1.0
C C:ASP36 4.8 79.1 1.0

Magnesium binding site 4 out of 4 in 5yxh

Go back to Magnesium Binding Sites List in 5yxh
Magnesium binding site 4 out of 4 in the Structure of Rheb-Gdp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of Rheb-Gdp within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg202

b:39.4
occ:1.00
OG D:SER20 2.2 33.6 1.0
O3B D:GDP201 2.2 36.3 1.0
O D:HOH311 2.2 42.8 1.0
O D:HOH305 2.2 36.8 1.0
O D:HOH301 2.2 36.4 1.0
O D:HOH330 2.2 41.9 1.0
CB D:SER20 3.2 33.0 1.0
PB D:GDP201 3.3 37.1 1.0
O2B D:GDP201 3.6 37.4 1.0
N D:SER20 3.9 32.4 1.0
OD2 D:ASP60 3.9 40.4 1.0
OD1 D:ASP60 4.1 40.0 1.0
CA D:SER20 4.1 31.9 1.0
O D:ASP36 4.2 84.4 1.0
CD2 D:TYR35 4.2 79.9 1.0
O2A D:GDP201 4.2 37.7 1.0
O D:ALA62 4.3 46.0 1.0
O1B D:GDP201 4.3 35.2 1.0
CE2 D:TYR35 4.4 80.7 1.0
O3A D:GDP201 4.4 36.3 1.0
CG D:ASP60 4.4 40.5 1.0
O D:THR61 4.5 38.4 1.0
PA D:GDP201 4.6 39.2 1.0
O1A D:GDP201 4.8 38.0 1.0
CB D:LYS19 4.8 30.7 1.0
CE D:LYS19 4.9 31.3 1.0
O D:PRO37 4.9 78.4 1.0
CA D:PRO37 4.9 81.6 1.0
C D:LYS19 5.0 31.6 1.0

Reference:

S.J.Mahoney, S.Narayan, L.Molz, L.A.Berstler, S.A.Kang, G.P.Vlasuk, E.Saiah. A Small Molecule Inhibitor of Rheb Selectively Targets MTORC1 Signaling. Nat Commun V. 9 548 2018.
ISSN: ESSN 2041-1723
PubMed: 29416044
DOI: 10.1038/S41467-018-03035-Z
Page generated: Mon Dec 14 22:15:34 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy