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 9 of 48 | « Previous | Next » | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3uzm A1743 Oph·Or 2   0.04   0.38   0.87 no 4dha A3002 Oph·Or 2   0.04   0.57   0.96 no 4kfh A2535 Oph·Or 2   0.04   0.39   0.69 no 4l6j A5074 Oph·Or 2   0.04   0.46   0.41 no 3i9b A1622 Oph·Or 2   0.04   0.54   0.66 no 3ohk A3145 Oph·Or 2   0.04   0.43   0.97 no 4dv7 A1814 Oph·Or 2   0.04   0.61   0.73 no 4dv1 A1698 Oph·Or 2   0.04   0.12   0.62 no 2v48 G2715 Oph·Or 2   0.04   0.10   0.24 no 3ohz A3138 Oph·Or 2   0.04   0.64   0.90 no 3f1f A5357 Oph·Or 2   0.04   0.27   0.85 no 3pyo A3185 Oph·Or 2   0.04   0.74   0.76 no 3kiy A3058 Oph·Or 2   0.04   0.52   0.69 no 4lfb A1720 Oph·Or 2   0.04   0.41   1.00 no 2j00 Z510 Oph·Or 2   0.04   0.43   0.86 no 1vvs A3237 Oph·Or 2   0.04   0.22   0.37 no 4ji7 A1763 Oph·Or 2   0.04   0.71   1.00 no 2wdg Z510 Oph·Or 2   0.04   0.35   0.94 no 3v2f A3071 Oph·Or 2   0.04   0.39   0.95 no 4ji1 A1847 Oph·Or 2   0.04   0.48   0.91 no 3uz6 A2340 Oph·Or 2   0.04   0.28   0.89 no 4qcp A3192 Oph·Or 2   0.04   0.54   0.96 no 3f1e A5192 Oph·Or 2   0.04   0.51   0.36 no 3oh5 A3127 Oph·Or 2   0.04   0.16   0.98 no 3uz7 A1901 Oph·Or 2   0.04   0.46   0.93 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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