MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs5:A1603, See in JSmolClick on the image to toggle views Site type: cis-2Oph·2Ob Schematic drawing for cis-2Oph·2Ob List of all 67 Mg2+ binding sites with the site type cis-2Oph·2Ob 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 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4gd1 A1629 cis-2Oph·2Ob 6   0.67   0.79  0 no 3t1h A1691 cis-2Oph·2Ob 4   0.37   0.76   0.21 no 3t1y A1709 cis-2Oph·2Ob 4   0.17   0.68   0.21 no 3t1y A1691 cis-2Oph·2Ob 4   0.46   0.82   0.21 no 3f1f A6012 cis-2Oph·2Ob 4   0.13   0.74   0.29 no 1hnw A1575 cis-2Oph·2Ob 4   0.53   0.72   0.46 no 4kvb A1724 cis-2Oph·2Ob 4   0.73   0.95   0.49 no 1hnx A1575 cis-2Oph·2Ob 4   0.38   0.59   0.52 no 3ofa A1561 cis-2Oph·2Ob 6   0.54   0.57   0.52 no 2j02 Z181 cis-2Oph·2Ob 4   0.67   0.69   0.53 yes 1fjg A1576 cis-2Oph·2Ob 4   0.43   0.65   0.55 no 4qd1 A3272 cis-2Oph·2Ob 4   0.14   0.44   0.57 no 2uub Z1075 cis-2Oph·2Ob 4   0.50   0.70   0.59 no 1hnz A1575 cis-2Oph·2Ob 4   0.40   0.74   0.60 no 4lf6 A1708 cis-2Oph·2Ob 4   0.45   0.76   0.61 no 2uua Z75 cis-2Oph·2Ob 4   0.57   0.71   0.62 yes 4lfa A1677 cis-2Oph·2Ob 4   0.51   0.91   0.65 yes 2uuc Z1134 cis-2Oph·2Ob 4   0.55   0.75   0.67 yes 4lf5 A1684 cis-2Oph·2Ob 4   0.39   0.44   0.68 no 2uxc Z164 cis-2Oph·2Ob 4   0.16   0.69   0.68 no 3i9b A1951 cis-2Oph·2Ob 4   0.49   0.65   0.68 no 4lf9 A1693 cis-2Oph·2Ob 4   0.54   0.72   0.68 yes 4b3m A2586 cis-2Oph·2Ob 4   0.43   0.59   0.69 no 4qcy A3022 cis-2Oph·2Ob 4   0.66   0.71   0.69 yes 3i1m A1562 cis-2Oph·2Ob 6   0.57   0.59   0.70 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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