Magnesium in PDB 6e1t: Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine

Protein crystallography data

The structure of Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine, PDB code: 6e1t 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) 57.53 / 1.80
Space group P 63 2 2
Cell size a, b, c (Å), α, β, γ (°) 115.054, 115.054, 58.792, 90.00, 90.00, 120.00
R / Rfree (%) 19.5 / 20.5

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine (pdb code 6e1t). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine, PDB code: 6e1t:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 6e1t

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Magnesium binding site 1 out of 4 in the Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-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 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg103

b:70.7
occ:1.00
OP2 A:A10 2.5 45.3 1.0
OP2 A:C9 3.2 60.8 1.0
O5' A:C9 3.4 58.6 1.0
P A:A10 3.4 49.5 1.0
C5' A:C9 3.5 51.2 1.0
C8 A:G8 3.5 45.2 1.0
N7 A:G8 3.7 47.1 1.0
O3' A:C9 3.7 58.7 1.0
C3' A:G8 3.8 48.1 1.0
OP1 A:A10 3.8 57.1 1.0
P A:C9 3.9 58.1 1.0
C3' A:C9 4.1 52.5 1.0
N9 A:G8 4.1 49.5 1.0
C2' A:G8 4.3 52.6 1.0
C5 A:G8 4.3 45.7 1.0
C4' A:C9 4.3 51.0 1.0
O5' A:G8 4.3 63.1 1.0
O3' A:G8 4.3 54.2 1.0
O A:HOH224 4.5 54.9 1.0
C4 A:G8 4.6 44.0 1.0
OP2 A:G8 4.7 61.5 1.0
C1' A:G8 4.8 53.0 1.0
O5' A:A10 4.8 51.7 1.0
C4' A:G8 5.0 51.7 1.0

Magnesium binding site 2 out of 4 in 6e1t

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Magnesium binding site 2 out of 4 in the Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine


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 A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg104

b:76.3
occ:1.00
OP2 A:G5 2.3 45.6 1.0
O A:HOH274 2.6 34.9 1.0
N7 A:G5 3.1 37.6 1.0
N1 A:HLV102 3.2 48.5 1.0
C8 A:G5 3.3 38.1 1.0
P A:G5 3.5 51.7 1.0
O A:HOH206 3.6 48.9 1.0
C3' A:G4 3.7 41.4 1.0
O5' A:G5 3.7 46.6 1.0
C8 A:G4 4.0 37.2 1.0
O3' A:G4 4.1 49.1 1.0
N7 A:G4 4.2 40.5 1.0
N9 A:G4 4.3 36.5 1.0
C2' A:G4 4.3 41.2 1.0
O5' A:G4 4.3 40.2 1.0
C5 A:G5 4.5 34.6 1.0
C5 A:G4 4.5 35.8 1.0
C4 A:G4 4.6 30.8 1.0
C14 A:HLV102 4.7 46.5 1.0
N9 A:G5 4.7 37.0 1.0
C4' A:G4 4.8 41.9 1.0
C1' A:G4 4.8 32.7 1.0
OP1 A:G5 4.8 47.1 1.0
C5' A:G4 5.0 47.4 1.0

Magnesium binding site 3 out of 4 in 6e1t

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Magnesium binding site 3 out of 4 in the Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg105

b:74.0
occ:1.00
OP2 A:C7 2.2 61.1 1.0
O5' A:U6 3.0 58.6 1.0
OP2 A:U6 3.1 44.8 1.0
C5 A:C7 3.4 39.2 1.0
O A:HOH224 3.4 54.9 1.0
P A:C7 3.4 57.8 1.0
P A:U6 3.5 55.0 1.0
C6 A:C7 3.6 42.3 1.0
O5' A:C7 3.7 56.7 1.0
C3' A:U6 3.8 48.6 1.0
OP1 A:U6 4.0 59.7 1.0
O3' A:U6 4.0 54.2 1.0
C5' A:U6 4.1 48.0 1.0
C6 A:U6 4.4 44.0 1.0
O A:HOH229 4.4 40.6 1.0
O A:HOH203 4.4 41.4 1.0
C4' A:U6 4.5 49.0 1.0
C4 A:C7 4.7 43.4 1.0
OP1 A:C7 4.7 57.5 1.0
C5 A:U6 4.8 42.2 1.0
N1 A:C7 4.9 45.4 1.0
O3' A:G5 5.0 50.0 1.0

Magnesium binding site 4 out of 4 in 6e1t

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Magnesium binding site 4 out of 4 in the Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of A Class I PREQ1 Riboswitch Complexed with A Synthetic Compound 1: 2-[(Dibenzo[B,D]Furan-2-Yl)Oxy]Ethan-1-Amine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg106

b:81.1
occ:1.00
OP2 A:A28 2.4 70.0 1.0
O2 A:U6 3.1 46.7 1.0
C8 A:A28 3.4 48.8 1.0
O5' A:A28 3.5 81.9 1.0
P A:A28 3.5 69.6 1.0
O4' A:C7 3.7 48.7 1.0
C2' A:A28 3.8 58.3 1.0
C4' A:C7 3.9 52.9 1.0
C2 A:U6 4.1 48.5 1.0
O2' A:C7 4.1 54.5 1.0
C1' A:C7 4.2 47.8 1.0
N7 A:A28 4.3 43.3 1.0
O2' A:A28 4.3 65.4 1.0
N9 A:A28 4.4 51.3 1.0
O2' A:U6 4.5 57.3 1.0
C1' A:A28 4.5 56.3 1.0
O3' A:A27 4.5 68.2 1.0
C2' A:U6 4.6 52.4 1.0
C3' A:A27 4.6 63.6 1.0
C2' A:A27 4.6 59.7 1.0
OP1 A:A28 4.6 70.9 1.0
C3' A:A28 4.6 69.2 1.0
C5' A:A28 4.7 79.7 1.0
N3 A:U6 4.7 43.0 1.0
C5' A:C7 4.7 55.8 1.0
C2' A:C7 4.7 48.6 1.0
O4' A:A28 4.8 64.0 1.0
C4' A:A28 5.0 71.6 1.0
C3' A:C7 5.0 54.7 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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