MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2v48:G2217, See in JSmolClick on the image to toggle views Site type: Oph·Ob·Nb Schematic drawing for Oph·Ob·Nb List of all 149 Mg2+ binding sites with the site type Oph·Ob·Nb 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 3 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vvq A3119 Oph·Ob·Nb 3   0.66   0.23   0.56 no 3oi5 A3110 Oph·Ob·Nb 3   0.05   0.48   0.88 no 3hux A3077 Oph·Ob·Nb 3   0.06   0.64   0.74 no 1vxl A3062 Oph·Ob·Nb 3   0.44   0.13   0.51 no 1vvy A3061 Oph·Ob·Nb 3   0.39   0.12   0.77 no 4kix A3056 Oph·Ob·Nb 5   0.37   0.55   0.46 no 1vy1 A3048 Oph·Ob·Nb 3   0.53   0.07   0.08 no 1vvy A3043 Oph·Ob·Nb 3   0.36   0.30   0.49 no 3oh7 A3040 Oph·Ob·Nb 3   0.05   0.51   0.90 no 4nvu A3036 Oph·Ob·Nb 3   0.09   0.39   0.98 no 4nvu A3035 Oph·Ob·Nb 3   0.16   0.26   0.82 no 4qcy A3034 Oph·Ob·Nb 3   0.15   0.25   0.79 no 3v23 A3027 Oph·Ob·Nb 3   0.05   0.50   0.99 no 4qcn A3021 Oph·Ob·Nb 3   0.05   0.59   0.86 no 4kj9 A3020 Oph·Ob·Nb 5   0.45   0.42   0.66 no 4qcx A3019 Oph·Ob·Nb 3   0.12   0.49   0.91 no 4qcy A3010 Oph·Ob·Nb 3   0.08   0.49   0.69 no 4nvz B3007 Oph·Ob·Nb 3   0.11   0.42   0.70 no 3pyr A3004 Oph·Ob·Nb 3   0.05   0.84   0.83 no 3ms1 A2968 Oph·Ob·Nb 3   0.06   0.56   0.50 no 3kno A2965 Oph·Ob·Nb 3   0.23   0.18   0.34 no 4b3m A2745 Oph·Ob·Nb 3   0.09   0.64   0.77 no 4b3t A2705 Oph·Ob·Nb 3   0.11   0.56   0.71 no 4b3r A2699 Oph·Ob·Nb 3   0.09   0.79   0.65 no 4b3m A2685 Oph·Ob·Nb 3   0.05   0.54   0.81 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/)
For any help please contact <dust@iwonka.med.virginia.edu>