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 1 of 48 | « 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 3v2f A3086 Oph·Or 2   0.02   0.20   0.82 no 4l6j A5436 Oph·Or 2   0.02   0.41   0.22 no 3d5b A3130 Oph·Or 2   0.02   0.34   0.18 no 4ji1 A1889 Oph·Or 2   0.02   0.21   0.79 no 4l6j A4356 Oph·Or 2   0.02   0.39   0.70 no 2wdh Z192 Oph·Or 2   0.02   0.23   0.81 no 2x9t Z506 Oph·Or 2   0.02   0.30   0.03 no 4dh9 A1689 Oph·Or 2   0.02   0.23   0.74 no 3f1f A5296 Oph·Or 2   0.02   0.35   0.86 no 4nvv A3736 Oph·Or 2   0.03   0.60   0.59 no 3t1h A1629 Oph·Or 2   0.03   0.41   0.04 no 4kfk A1850 Oph·Or 2   0.03   0.25   0.98 no 4dv1 A1770 Oph·Or 2   0.03   0.21   0.90 no 3kix a1685 Oph·Or 2   0.03   0.18   0.59 no 4duy A1676 Oph·Or 2   0.03   0.12   0.90 no 4b3t A2639 Oph·Or 2   0.03   0.44   0.94 no 4dr1 A1827 Oph·Or 2   0.03   0.25   0.93 no 3v29 A3051 Oph·Or 2   0.03   0.51   0.99 no 4l6j A6772 Oph·Or 2   0.03   0.23   0.93 no 3pyo A3434 Oph·Or 2   0.03   0.51   0.88 no 3d5d A3046 Oph·Or 2   0.03   0.31   0.15 no 4qcz A3237 Oph·Or 2   0.03   0.21   0.90 no 4l6j A7981 Oph·Or 2   0.03   0.78   0.78 no 4dv7 A1789 Oph·Or 2   0.03   0.30   0.96 no 4kfk A2258 Oph·Or 2   0.03   0.18   0.97 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>