Magnesium in PDB 5swd: Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State

The structure of Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State, PDB code: 5swd was solved by J.R.Stagno, Y.-X.Wang, Y.Liu, Y.R.Bhandari, C.E.Conrad, G.Nelson, C.Li, D.R.Wendel, T.A.White, A.Barty, R.A.Tuckey, N.A.Zatsepin, T.D.Grant, P.Fromme, K.Tan, X.Ji, J.C.H.Spence, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.92 / 2.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	47.910, 46.720, 92.250, 90.00, 94.06, 90.00
R / Rfree (%)	19.5 / 22.9

The binding sites of Magnesium atom in the Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State (pdb code 5swd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State, PDB code: 5swd:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:62.4 occ:1.00 O B:HOH204 1.9 73.9 1.0 O B:HOH207 2.0 70.8 1.0 OP1 B:U68 2.3 57.4 1.0 OP1 A:G37 2.3 61.0 1.0 O A:HOH206 2.4 71.6 1.0 O A:HOH205 2.5 69.0 1.0 P A:G37 3.7 68.1 1.0 P B:U68 3.7 65.9 1.0 OP1 B:C27 3.9 58.0 1.0 OP2 A:G38 4.1 57.7 1.0 C5' B:U68 4.3 60.8 1.0 O3' B:C67 4.4 60.7 1.0 C5' A:G37 4.4 64.7 1.0 O5' A:G37 4.5 66.0 1.0 O5' B:U68 4.5 54.3 1.0 OP2 A:G37 4.5 80.4 1.0 O3' A:U36 4.7 70.5 1.0 OP2 B:U68 4.8 56.0 1.0

Magnesium binding site 2 out of 3 in the Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:66.6 occ:1.00 OP1 A:A52 1.8 72.8 1.0 O B:HOH206 2.1 60.8 1.0 O A:HOH201 2.2 65.0 1.0 O B:HOH205 2.2 64.4 1.0 O A:HOH207 2.6 66.8 1.0 P A:A52 3.0 64.7 1.0 O3' A:U51 3.2 61.8 1.0 O5' A:A52 4.0 64.3 1.0 C5' A:A52 4.0 65.4 1.0 OP2 A:A52 4.2 58.6 1.0 O2' A:U51 4.2 66.4 1.0 OP1 B:G46 4.3 55.9 1.0 OP1 B:U47 4.4 63.0 1.0 C3' A:U51 4.5 63.9 1.0 OP2 A:C53 4.5 72.3 1.0 OP2 B:U47 4.6 58.1 1.0 P B:U47 4.9 64.2 1.0 C2' A:U51 4.9 62.1 1.0

Magnesium binding site 3 out of 3 in the Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Structure of the Adenine Riboswitch Aptamer Domain in An Intermediate- Bound State within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:82.9 occ:1.00 O B:HOH202 1.9 70.3 1.0 O B:HOH203 1.9 74.7 1.0 OP2 B:A24 2.2 88.0 1.0 O B:HOH201 2.6 74.4 1.0 P B:A24 3.4 74.8 1.0 O5' B:A24 3.9 63.2 1.0 OP1 B:A24 3.9 83.2 1.0 N7 B:G72 4.2 76.8 1.0 N7 B:A24 4.2 78.1 1.0 O2' B:U22 4.2 80.7 1.0 C8 B:A24 4.2 79.4 1.0 O6 B:G72 4.2 79.4 1.0 OP1 B:A23 4.2 84.2 1.0 O3' B:A23 4.7 81.1 1.0 O4 B:U71 4.8 82.4 1.0 O3' B:U22 4.8 87.3 1.0 C5 B:G72 4.9 73.6 1.0 C6 B:G72 4.9 80.0 1.0

J.R.Stagno, Y.Liu, Y.R.Bhandari, C.E.Conrad, S.Panja, M.Swain, L.Fan, G.Nelson, C.Li, D.R.Wendel, T.A.White, J.D.Coe, M.O.Wiedorn, J.Knoska, D.Oberthuer, R.A.Tuckey, P.Yu, M.Dyba, S.G.Tarasov, U.Weierstall, T.D.Grant, C.D.Schwieters, J.Zhang, A.R.Ferre-D'amare, P.Fromme, D.E.Draper, M.Liang, M.S.Hunter, S.Boutet, K.Tan, X.Zuo, X.Ji, A.Barty, N.A.Zatsepin, H.N.Chapman, J.C.Spence, S.A.Woodson, Y.X.Wang. Structures of Riboswitch Rna Reaction States By Mix-and-Inject Xfel Serial Crystallography. Nature V. 541 242 2017.
ISSN: ESSN 1476-4687
PubMed: 27841871
DOI: 10.1038/NATURE20599