Magnesium in PDB 5kpy: Structure of A 5-Hydroxytryptophan Aptamer

The structure of Structure of A 5-Hydroxytryptophan Aptamer, PDB code: 5kpy was solved by R.T.Batey, E.Porter, M.Merck, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.33 / 2.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	127.553, 26.594, 63.367, 90.00, 106.32, 90.00
R / Rfree (%)	21.7 / 25.8

The structure of Structure of A 5-Hydroxytryptophan Aptamer also contains other interesting chemical elements:

Iridium

(Ir)

12 atoms

The binding sites of Magnesium atom in the Structure of A 5-Hydroxytryptophan Aptamer (pdb code 5kpy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Structure of A 5-Hydroxytryptophan Aptamer, PDB code: 5kpy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg114 b:17.3 occ:1.00 O2 A:C77 4.3 25.3 1.0 O2' A:C77 4.5 29.7 1.0

Magnesium binding site 2 out of 6 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg115 b:40.2 occ:1.00 O A:HOH251 3.0 36.2 0.8 O A:HOH308 3.4 33.9 1.0 OP2 A:C77 3.6 28.7 1.0 O A:HOH268 4.1 27.8 0.8 N7 A:G78 4.2 28.3 1.0 P A:C77 4.5 30.6 1.0 OP1 A:C77 4.5 32.9 1.0 O6 A:G78 4.5 27.3 1.0 O5' A:C77 4.9 28.2 1.0

Magnesium binding site 3 out of 6 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg116 b:30.3 occ:1.00 O A:HOH252 2.5 19.6 1.0 O A:HOH249 2.7 20.0 1.0 O A:HOH247 2.9 19.1 0.9 O6 A:G20 3.9 19.8 1.0 OP2 A:C18 4.6 30.3 1.0 OP2 A:A74 4.7 16.5 1.0 O4 A:U19 4.7 22.3 1.0

Magnesium binding site 4 out of 6 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg117 b:38.3 occ:1.00 O2 A:C60 2.3 35.4 1.0 C2 A:A66 3.1 41.8 1.0 C2 A:U67 3.2 35.4 1.0 O2 A:U67 3.3 36.6 1.0 O4' A:C61 3.3 39.7 1.0 O2' A:C60 3.3 35.3 1.0 N2 A:G38 3.3 37.1 1.0 C1' A:C61 3.4 39.0 1.0 C2 A:C60 3.5 34.4 1.0 N1 A:A66 3.5 40.9 1.0 N1 A:U67 3.6 37.9 1.0 C2' A:C60 3.6 36.0 1.0 N3 A:U67 3.6 33.7 1.0 N1 A:C61 3.7 37.2 1.0 C1' A:C60 3.8 34.2 1.0 C1' A:U67 4.0 39.6 1.0 C6 A:C61 4.1 37.8 1.0 N3 A:A66 4.1 45.1 1.0 N1 A:C60 4.2 33.5 1.0 C6 A:U67 4.2 38.2 1.0 C4 A:U67 4.3 35.1 1.0 C2 A:C61 4.3 37.5 1.0 N3 A:C60 4.5 34.1 1.0 O2 A:C61 4.5 39.5 1.0 C5 A:U67 4.6 38.2 1.0 C2 A:G38 4.6 36.8 1.0 C4' A:C61 4.6 40.8 1.0 O4' A:U67 4.7 42.3 1.0 C2' A:C61 4.8 41.4 1.0 C6 A:A66 4.9 42.5 1.0 N1 A:A59 5.0 29.9 1.0 C5 A:C61 5.0 37.0 1.0 O2' A:C61 5.0 43.0 1.0

Magnesium binding site 5 out of 6 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg118 b:20.1 occ:1.00 O2' A:A48 2.7 15.7 1.0 N3 A:A48 3.0 15.7 1.0 C2' A:A48 3.1 16.6 1.0 OP2 A:U51 3.3 19.8 1.0 C1' A:A48 3.4 15.9 1.0 CH2 A:4PQ101 3.7 15.6 1.0 O A:HOH269 3.7 17.9 0.9 C4 A:A48 3.8 16.1 1.0 C2 A:A48 3.9 16.5 1.0 O5' A:U51 4.0 18.5 1.0 N9 A:A48 4.0 16.0 1.0 P A:U51 4.0 21.1 1.0 CZ3 A:4PQ101 4.3 16.3 1.0 CZ2 A:4PQ101 4.3 15.9 1.0 OAD A:4PQ101 4.4 17.3 1.0 OP1 A:U51 4.4 17.7 1.0 O2 A:C75 4.5 18.4 1.0 C5' A:A49 4.5 16.6 1.0 C3' A:A48 4.6 15.2 1.0 O4' A:U51 4.6 19.6 1.0 O4' A:A48 4.7 15.4 1.0 C2 A:C75 4.9 19.2 1.0 O A:HOH294 4.9 20.6 0.8 N2 A:G47 5.0 16.5 1.0

Magnesium binding site 6 out of 6 in the Structure of A 5-Hydroxytryptophan Aptamer


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of A 5-Hydroxytryptophan Aptamer within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg119 b:25.6 occ:1.00 HN43 A:IRI106 2.0 21.8 1.0 HN52 A:IRI106 2.4 19.8 1.0 O A:4PQ101 2.6 17.6 1.0 N4 A:IRI106 2.9 18.2 1.0 N5 A:IRI106 3.2 16.5 1.0 HN41 A:IRI106 3.3 21.8 1.0 HN42 A:IRI106 3.3 21.8 1.0 C A:4PQ101 3.4 16.6 1.0 C4' A:U46 3.5 16.5 1.0 OXT A:4PQ101 3.5 16.1 1.0 HN51 A:IRI106 3.5 19.8 1.0 O4' A:U46 3.6 15.4 1.0 O A:HOH236 3.7 22.2 0.8 HN53 A:IRI106 3.9 19.8 1.0 O2' A:U45 3.9 18.7 1.0 C5' A:U46 3.9 17.7 1.0 HN31 A:IRI106 4.0 18.7 1.0 IR A:IRI106 4.3 17.4 1.0 C1' A:U46 4.5 17.0 1.0 CD1 A:4PQ101 4.6 16.4 1.0 N3 A:IRI106 4.6 15.6 1.0 O A:HOH240 4.7 17.1 0.7 O2' A:U46 4.7 16.8 1.0 C2' A:U45 4.7 17.0 1.0 HN13 A:IRI106 4.7 16.6 1.0 C3' A:U46 4.8 16.3 1.0 CA A:4PQ101 4.8 16.5 1.0 O2 A:U45 5.0 15.5 1.0 C2' A:U46 5.0 15.8 1.0

E.B.Porter, J.T.Polaski, M.M.Morck, R.T.Batey. Recurrent Rna Motifs As Scaffolds For Genetically Encodable Small-Molecule Biosensors. Nat. Chem. Biol. V. 13 295 2017.
ISSN: ESSN 1552-4469
PubMed: 28092358
DOI: 10.1038/NCHEMBIO.2278