Magnesium in PDB 5do4: Thrombin-Rna Aptamer Complex

All present enzymatic activity of Thrombin-Rna Aptamer Complex:
3.4.21.5;

The structure of Thrombin-Rna Aptamer Complex, PDB code: 5do4 was solved by P.S.Pallan, M.Egli, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.30 / 1.86
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	83.663, 139.166, 44.511, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.4

The structure of Thrombin-Rna Aptamer Complex also contains other interesting chemical elements:

Fluorine	(F)	8 atoms
Calcium	(Ca)	1 atom

The binding sites of Magnesium atom in the Thrombin-Rna Aptamer Complex (pdb code 5do4). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total only one binding site of Magnesium was determined in the Thrombin-Rna Aptamer Complex, PDB code: 5do4:

Magnesium binding site 1 out of 1 in the Thrombin-Rna Aptamer Complex


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Thrombin-Rna Aptamer Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg102 b:22.8 occ:1.00 O A:HOH211 2.1 34.4 1.0 O A:HOH215 2.2 33.9 1.0 OP2 A:A9 2.2 42.3 1.0 OP2 A:A8 2.3 32.4 1.0 O A:HOH210 2.3 35.6 1.0 O A:HOH202 2.5 17.0 0.5 P A:A8 3.5 34.0 1.0 P A:A9 3.7 37.1 1.0 O3' A:A7 3.8 34.2 1.0 O5' A:A8 4.0 36.4 1.0 N7 A:A9 4.2 38.8 1.0 C3' A:A8 4.3 37.9 1.0 O3' A:A8 4.4 35.1 1.0 ND2 H:ASN184 4.4 28.2 1.0 O A:HOH213 4.5 33.0 1.0 O H:HOH499 4.5 12.6 0.5 O2' A:A7 4.5 30.5 1.0 O5' A:A9 4.5 44.5 1.0 OP1 A:A9 4.6 33.9 1.0 C8 A:A9 4.6 45.2 1.0 O H:HOH411 4.6 31.1 1.0 NH2 H:ARG98 4.6 31.7 1.0 OP1 A:A8 4.8 32.0 1.0 C5' A:A8 5.0 37.2 1.0 OD2 H:ASP183 5.0 32.1 1.0 N7 A:G10 5.0 38.3 1.0 CB H:ASP183 5.0 29.6 1.0

N.D.Abeydeera, M.Egli, N.Cox, K.Mercier, J.N.Conde, P.S.Pallan, D.M.Mizurini, M.Sierant, F.E.Hibti, T.Hassell, T.Wang, F.W.Liu, H.M.Liu, C.Martinez, A.K.Sood, T.P.Lybrand, C.Frydman, R.Q.Monteiro, R.H.Gomer, B.Nawrot, X.Yang. Evoking Picomolar Binding in Rna By A Single Phosphorodithioate Linkage. Nucleic Acids Res. V. 44 8052 2016.
ISSN: ESSN 1362-4962
PubMed: 27566147
DOI: 10.1093/NAR/GKW725