Magnesium in PDB 6e1u: Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 2: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]-N,N- Dimethylethan-1-Amine

Protein crystallography data

The structure of Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 2: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]-N,N- Dimethylethan-1-Amine, PDB code: 6e1u was solved by T.Numata, C.M.Connelly, J.S.Schneekloth, A.R.Ferre-D'amare, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.68 / 1.94
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.361, 115.361, 58.463, 90.00, 90.00, 120.00
R / Rfree (%) 19 / 20.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 2: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]-N,N- Dimethylethan-1-Amine (pdb code 6e1u). 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 Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 2: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]-N,N- Dimethylethan-1-Amine, PDB code: 6e1u:

Magnesium binding site 1 out of 1 in 6e1u

Go back to Magnesium Binding Sites List in 6e1u
Magnesium binding site 1 out of 1 in the Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 2: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]-N,N- Dimethylethan-1-Amine


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 A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 2: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]-N,N- Dimethylethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg102

b:73.4
occ:1.00
OP2 A:G3 2.5 49.2 1.0
OP2 A:G4 3.1 57.4 1.0
O5' A:G3 3.1 55.6 1.0
O A:HOH218 3.2 48.5 1.0
P A:G3 3.2 57.0 1.0
O A:HOH230 3.7 50.6 1.0
OP1 A:G3 3.9 68.3 1.0
C8 A:G3 4.2 41.0 1.0
C3' A:G3 4.3 46.7 1.0
C5' A:G3 4.3 49.2 1.0
P A:G4 4.4 59.3 1.0
N7 A:G3 4.6 39.5 1.0
O3' A:U2 4.7 59.7 1.0
O3' A:G3 4.7 54.4 1.0
C4' A:G3 4.8 46.1 1.0

Reference:

C.M.Connelly, T.Numata, R.E.Boer, M.H.Moon, R.S.Sinniah, J.J.Barchi, A.R.Ferre-D'amare, J.S.Schneekloth Jr.. Synthetic Ligands For PREQ1RIBOSWITCHES Provide Structural and Mechanistic Insights Into Targeting Rna Tertiary Structure. Nat Commun V. 10 1501 2019.
ISSN: ESSN 2041-1723
PubMed: 30940810
DOI: 10.1038/S41467-019-09493-3
Page generated: Mon Dec 14 22:37:49 2020

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