Atomistry » Magnesium » PDB 4qh0-4qpm » 4qlm
Atomistry »
  Magnesium »
    PDB 4qh0-4qpm »
      4qlm »

Magnesium in PDB 4qlm: Ydao Riboswitch Binding to C-Di-Amp

Protein crystallography data

The structure of Ydao Riboswitch Binding to C-Di-Amp, PDB code: 4qlm was solved by A.M.Ren, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.64 / 2.72
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 78.767, 87.975, 145.235, 90.00, 90.00, 90.00
R / Rfree (%) 21.3 / 24.4

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Ydao Riboswitch Binding to C-Di-Amp (pdb code 4qlm). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Ydao Riboswitch Binding to C-Di-Amp, PDB code: 4qlm:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 4qlm

Go back to Magnesium Binding Sites List in 4qlm
Magnesium binding site 1 out of 2 in the Ydao Riboswitch Binding to C-Di-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ydao Riboswitch Binding to C-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg201

b:88.8
occ:1.00
OP2 A:G28 2.0 71.5 1.0
O A:HOH332 2.0 62.7 1.0
O A:HOH331 2.1 0.8 1.0
OP1 A:G96 2.1 0.6 1.0
O4 A:U98 2.1 91.7 1.0
OP2 A:C97 2.1 78.4 1.0
C4 A:U98 3.0 82.2 1.0
P A:G28 3.4 83.0 1.0
C5 A:U98 3.4 72.0 1.0
P A:G96 3.5 0.7 1.0
P A:C97 3.6 80.9 1.0
N7 A:G28 3.8 73.6 1.0
O5' A:G28 3.9 80.1 1.0
O3' A:A95 3.9 0.7 1.0
C8 A:G28 4.1 65.2 1.0
O5' A:G27 4.1 64.7 1.0
C5 A:C97 4.2 0.5 1.0
OP1 A:C97 4.3 86.8 1.0
N3 A:U98 4.3 85.0 1.0
OP2 A:G96 4.3 82.5 1.0
OP1 A:G28 4.3 85.5 1.0
O3' A:G27 4.4 81.3 1.0
C3' A:G27 4.5 73.2 1.0
O5' A:C97 4.5 92.7 1.0
O3' A:G96 4.5 83.1 1.0
O5' A:G96 4.6 97.8 1.0
C3' A:G96 4.7 86.6 1.0
C5' A:G27 4.7 70.7 1.0
C6 A:U98 4.8 71.7 1.0
OP1 A:G27 4.8 77.9 1.0
C6 A:C97 4.8 0.3 1.0
OP2 A:A29 4.8 82.5 1.0
P A:G27 4.8 76.8 1.0
O A:HOH321 5.0 81.4 1.0

Magnesium binding site 2 out of 2 in 4qlm

Go back to Magnesium Binding Sites List in 4qlm
Magnesium binding site 2 out of 2 in the Ydao Riboswitch Binding to C-Di-Amp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ydao Riboswitch Binding to C-Di-Amp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg202

b:69.5
occ:1.00
O4' A:A73 2.4 75.7 1.0
OP1 A:U72 3.2 72.5 1.0
C4' A:A73 3.3 70.9 1.0
C1' A:A73 3.3 74.9 1.0
OP1 A:U75 3.6 91.4 1.0
N9 A:A73 3.7 76.8 1.0
C5' A:A73 4.0 68.7 1.0
C4 A:A73 4.3 83.7 1.0
C8 A:A73 4.4 76.4 1.0
P A:U75 4.4 89.1 1.0
C3' A:A73 4.5 76.1 1.0
P A:U72 4.5 75.8 1.0
OP1 A:C7 4.5 83.1 1.0
N3 A:A73 4.5 90.3 1.0
C2' A:A73 4.6 79.0 1.0
O3' A:C74 4.6 82.1 1.0
O3' A:A73 4.6 85.9 1.0
OP2 A:U75 4.7 84.5 1.0
OP2 A:U72 4.8 63.1 1.0
O3' A:G6 4.8 95.7 1.0
O5' A:A73 4.9 71.3 1.0

Reference:

A.Ren, D.J.Patel. C-Di-Amp Binds the Ydao Riboswitch in Two Pseudo-Symmetry-Related Pockets. Nat.Chem.Biol. V. 10 780 2014.
ISSN: ISSN 1552-4450
PubMed: 25086509
DOI: 10.1038/NCHEMBIO.1606
Page generated: Tue Aug 20 02:03:05 2024

Last articles

Sr in 3BNQ
Sr in 2X53
Sr in 2SPT
Sr in 2QJY
Sr in 2XRM
Sr in 2WOH
Sr in 2RIO
Sr in 2PN4
Sr in 2QJP
Sr in 2HMP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy