Atomistry » Magnesium » PDB 6d9m-6dlu » 6dlr
Atomistry »
  Magnesium »
    PDB 6d9m-6dlu »
      6dlr »

Magnesium in PDB 6dlr: Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure

Protein crystallography data

The structure of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure, PDB code: 6dlr 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) 19.54 / 2.66
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 83.520, 92.677, 74.487, 90.00, 121.21, 90.00
R / Rfree (%) 19.7 / 22.2

Other elements in 6dlr:

The structure of Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure also contains other interesting chemical elements:

Potassium (K) 3 atoms
Iridium (Ir) 18 atoms

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked Structure (pdb code 6dlr). 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, Iridium-Hexamine Soaked Structure, PDB code: 6dlr:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6dlr

Go back to Magnesium Binding Sites List in 6dlr
Magnesium binding site 1 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked 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, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg220

b:56.0
occ:1.00
OP2 A:C91 2.2 60.3 1.0
OP1 A:G48 2.2 51.3 1.0
OP1 A:C90 2.2 59.6 1.0
P A:C90 3.4 46.6 1.0
P A:C91 3.5 50.4 1.0
P A:G48 3.6 56.5 1.0
OP2 A:C90 3.8 47.0 1.0
N7 A:G48 4.0 56.5 1.0
O3' A:A47 4.1 55.2 1.0
OP1 A:C91 4.1 56.3 1.0
C8 A:G48 4.3 50.6 1.0
O5' A:C90 4.3 44.6 1.0
O5' A:C91 4.4 48.9 1.0
O2' A:A93 4.5 52.2 1.0
OP2 A:G48 4.5 53.0 1.0
O5' A:G48 4.6 51.4 1.0
O3' A:G89 4.6 51.3 1.0
O3' A:C90 4.6 58.9 1.0
C5' A:C90 4.6 49.3 1.0
OP2 A:G94 4.7 50.7 1.0
O3' A:A93 4.8 47.5 1.0
C3' A:C90 4.9 46.8 1.0

Magnesium binding site 2 out of 3 in 6dlr

Go back to Magnesium Binding Sites List in 6dlr
Magnesium binding site 2 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked 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, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg221

b:75.7
occ:1.00
OP1 A:C91 2.1 56.3 1.0
OP2 A:G48 2.2 53.0 1.0
P A:G48 3.4 56.5 1.0
P A:C91 3.6 50.4 1.0
OP1 A:G48 3.7 51.3 1.0
C5' A:G48 4.0 46.7 1.0
O5' A:G48 4.1 51.4 1.0
O3' A:C90 4.3 58.9 1.0
OP2 A:C91 4.3 60.3 1.0
N2 A:IRI205 4.3 54.9 0.6
O5' A:C91 4.6 48.9 1.0
O3' A:A47 4.6 55.2 1.0
C5' A:C91 4.9 46.2 1.0

Magnesium binding site 3 out of 3 in 6dlr

Go back to Magnesium Binding Sites List in 6dlr
Magnesium binding site 3 out of 3 in the Prpp Riboswitch Bound to Prpp, Iridium-Hexamine Soaked 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, Iridium-Hexamine Soaked Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg222

b:60.6
occ:1.00
O2P A:PRP201 2.0 49.4 1.0
OP2 A:C75 2.4 53.9 1.0
O2 A:U49 2.4 61.3 1.0
P A:PRP201 2.9 46.2 1.0
O3P A:PRP201 3.0 48.9 1.0
O1P A:PRP201 3.5 47.1 1.0
C2 A:U49 3.6 61.4 1.0
P A:C75 3.8 58.3 1.0
O2' A:A74 4.1 45.7 1.0
N3 A:U49 4.2 58.3 1.0
O5' A:C75 4.2 58.1 1.0
O5 A:PRP201 4.3 45.7 1.0
O3' A:A74 4.3 57.9 1.0
C5 A:C75 4.4 49.9 1.0
C2' A:A74 4.5 52.1 1.0
N2 A:G48 4.7 48.2 1.0
N1 A:U49 4.7 54.8 1.0
C6 A:C75 4.7 54.3 1.0
N1 A:G48 4.7 53.8 1.0
N3 A:IRI208 4.7 39.1 0.8
N6 A:IRI208 4.8 76.6 0.8
OP2 A:C76 4.8 54.4 1.0
C5 A:C76 4.8 42.0 1.0
C1' A:U49 4.9 53.7 1.0
OP1 A:C75 5.0 56.0 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 23:10:42 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy