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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

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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

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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

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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

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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

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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

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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

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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

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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

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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

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