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 5 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 4qd1 A3253 Oph·Ob·Nb 3   0.35   0.28   0.75 no 4nvz A3258 Oph·Ob·Nb 3   0.07   0.51   0.63 no 4dv4 A1862 Oph·Ob·Nb 3   0.05   0.82   0.86 no 4nvv A3263 Oph·Ob·Nb 3   0.08   0.41   0.73 no 2xfz Z602 Oph·Ob·Nb 3   0.09   0.66   0.84 no 4dr6 A1912 Oph·Ob·Nb 3   0.10   0.82   0.91 no 4l6j A4771 Oph·Ob·Nb 3   0.07   0.78   0.41 no 3u5h 53849 Oph·Ob·Nb 3   0.06   0.25   0.73 no 3i8h A1875 Oph·Ob·Nb 3   0.10   0.51   0.95 no 3u5d 13848 Oph·Ob·Nb 3   0.08   0.67   0.78 no 3i8g A2105 Oph·Ob·Nb 3   0.19   0.23   0.80 no 4nvz B3007 Oph·Ob·Nb 3   0.11   0.42   0.70 no 3f1f A5973 Oph·Ob·Nb 3   0.06   0.74   0.89 no 3u5h 54525 Oph·Ob·Nb 3   0.07   0.58   0.70 no 4l6j A7548 Oph·Ob·Nb 3   0.06   0.57   0.88 no 4qcy A3034 Oph·Ob·Nb 3   0.15   0.25   0.79 no 3f1g A5061 Oph·Ob·Nb 3   0.04   0.44   0.03 no 3oh7 A3040 Oph·Ob·Nb 3   0.05   0.51   0.90 no 4dr3 A1799 Oph·Ob·Nb 3   0.05   0.61   0.50 no 4dr6 A1797 Oph·Ob·Nb 3   0.06   0.36   0.91 no 1vy3 A3203 Oph·Ob·Nb 3   0.13   0.25   0.56 no 4qcz A3277 Oph·Ob·Nb 3   0.10   0.41   0.65 no 3oi5 A3173 Oph·Ob·Nb 3   0.07   0.45   0.74 no 3i8g A1989 Oph·Ob·Nb 3   0.16   0.26   0.62 no 3i8g A2144 Oph·Ob·Nb 3   0.08   0.51   0.75 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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