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Magnesium in PDB 6dlt: Prpp Riboswitch Bound to Prpp, Native Structure

Protein crystallography data

The structure of Prpp Riboswitch Bound to Prpp, Native Structure, PDB code: 6dlt was solved by A.Peselis, A.Serganov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.567, 90.756, 74.174, 90.00, 122.00, 90.00
R / Rfree (%) 22.5 / 24.3

Other elements in 6dlt:

The structure of Prpp Riboswitch Bound to Prpp, Native Structure also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Prpp Riboswitch Bound to Prpp, Native Structure (pdb code 6dlt). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Prpp Riboswitch Bound to Prpp, Native Structure, PDB code: 6dlt:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6dlt

Go back to Magnesium Binding Sites List in 6dlt
Magnesium binding site 1 out of 3 in the Prpp Riboswitch Bound to Prpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Prpp Riboswitch Bound to Prpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:53.1
occ:1.00
OP2 A:C91 2.1 45.6 1.0
OP1 A:C90 2.1 51.0 1.0
OP1 A:G48 2.2 53.6 1.0
P A:C90 3.3 49.8 1.0
P A:C91 3.5 55.2 1.0
P A:G48 3.6 54.4 1.0
OP2 A:C90 3.7 42.0 1.0
O A:HOH301 3.7 42.9 1.0
O3' A:A47 4.1 49.3 1.0
OP1 A:C91 4.1 49.3 1.0
O5' A:C90 4.1 45.6 1.0
N7 A:G48 4.2 52.5 1.0
O5' A:C91 4.3 40.1 1.0
OP2 A:G48 4.5 55.9 1.0
C8 A:G48 4.5 48.3 1.0
O3' A:G89 4.5 42.9 1.0
O2' A:A93 4.5 44.6 1.0
O3' A:C90 4.6 49.6 1.0
OP2 A:G94 4.6 43.5 1.0
C5' A:C90 4.6 44.3 1.0
O5' A:G48 4.7 54.9 1.0
O3' A:A93 4.8 49.6 1.0
C3' A:C90 4.8 40.9 1.0

Magnesium binding site 2 out of 3 in 6dlt

Go back to Magnesium Binding Sites List in 6dlt
Magnesium binding site 2 out of 3 in the Prpp Riboswitch Bound to Prpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Prpp Riboswitch Bound to Prpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:53.1
occ:1.00
OP1 A:C91 2.2 49.3 1.0
OP2 A:G48 2.5 55.9 1.0
P A:C91 3.6 55.2 1.0
P A:G48 3.8 54.4 1.0
O3' A:C90 4.1 49.6 1.0
OP1 A:G48 4.4 53.6 1.0
C5' A:G48 4.4 54.6 1.0
O5' A:C91 4.6 40.1 1.0
O5' A:G48 4.6 54.9 1.0
OP2 A:C91 4.6 45.6 1.0
C5' A:C91 4.7 36.0 1.0

Magnesium binding site 3 out of 3 in 6dlt

Go back to Magnesium Binding Sites List in 6dlt
Magnesium binding site 3 out of 3 in the Prpp Riboswitch Bound to Prpp, Native Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Prpp Riboswitch Bound to Prpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg203

b:59.6
occ:1.00
O2P A:PRP207 2.2 49.2 1.0
O2 A:U49 2.7 53.5 1.0
OP2 A:C75 2.8 55.5 1.0
P A:PRP207 3.1 52.9 1.0
O3P A:PRP207 3.2 53.2 1.0
C2 A:U49 3.8 56.6 1.0
O1P A:PRP207 3.8 47.9 1.0
P A:C75 4.0 58.3 1.0
O5' A:C75 4.1 56.3 1.0
N3 A:U49 4.2 54.5 1.0
OP2 A:C76 4.2 44.8 1.0
C5 A:C75 4.4 51.4 1.0
O2' A:A74 4.5 54.5 1.0
O5 A:PRP207 4.5 55.1 1.0
C6 A:C75 4.6 48.6 1.0
O3' A:A74 4.6 55.5 1.0
C5 A:C76 4.7 44.4 1.0
N1 A:U49 5.0 57.0 1.0

Reference:

A.Peselis, A.Serganov. Ykkc Riboswitches Employ An Add-on Helix to Adjust Specificity For Polyanionic Ligands. Nat. Chem. Biol. V. 14 887 2018.
ISSN: ESSN 1552-4469
PubMed: 30120360
DOI: 10.1038/S41589-018-0114-4
Page generated: Mon Sep 30 23:12:00 2024

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