MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2i2t:B2987, See in JSmolClick on the image to toggle views Site type: cis-2Oph·Ob Schematic drawing for cis-2Oph·Ob List of all 312 Mg2+ binding sites with the site type cis-2Oph·Ob 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 4 of 13 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2qam B3505 cis-2Oph·Ob 6   0.91   0.77   0.86 yes 2qam B3480 cis-2Oph·Ob 6   0.92   0.71   0.71 yes 2qao B3496 cis-2Oph·Ob 6   0.95   0.84   0.91 yes 2qao B3521 cis-2Oph·Ob 6   0.85   0.76   0.66 yes 2qba B3480 cis-2Oph·Ob 6   0.95   0.77   0.98 yes 2qbc B3521 cis-2Oph·Ob 6   0.95   0.81   0.67 yes 2qbc B3496 cis-2Oph·Ob 6   0.99   0.90   0.60 yes 2qbe B3480 cis-2Oph·Ob 6   0.81   0.80   0.79 yes 2qbe B3505 cis-2Oph·Ob 6   0.88   0.80   0.93 yes 2qbg B2989 cis-2Oph·Ob 6   0.95   0.87   0.29 no 2qbg B2995 cis-2Oph·Ob 6   0.89   0.79   0.77 yes 2qbi B2987 cis-2Oph·Ob 6   0.72   0.76   0.73 yes 2qbk B2995 cis-2Oph·Ob 6   0.96   0.72   0.56 yes 2qbk B2989 cis-2Oph·Ob 6   0.94   0.95   0.56 yes 2qex 08002 cis-2Oph·Ob 6   0.93   0.89   0.92 yes 2qov B2987 cis-2Oph·Ob 6   0.87   0.71   0.83 yes 2qox B2994 cis-2Oph·Ob 6   0.85   0.69   0.72 yes 2qox B2988 cis-2Oph·Ob 6   0.88   0.87   0.62 yes 2qoz B2987 cis-2Oph·Ob 6   0.95   0.89   0.77 yes 2qp1 B2989 cis-2Oph·Ob 6   0.93   0.90   0.66 yes 2uu9 Z1049 cis-2Oph·Ob 3   0.10   0.64   0.32 no 2uua Z51 cis-2Oph·Ob 3   0.17   0.54   0.63 no 2uub Z1089 cis-2Oph·Ob 3   0.18   0.48   0.83 no 2uub Z1051 cis-2Oph·Ob 3   0.13   0.70   0.65 no 2uuc Z1046 cis-2Oph·Ob 3   0.12   0.72   0.66 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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