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Manganese 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:

Magnesium (Mg) 8 atoms
Potassium (K) 1 atom
Sodium (Na) 8 atoms

Manganese Binding Sites:

The binding sites of Manganese 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 Manganese atom.
In total 10 binding sites of Manganese where determined in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure, PDB code: 6dmd:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Manganese binding site 1 out of 10 in 6dmd

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Manganese binding site 1 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn202

b:25.9
occ:1.00
 O1B A:G4P201 2.1 28.1 1.0
O2A A:G4P201 2.2 26.3 1.0
N7 A:A3 2.6 30.7 1.0
PB A:G4P201 3.3 27.7 1.0
PA A:G4P201 3.3 26.2 1.0
C8 A:A3 3.3 29.4 1.0
O3A A:G4P201 3.6 26.3 1.0
C5 A:A3 3.7 30.3 1.0
O3B A:G4P201 3.9 26.7 1.0
O5' A:G4P201 3.9 26.9 1.0
N6 A:A3 4.1 32.3 1.0
OP2 A:A3 4.2 27.6 1.0
C6 A:A3 4.3 31.4 1.0
N7 A:A4 4.4 27.1 1.0
O A:HOH307 4.5 17.8 1.0
O2B A:G4P201 4.5 27.7 1.0
N9 A:A3 4.6 29.1 1.0
O1A A:G4P201 4.6 30.2 1.0
O6 A:G5 4.7 29.1 1.0
C4 A:A3 4.7 30.1 1.0
N7 A:G2 4.8 19.9 1.0

Manganese binding site 2 out of 10 in 6dmd

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Manganese binding site 2 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn203

b:37.2
occ:1.00
 OP2 A:A13 2.1 25.9 1.0
N7 A:G14 2.4 24.3 1.0
C8 A:G14 3.3 24.8 1.0
C5 A:G14 3.4 23.6 1.0
P A:A13 3.5 25.2 1.0
O6 A:G14 3.6 25.7 1.0
C6 A:G14 3.9 24.4 1.0
O3' A:U12 4.2 24.3 1.0
OP1 A:A13 4.3 26.8 1.0
N1 A:A41 4.3 22.0 1.0
C3' A:U12 4.5 24.2 1.0
N9 A:G14 4.5 24.9 1.0
C4 A:G14 4.6 23.7 1.0
O5' A:A13 4.6 25.3 1.0
O5' A:U12 4.6 28.9 1.0
C2 A:A41 4.9 21.6 1.0

Manganese binding site 3 out of 10 in 6dmd

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Manganese binding site 3 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn204

b:72.5
occ:1.00
 OP1 A:A13 2.4 26.8 1.0
OP2 A:G14 2.4 30.2 1.0
P A:A13 3.7 25.2 1.0
P A:G14 3.8 30.3 1.0
O5' A:G14 4.3 30.4 1.0
O5' A:A13 4.3 25.3 1.0
OP2 A:A13 4.3 25.9 1.0
C5' A:A13 4.5 26.0 1.0
OP1 A:G14 4.6 28.3 1.0
O3' A:U12 4.9 24.3 1.0
O3' A:A13 4.9 27.5 1.0

Manganese binding site 4 out of 10 in 6dmd

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Manganese binding site 4 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn205

b:50.4
occ:1.00
 OP1 A:A87 2.1 32.8 1.0
OP1 A:G43 2.2 25.9 1.0
OP2 A:C88 2.4 28.6 1.0
P A:A87 3.4 29.3 1.0
P A:G43 3.7 23.9 1.0
N7 A:G43 3.7 21.9 1.0
P A:C88 3.9 31.4 1.0
OP2 A:A87 3.9 29.0 1.0
C8 A:G43 4.0 22.0 1.0
O3' A:A42 4.3 23.6 1.0
O5' A:A87 4.4 27.2 1.0
O3' A:G86 4.4 32.0 1.0
OP2 A:G43 4.5 24.1 1.0
OP1 A:C88 4.5 30.7 1.0
O5' A:G43 4.6 21.4 1.0
C5' A:A87 4.6 26.4 1.0
O5' A:C88 4.7 29.6 1.0
O3' A:A87 4.8 29.8 1.0
C3' A:A87 5.0 27.9 1.0
N4 A:C44 5.0 20.1 1.0

Manganese binding site 5 out of 10 in 6dmd

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Manganese binding site 5 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn206

b:89.1
occ:1.00
 OP2 A:U81 3.8 39.2 1.0
OP1 A:U81 4.2 44.3 1.0
OP2 A:A83 4.3 35.9 1.0
P A:U81 4.3 44.4 1.0
OP2 A:A82 4.3 38.7 1.0
OP1 A:A83 4.5 36.0 1.0
O5' A:U81 4.6 42.8 1.0
P A:A83 4.8 37.1 1.0

Manganese binding site 6 out of 10 in 6dmd

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Manganese binding site 6 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn207

b:59.5
occ:1.00
 O2 A:C44 2.3 25.1 1.0
OP2 A:C72 2.4 30.1 1.0
C2 A:C44 3.2 22.2 1.0
N3 A:C44 3.4 20.1 1.0
O1D A:G4P201 3.8 26.6 1.0
P A:C72 3.8 28.6 1.0
O A:HOH311 4.4 25.6 1.0
O3' A:A71 4.4 30.3 1.0
N1 A:C44 4.5 21.8 1.0
N1 A:G43 4.6 20.9 1.0
O2' A:A71 4.7 31.4 1.0
C4 A:C44 4.7 19.5 1.0
O5' A:C72 4.7 30.2 1.0
OP1 A:C72 4.8 26.8 1.0
C2' A:A71 4.9 30.4 1.0
C1' A:C44 4.9 22.5 1.0
O6 A:G43 4.9 22.6 1.0

Manganese binding site 7 out of 10 in 6dmd

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Manganese binding site 7 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn202

b:60.5
occ:1.00
 O1B B:G4P201 2.3 43.5 1.0
O2A B:G4P201 2.4 48.9 1.0
N7 B:A3 2.6 38.1 1.0
C8 B:A3 3.3 39.1 1.0
PA B:G4P201 3.6 53.3 1.0
C5 B:A3 3.6 37.7 1.0
PB B:G4P201 3.6 46.3 1.0
O3A B:G4P201 3.8 51.0 1.0
OP2 B:A3 3.9 43.0 1.0
N6 B:A3 4.0 35.9 1.0
N7 B:A4 4.0 36.0 1.0
C6 B:A3 4.2 36.2 1.0
O5' B:G4P201 4.4 56.0 1.0
N9 B:A3 4.5 40.1 1.0
O2B B:G4P201 4.6 51.6 1.0
O3B B:G4P201 4.6 44.1 1.0
C4 B:A3 4.7 38.8 1.0
C8 B:A4 4.7 36.8 1.0
OP2 B:G2 4.8 41.3 1.0
N7 B:G2 4.8 28.2 1.0
O6 B:G5 4.8 38.3 1.0
O1A B:G4P201 4.8 55.5 1.0
O5' B:A3 4.9 43.8 1.0
C8 B:G2 5.0 30.0 1.0

Manganese binding site 8 out of 10 in 6dmd

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Manganese binding site 8 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn 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:Mn203

b:74.2
occ:1.00
 OP2 B:C88 2.2 53.2 1.0
OP1 B:G43 2.3 42.3 1.0
OP1 B:A87 2.3 72.9 1.0
P B:A87 3.5 66.8 1.0
N7 B:G43 3.6 55.7 1.0
P B:C88 3.6 55.2 1.0
P B:G43 3.7 40.9 1.0
OP2 B:A87 3.8 67.8 1.0
C8 B:G43 3.8 55.1 1.0
OP1 B:C88 4.2 56.5 1.0
O3' B:A42 4.4 41.8 1.0
O3' B:A87 4.4 58.6 1.0
O3' B:G86 4.5 65.5 1.0
OP2 B:G43 4.6 42.1 1.0
O5' B:C88 4.6 61.6 1.0
O5' B:A87 4.6 60.5 1.0
O5' B:G43 4.7 41.7 1.0
C3' B:A87 4.8 58.9 1.0
N4 B:C44 4.9 44.8 1.0
C5 B:G43 5.0 55.8 1.0
C5' B:A87 5.0 59.3 1.0
OP2 B:C89 5.0 77.0 1.0

Manganese binding site 9 out of 10 in 6dmd

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Manganese binding site 9 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 9 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn204

b:84.1
occ:1.00
 OP2 B:C72 2.4 48.5 1.0
O2 B:C44 2.4 44.9 1.0
C2 B:C44 3.5 46.4 1.0
P B:C72 3.6 51.6 1.0
O3D B:G4P201 3.7 60.2 1.0
O3' B:A71 3.7 51.6 1.0
N3 B:C44 3.9 46.9 1.0
O2' B:A71 4.1 49.0 1.0
N1 B:G43 4.3 56.3 1.0
O5' B:C72 4.3 54.1 1.0
C2' B:A71 4.4 48.9 1.0
C3' B:A71 4.6 49.5 1.0
N2 B:G43 4.7 59.2 1.0
O1D B:G4P201 4.7 59.4 1.0
N1 B:C44 4.7 47.0 1.0
C5 B:C72 4.8 54.7 1.0
PD B:G4P201 4.8 54.3 1.0
OP1 B:C72 4.8 52.3 1.0
C2 B:G43 4.9 57.1 1.0
O6 B:G43 4.9 59.2 1.0
C6 B:G43 5.0 57.4 1.0
C1' B:C44 5.0 46.0 1.0

Manganese binding site 10 out of 10 in 6dmd

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Manganese binding site 10 out of 10 in the Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 10 of Ppgpp Riboswitch Bound to Ppgpp, Manganese Chloride Structure within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn205

b:65.3
occ:1.00
 OP1 B:C88 2.1 56.5 1.0
OP2 B:G43 2.3 42.1 1.0
P B:C88 3.5 55.2 1.0
P B:G43 3.6 40.9 1.0
O3' B:A87 4.1 58.6 1.0
OP1 B:G43 4.1 42.3 1.0
C5' B:G43 4.2 43.0 1.0
OP2 B:C88 4.4 53.2 1.0
O5' B:G43 4.4 41.7 1.0
O5' B:C88 4.5 61.6 1.0
C5' B:C88 4.6 63.9 1.0
O3' B:A42 4.7 41.8 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: Sun Oct 6 04:04:56 2024

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