Magnesium in PDB 6d5j: Ras:Sos:Ras in Complex with A Small Molecule Activator

Protein crystallography data

The structure of Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6d5j was solved by J.Phan, T.Hodges, S.W.Fesik, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.72 / 1.75
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 183.627, 183.627, 179.056, 90.00, 90.00, 90.00
R / Rfree (%) 15.7 / 17.5

Other elements in 6d5j:

The structure of Ras:Sos:Ras in Complex with A Small Molecule Activator also contains other interesting chemical elements:

Fluorine (F) 1 atom
Chlorine (Cl) 1 atom
Sodium (Na) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ras:Sos:Ras in Complex with A Small Molecule Activator (pdb code 6d5j). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Ras:Sos:Ras in Complex with A Small Molecule Activator, PDB code: 6d5j:

Magnesium binding site 1 out of 1 in 6d5j

Go back to Magnesium Binding Sites List in 6d5j
Magnesium binding site 1 out of 1 in the Ras:Sos:Ras in Complex with A Small Molecule Activator


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ras:Sos:Ras in Complex with A Small Molecule Activator within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:3.7
occ:1.00
O1G A:GNP201 2.0 17.2 1.0
OG1 A:THR35 2.0 17.4 1.0
O1B A:GNP201 2.0 16.4 1.0
OG A:SER17 2.0 15.8 1.0
O A:HOH344 2.2 18.2 1.0
O A:HOH312 2.2 36.2 1.0
CB A:THR35 3.1 15.2 1.0
CB A:SER17 3.1 14.8 1.0
PB A:GNP201 3.2 15.1 1.0
PG A:GNP201 3.2 16.6 1.0
N3B A:GNP201 3.4 13.6 1.0
N A:THR35 3.8 14.4 1.0
N A:SER17 3.8 13.8 1.0
OD2 A:ASP57 4.0 22.8 1.0
CA A:SER17 4.1 14.0 1.0
CA A:THR35 4.1 14.4 1.0
O A:HOH389 4.1 32.4 1.0
O3G A:GNP201 4.1 17.7 1.0
O2A A:GNP201 4.1 17.9 1.0
OD1 A:ASP57 4.2 19.4 1.0
CG2 A:THR35 4.2 19.0 1.0
O2B A:GNP201 4.3 15.2 1.0
O3A A:GNP201 4.3 15.0 1.0
O2G A:GNP201 4.3 20.1 1.0
O A:ASP33 4.4 17.6 1.0
O A:THR58 4.4 17.5 1.0
CG A:ASP57 4.5 20.8 1.0
PA A:GNP201 4.5 15.9 1.0
O1A A:GNP201 4.6 16.6 1.0
C A:PRO34 4.8 17.4 1.0
CB A:LYS16 4.9 13.0 1.0
C A:LYS16 4.9 13.9 1.0
CE A:LYS16 5.0 14.6 1.0
NZ A:LYS16 5.0 14.6 1.0
CA A:PRO34 5.0 16.9 1.0

Reference:

T.R.Hodges, J.R.Abbott, A.J.Little, D.Sarkar, J.M.Salovich, J.E.Howes, D.T.Akan, J.Sai, A.L.Arnold, C.Browning, M.C.Burns, T.Sobolik, Q.Sun, Y.Beesetty, J.A.Coker, D.Scharn, H.Stadtmueller, O.W.Rossanese, J.Phan, A.G.Waterson, D.B.Mcconnell, S.W.Fesik. Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on Ras. J. Med. Chem. V. 61 8875 2018.
ISSN: ISSN 1520-4804
PubMed: 30205005
DOI: 10.1021/ACS.JMEDCHEM.8B01108
Page generated: Mon Dec 14 22:33:37 2020

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