MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3428, See in JSmolClick on the image to toggle views Site type: Oph·Or Schematic drawing for Oph·Or List of all 1185 Mg2+ binding sites with the site type Oph·Or in RNA crystal structures in the full dataset (switch to benchmark dataset) Sites in the table can be ordered by the following fields by clicking the column header: "benchmark dataset", "Coordination Number", "Qv #", "Qs #", "Qe #", "PDB ID" or "Mg2+ ID" Page 6 of 48 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vxm A1611 Oph·Or 2   0.13   0.18   0.13 no 1vxm A1640 Oph·Or 4   0.95   0.55   0.42 no 1vxm A1633 Oph·Or 2   0.04   0.16   0.43 no 1vxn A3139 Oph·Or 2   0.11   0.23   0.61 no 1vxn A3245 Oph·Or 2   0.04   0.20   0.57 no 1vxn A3168 Oph·Or 2   0.07   0.18   0.76 no 1vxq A3093 Oph·Or 2   0.09   0.22   0.31 no 1vxq A3228 Oph·Or 2   0.04   0.11   0.86 no 1vxs A1613 Oph·Or 2   0.15   0.12   0.33 no 1vxt A3222 Oph·Or 2   0.11   0.23   0.77 no 1vxt A3115 Oph·Or 2   0.08   0.79   0.84 no 1vxt A3213 Oph·Or 2   0.06   0.46   0.81 no 1vxt A3088 Oph·Or 2   0.06   0.14   0.06 no 1vxt A3161 Oph·Or 2   0.07   0.28   0.89 no 1vy1 A3178 Oph·Or 2   0.07   0.33   0.43 no 1vy1 A3165 Oph·Or 2   0.08   0.79   0.67 no 1vy1 A3147 Oph·Or 2   0.08   0.24   0.63 no 1vy1 A3097 Oph·Or 2   0.09   0.12   0.17 no 1vy2 A1671 Oph·Or 2   0.21   0.17   0.82 no 1vy2 A1612 Oph·Or 2   0.23   0.03   0.23 no 1vy3 A3115 Oph·Or 2   0.09   0.68   0.69 no 1vy3 A3087 Oph·Or 2   0.09   0.13   0.20 no 1vy3 A3201 Oph·Or 2   0.11   0.53   0.58 no 1w2b 38093 Oph·Or 6   0.25   0.97   0.60 no 1xmo A1578 Oph·Or 2   0.31   0.09   0.29 no

^# Validation parameters Q_v, Q_s, Q_e are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Q_v measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg²⁺ (+2)
Q_s measures the geometrical symmetry of the ligands distribution around the Mg²⁺ required for octahedral geometry
Q_e measures the agreement of the isotropic atomic displacement (B) factor and occupancy of the Mg²⁺ compared to those of all atoms in its environment

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
Abbreviations used for Mg2+ "Site type"	Mg2+ inner-sphere ligands	Geometry for inner-sphere OP	Mg2+ outer-sphere moieties
	Oph phosphate oxygen (OP1/OP2) Or ribose oxygen (O2'/O4')      or oxygen bridging phosphate and ribose (O3'/O5') Ob nucleobase oxygen      Nb nucleobase nitrogen	cis- two OP ligands adopt cis- isoform trans- two OP ligands adopt trans- isoform fac- three OP ligands adopt fac- isoform mer- three OP ligands adopt mer- isoform	Pout phosphate moiety Rout ribose moiety Bout nucleobase moiety
Reference:	Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W. (2015) Magnesium binding architectures in RNA crystal structures: validation, binding preferences, classification, and motif detection. Nucleic Acid Research 43(7):3789-801 [Pubmed].

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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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