Atomistry » Sodium » PDB 6d50-6dmi » 6dmc
Atomistry »
  Sodium »
    PDB 6d50-6dmi »
      6dmc »

Sodium in PDB 6dmc: Ppgpp Riboswitch Bound to Ppgpp, Native Structure

Protein crystallography data

The structure of Ppgpp Riboswitch Bound to Ppgpp, Native Structure, PDB code: 6dmc 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 / 2.20
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.162, 48.917, 78.723, 90.00, 97.33, 90.00
R / Rfree (%) 22.8 / 25.9

Other elements in 6dmc:

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

Magnesium (Mg) 21 atoms
Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure (pdb code 6dmc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 10 binding sites of Sodium where determined in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure, PDB code: 6dmc:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Sodium binding site 1 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 1 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na214

b:58.5
occ:1.00
 OP2 A:C11 2.8 47.6 1.0
N7 A:A41 3.7 26.0 1.0
P A:C11 4.2 49.9 1.0
OP2 A:A41 4.3 29.1 1.0
O A:HOH376 4.4 29.6 1.0
C8 A:A41 4.4 26.2 1.0
O A:HOH335 4.6 29.1 1.0
N6 A:A41 4.6 26.6 1.0
C5 A:A41 4.6 25.9 1.0
OP2 A:C40 4.7 32.5 1.0
OP1 A:C11 4.8 49.0 1.0
O5' A:C11 4.8 45.4 1.0

Sodium binding site 2 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 2 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na215

b:36.0
occ:1.00
 O A:HOH425 2.0 33.8 1.0
O A:HOH374 2.2 34.1 1.0
O A:HOH321 2.3 33.1 1.0
O A:HOH338 4.0 45.0 1.0
O A:HOH342 4.6 34.8 1.0
OP2 A:A31 4.7 45.9 1.0
N7 A:G32 4.8 32.3 1.0
O6 A:G32 4.9 30.3 1.0
O A:HOH414 4.9 13.6 1.0
O6 A:G33 5.0 26.9 1.0

Sodium binding site 3 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 3 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na216

b:58.2
occ:1.00
 O6 A:G26 4.9 43.5 1.0
N7 A:G26 4.9 40.8 1.0

Sodium binding site 4 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 4 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na217

b:27.9
occ:1.00
 O A:HOH424 2.0 18.0 1.0
O A:HOH332 2.0 22.4 1.0
O A:HOH330 2.1 32.5 1.0
O A:HOH327 2.2 14.4 1.0
O A:HOH347 2.2 23.8 1.0
O A:HOH419 2.3 31.2 1.0
OP1 A:C44 3.9 24.4 1.0
OP2 A:C44 4.1 22.4 1.0
N7 A:G45 4.1 29.1 1.0
O A:HOH420 4.2 41.2 1.0
O6 A:G45 4.2 25.6 1.0
N7 A:G46 4.3 29.8 1.0
O6 A:G46 4.3 27.6 1.0
P A:C44 4.5 24.7 1.0
C5 A:G45 4.6 28.2 1.0
C6 A:G45 4.6 27.3 1.0
O A:HOH390 4.7 40.1 1.0
O A:HOH355 4.8 27.6 1.0

Sodium binding site 5 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 5 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na218

b:56.0
occ:1.00
 O2 A:C19 3.7 37.7 1.0
N2 A:G37 3.9 31.9 1.0
O2' A:C19 4.0 41.5 1.0
O2' A:A38 4.4 32.1 1.0
C2' A:C19 4.7 41.2 1.0
C2 A:C19 4.9 38.2 1.0

Sodium binding site 6 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 6 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na219

b:45.8
occ:1.00
 C4' A:U100 4.6 45.9 1.0
O2' A:C53 4.9 72.3 1.0
C5' A:U100 5.0 48.3 1.0

Sodium binding site 7 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 7 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 7 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na211

b:53.1
occ:1.00
 O B:HOH306 2.3 34.7 1.0
O B:HOH330 2.3 42.3 1.0
O B:HOH329 2.4 49.8 1.0
O6 B:G46 4.1 50.1 1.0
O6 B:G45 4.3 46.3 1.0
O B:HOH340 4.3 38.5 1.0
N7 B:G46 4.5 53.8 1.0
O4 B:U47 4.6 56.8 1.0
OP1 B:C44 4.6 34.3 1.0
O B:HOH307 4.6 39.6 1.0
OP2 B:C44 4.7 35.5 1.0
N6 B:A9 4.8 54.8 1.0
C5' B:A42 4.8 44.1 1.0
N7 B:G45 4.9 42.1 1.0
C6 B:G45 4.9 43.5 1.0
O5' B:A42 5.0 46.4 1.0

Sodium binding site 8 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 8 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 8 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na212

b:48.8
occ:1.00
 O B:HOH327 2.3 46.1 1.0
O B:HOH342 2.4 46.0 1.0
N7 B:G32 2.9 34.4 1.0
O B:HOH323 2.9 36.5 1.0
O B:HOH328 3.4 40.7 1.0
C8 B:G32 3.8 35.2 1.0
O6 B:G32 3.8 31.7 1.0
C5 B:G32 3.9 34.5 1.0
N7 B:A31 3.9 34.2 1.0
C6 B:G32 4.2 32.9 1.0
C5 B:A31 4.4 34.2 1.0
C8 B:A31 4.5 34.6 1.0
N6 B:A31 4.6 34.5 1.0
C6 B:A31 4.7 34.7 1.0
OP2 B:G32 5.0 41.1 1.0

Sodium binding site 9 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 9 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 9 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na213

b:58.5
occ:1.00
 OP1 B:G66 2.2 43.0 1.0
O B:HOH312 2.3 37.2 1.0
O B:HOH314 2.4 35.0 1.0
P B:G66 3.6 43.5 1.0
O5' B:G66 4.4 41.5 1.0
C5' B:G66 4.4 41.6 1.0
OP2 B:G66 4.4 41.7 1.0
O3' B:G65 4.6 45.1 1.0
OP2 B:U67 4.6 41.6 1.0

Sodium binding site 10 out of 10 in 6dmc

Go back to Sodium Binding Sites List in 6dmc
Sodium binding site 10 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Native Structure


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 10 of Ppgpp Riboswitch Bound to Ppgpp, Native Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na214

b:60.9
occ:1.00
 C4' B:G61 5.0 78.6 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: Tue Oct 8 07:44:20 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy