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 1 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 1ffk 02926 cis-2Oph·Ob 6   0.52   0.84   0.93 yes 1fjg A1564 cis-2Oph·Ob 3   0.14   0.55   0.65 no 1hnx A1563 cis-2Oph·Ob 3   0.14   0.60   0.56 no 1i94 A1543 cis-2Oph·Ob 3   0.22   0.60   0.88 no 1i97 A1546 cis-2Oph·Ob 3   0.14   0.48   0.97 no 1ibl A1562 cis-2Oph·Ob 3   0.12   0.51   0.40 no 1ibm A1561 cis-2Oph·Ob 3   0.13   0.61   0.39 no 1jj2 08002 cis-2Oph·Ob 6   0.95   0.95   0.92 yes 1k73 A8002 cis-2Oph·Ob 6   0.93   0.88   0.81 yes 1k8a A8002 cis-2Oph·Ob 6   0.92   0.90   0.75 yes 1k9m A8002 cis-2Oph·Ob 6   0.72   0.67   0.66 yes 1kc8 A8002 cis-2Oph·Ob 6   0.93   0.79   0.97 yes 1kd1 A8002 cis-2Oph·Ob 6   0.96   0.81   0.93 yes 1kqs 08002 cis-2Oph·Ob 6   0.80   0.80   0.71 yes 1m1k A8002 cis-2Oph·Ob 6   0.79   0.98   0.96 yes 1m90 A8002 cis-2Oph·Ob 6   0.79   0.97   0.93 yes 1n32 A1562 cis-2Oph·Ob 3   0.16   0.47   0.42 no 1n33 A1561 cis-2Oph·Ob 3   0.15   0.54   0.52 no 1n8r A8002 cis-2Oph·Ob 6   0.94   0.90   0.63 yes 1nji A8002 cis-2Oph·Ob 6   0.70   0.92   0.84 yes 1q7y A8002 cis-2Oph·Ob 6   0.67   0.67   0.49 no 1q81 A8002 cis-2Oph·Ob 6   0.94   0.65   0.86 yes 1q82 A8002 cis-2Oph·Ob 6   0.92   0.93   0.82 yes 1q86 A8002 cis-2Oph·Ob 6   0.82   0.92   0.92 yes 1qvf 08002 cis-2Oph·Ob 6   0.86   0.87   0.78 yes

^# 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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