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Magnesium in PDB 6dmd: Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure

Protein crystallography data

The structure of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure, PDB code: 6dmd 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) 30.00 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.741, 49.595, 79.365, 90.00, 97.29, 90.00
R / Rfree (%) 21.7 / 27.2

Other elements in 6dmd:

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

Potassium (K) 1 atom
Manganese (Mn) 10 atoms
Sodium (Na) 8 atoms

Magnesium Binding Sites:

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

Magnesium binding site 1 out of 8 in 6dmd

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Magnesium binding site 1 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg213

b:50.2
occ:1.00
 N7 A:G91 4.2 32.5 1.0
O4 A:U92 4.2 27.6 1.0
O6 A:G43 4.3 22.6 1.0
O6 A:G91 4.4 31.7 1.0
O2D A:G4P201 4.4 26.6 1.0
N4 A:C90 4.7 40.2 1.0
O6 A:G76 4.8 40.7 1.0
O A:HOH311 4.9 25.6 1.0

Magnesium binding site 2 out of 8 in 6dmd

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Magnesium binding site 2 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg214

b:28.1
occ:1.00
 OP1 A:C88 2.1 30.7 1.0
OP2 A:G43 2.2 24.1 1.0
P A:C88 3.5 31.4 1.0
P A:G43 3.7 23.9 1.0
O3' A:A87 4.0 29.8 1.0
C5' A:G43 4.3 21.1 1.0
OP2 A:C88 4.3 28.6 1.0
OP1 A:G43 4.3 25.9 1.0
O5' A:G43 4.5 21.4 1.0
O5' A:C88 4.6 29.6 1.0
O3' A:A42 4.7 23.6 1.0
C5' A:C88 5.0 30.7 1.0

Magnesium binding site 3 out of 8 in 6dmd

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Magnesium binding site 3 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg215

b:26.0
occ:1.00
 O1C A:G4P201 2.3 29.9 1.0
PC A:G4P201 3.6 25.2 1.0
O3' A:G4P201 3.9 26.5 1.0
O4 A:U92 4.0 27.6 1.0
O3D A:G4P201 4.0 25.4 1.0
C4 A:U92 4.4 27.6 1.0
O2D A:G4P201 4.4 26.6 1.0
N7 A:G93 4.5 30.1 1.0
O3C A:G4P201 4.5 26.8 1.0
O6 A:G94 4.6 36.4 1.0
O6 A:G93 4.6 34.5 1.0
PD A:G4P201 4.6 27.0 1.0
O2C A:G4P201 4.6 25.4 1.0
N3 A:U92 4.8 28.6 1.0

Magnesium binding site 4 out of 8 in 6dmd

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Magnesium binding site 4 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg216

b:22.6
occ:1.00
 OP2 A:G37 2.2 35.6 1.0
P A:G37 3.6 33.9 1.0
OP1 A:G37 4.2 33.0 1.0
C5' A:G36 4.4 32.8 1.0
O5' A:G37 4.5 33.9 1.0
N7 A:A38 4.5 32.9 1.0
OP2 A:G36 4.6 34.0 1.0
O3' A:G36 4.6 32.8 1.0
OP2 A:A38 4.7 35.7 1.0
N4 A:C39 4.8 26.5 1.0
C3' A:G36 4.9 32.3 1.0
N6 A:A38 5.0 34.1 1.0

Magnesium binding site 5 out of 8 in 6dmd

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Magnesium binding site 5 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg217

b:40.4
occ:1.00
 OP2 A:A97 2.0 37.9 1.0
OP1 A:A96 2.2 50.7 1.0
P A:A97 3.5 41.8 1.0
P A:A96 3.5 48.4 1.0
O5' A:A96 4.2 45.3 1.0
O5' A:A97 4.2 40.4 1.0
OP2 A:A96 4.2 48.1 1.0
O3' A:A96 4.3 41.7 1.0
C3' A:A96 4.3 40.8 1.0
OP1 A:A97 4.5 43.5 1.0
N7 A:A97 4.6 31.2 1.0
O3' A:C95 4.7 56.0 1.0
C8 A:A97 4.7 31.8 1.0
C5' A:A96 4.8 42.6 1.0

Magnesium binding site 6 out of 8 in 6dmd

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Magnesium binding site 6 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg218

b:35.4
occ:1.00
 O2G A:GTP1 2.5 76.1 1.0
O2B A:G4P201 2.7 27.7 1.0
O3A A:GTP1 3.0 63.0 1.0
O1A A:GTP1 3.0 59.3 1.0
O3A A:G4P201 3.4 26.3 1.0
PA A:GTP1 3.6 58.0 1.0
PB A:G4P201 3.6 27.7 1.0
PG A:GTP1 3.8 84.2 1.0
O1A A:G4P201 4.0 30.2 1.0
O1B A:G4P201 4.1 28.1 1.0
O3G A:GTP1 4.1 89.6 1.0
PA A:G4P201 4.2 26.2 1.0
O5' A:GTP1 4.3 46.4 1.0
PB A:GTP1 4.4 77.0 1.0
OP2 A:G2 4.4 28.6 1.0
O3B A:GTP1 4.6 81.8 1.0
O2A A:G4P201 4.6 26.3 1.0
O1B A:GTP1 4.9 70.8 1.0
O2A A:GTP1 4.9 64.9 1.0
O3B A:G4P201 4.9 26.7 1.0
O1G A:GTP1 5.0 77.3 1.0

Magnesium binding site 7 out of 8 in 6dmd

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Magnesium binding site 7 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg209

b:39.2
occ:1.00
 O1C B:G4P201 2.6 55.4 1.0
O2D B:G4P201 3.7 52.9 1.0
O6 B:G94 3.9 54.6 1.0
PC B:G4P201 3.9 54.7 1.0
O3' B:G4P201 4.1 54.0 1.0
O6 B:G93 4.4 50.4 1.0
N7 B:G93 4.5 54.1 1.0
O4 B:U92 4.6 53.6 1.0
O3C B:G4P201 4.8 55.3 1.0
C4 B:U92 4.8 52.6 1.0
PD B:G4P201 4.9 54.3 1.0
N4 B:C72 4.9 51.2 1.0
N3 B:U92 5.0 52.9 1.0
C6 B:G94 5.0 57.1 1.0

Magnesium binding site 8 out of 8 in 6dmd

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Magnesium binding site 8 out of 8 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg210

b:56.2
occ:1.00
 O2A B:GTP1 1.9 63.5 1.0
O2B B:G4P201 2.0 51.6 1.0
O1G B:GTP1 3.2 96.6 1.0
PB B:G4P201 3.3 46.3 1.0
O1A B:G4P201 3.4 55.5 1.0
PA B:GTP1 3.4 60.5 1.0
OP2 B:G2 3.6 41.3 1.0
O3A B:G4P201 3.7 51.0 1.0
PA B:G4P201 4.0 53.3 1.0
O1B B:G4P201 4.0 43.5 1.0
C5' B:GTP1 4.0 44.0 1.0
O1A B:GTP1 4.2 66.0 1.0
O5' B:GTP1 4.3 48.3 1.0
O B:HOH316 4.4 32.0 1.0
O3A B:GTP1 4.4 72.0 1.0
O2A B:G4P201 4.4 48.9 1.0
O3B B:G4P201 4.4 44.1 1.0
PG B:GTP1 4.5 99.9 1.0
O3G B:GTP1 4.7 80.0 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 23:12:50 2024

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