Magnesium in PDB 5e54: Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser

The structure of Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser, PDB code: 5e54 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)	25.02 / 2.30
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 (%)	21.3 / 25.6

The binding sites of Magnesium atom in the Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser (pdb code 5e54). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser, PDB code: 5e54:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg101 b:49.4 occ:1.00 O B:HOH209 1.9 58.1 1.0 OP1 A:G37 2.0 54.6 1.0 OP1 B:U68 2.2 51.1 1.0 O A:HOH201 2.2 61.9 1.0 O A:HOH204 2.2 53.4 1.0 O B:HOH206 2.2 48.5 1.0 P A:G37 3.5 57.9 1.0 P B:U68 3.7 53.9 1.0 OP2 A:G38 4.2 51.0 1.0 C5' B:U68 4.2 54.0 1.0 O5' A:G37 4.2 54.5 1.0 OP1 B:C27 4.3 47.3 1.0 C5' A:G37 4.3 51.9 1.0 OP2 A:G37 4.3 59.4 1.0 O3' B:C67 4.4 56.0 1.0 O5' B:U68 4.4 50.8 1.0 O3' A:U36 4.4 60.0 1.0 OP2 B:U68 4.7 48.4 1.0

Magnesium binding site 2 out of 4 in the Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:55.4 occ:1.00 O A:HOH203 1.8 55.9 1.0 OP1 A:A52 1.9 59.7 1.0 O B:HOH203 1.9 47.8 1.0 O B:HOH208 2.1 54.3 1.0 O A:HOH202 2.3 60.0 1.0 O B:HOH205 2.3 48.4 1.0 P A:A52 3.2 57.3 1.0 O3' A:U51 3.5 59.0 1.0 C5' A:A52 3.9 55.5 1.0 O5' A:A52 4.0 56.7 1.0 OP1 B:U47 4.2 53.3 1.0 OP1 B:G46 4.3 46.4 1.0 OP2 A:A52 4.3 54.3 1.0 OP2 A:C53 4.4 60.1 1.0 OP2 B:U47 4.4 46.2 1.0 O2' A:U51 4.6 58.2 1.0 P B:U47 4.7 49.8 1.0 C3' A:U51 4.8 58.9 1.0

Magnesium binding site 3 out of 4 in the Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg103 b:77.3 occ:1.00 OP1 A:U22 2.2 93.8 1.0 OP1 A:A23 3.2 0.7 1.0 O3' A:U22 3.4 0.2 1.0 P A:U22 3.5 90.1 1.0 OP1 A:U48 3.6 67.1 1.0 P A:A23 3.9 0.1 1.0 OP2 A:U22 4.0 82.7 1.0 C3' A:U22 4.3 0.4 1.0 O4' A:U47 4.3 58.4 1.0 C4' A:U47 4.3 55.6 1.0 C5 A:U48 4.3 70.4 1.0 O3' A:A21 4.4 97.8 1.0 O5' A:A23 4.4 0.3 1.0 C5' A:A23 4.4 0.5 1.0 O5' A:U22 4.6 92.8 1.0 C5' A:U22 4.6 1.0 1.0 O3' A:U47 4.8 62.9 1.0 P A:U48 4.8 65.4 1.0 C3' A:A21 4.9 97.6 1.0 C4' A:U22 4.9 0.9 1.0 C6 A:U48 4.9 75.5 1.0 C2' A:A21 4.9 93.0 1.0 C1' A:U47 5.0 57.1 1.0

Magnesium binding site 4 out of 4 in the Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Two Apo Structures of the Adenine Riboswitch Aptamer Domain Determined Using An X-Ray Free Electron Laser within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg101 b:68.2 occ:1.00 O B:HOH201 2.0 65.2 1.0 OP2 B:A24 2.1 67.0 1.0 O B:HOH207 2.1 54.8 1.0 O B:HOH202 2.2 78.0 1.0 P B:A24 3.3 62.0 1.0 O5' B:A24 3.9 58.3 1.0 N7 B:A24 4.0 65.9 1.0 OP1 B:A24 4.0 59.8 1.0 O6 B:G72 4.1 67.7 1.0 C8 B:A24 4.1 64.1 1.0 N7 B:G72 4.1 65.3 1.0 O2' B:U22 4.5 68.8 1.0 OP1 B:A23 4.5 67.0 1.0 O3' B:A23 4.6 65.9 1.0 O3' B:U22 4.6 68.0 1.0 C6 B:G72 4.7 69.2 1.0 C5 B:G72 4.7 66.9 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