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 1fjg A1576 cis-2Oph·2Ob 4   0.43   0.65   0.55 no 1hnw A1575 cis-2Oph·2Ob 4   0.53   0.72   0.46 no 1hnx A1575 cis-2Oph·2Ob 4   0.38   0.59   0.52 no 1hnz A1575 cis-2Oph·2Ob 4   0.40   0.74   0.60 no 1hr0 A1574 cis-2Oph·2Ob 4   0.32   0.58   0.82 no 1vs5 A1603 cis-2Oph·2Ob 6   0.92   0.85   0.97 yes 1vs7 A1582 cis-2Oph·2Ob 6   0.92   0.61   0.85 yes 2avy A1576 cis-2Oph·2Ob 6   0.93   0.84   0.97 yes 2aw7 A1581 cis-2Oph·2Ob 6   0.90   0.53   0.88 no 2i2p A1577 cis-2Oph·2Ob 6   0.95   0.58   0.98 no 2j02 Z181 cis-2Oph·2Ob 4   0.67   0.69   0.53 yes 2qal A2210 cis-2Oph·2Ob 6   0.81   0.72   0.95 yes 2qan A2236 cis-2Oph·2Ob 6   0.74   0.84   0.80 yes 2qb9 A2210 cis-2Oph·2Ob 6   0.66   0.57   0.85 no 2qbb A2236 cis-2Oph·2Ob 6   0.59   0.77   0.98 yes 2qbd A2210 cis-2Oph·2Ob 6   0.80   0.82   0.89 yes 2qbf A1580 cis-2Oph·2Ob 6   0.84   0.77   0.97 yes 2qbh A1577 cis-2Oph·2Ob 6   0.69   0.54   1.00 no 2qbj A1580 cis-2Oph·2Ob 6   0.61   0.77   0.85 yes 2qou A1577 cis-2Oph·2Ob 6   0.56   0.56   0.99 no 2uua Z75 cis-2Oph·2Ob 4   0.57   0.71   0.62 yes 2uub Z1075 cis-2Oph·2Ob 4   0.50   0.70   0.59 no 2uuc Z1134 cis-2Oph·2Ob 4   0.55   0.75   0.67 yes 2uxc Z164 cis-2Oph·2Ob 4   0.16   0.69   0.68 no 2vqe Z154 cis-2Oph·2Ob 4   0.39   0.78   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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