MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2991, See in JSmolClick on the image to toggle views Site type: trans,cis-4Oph Schematic drawing for trans,cis-4Oph List of all 107 Mg2+ binding sites with the site type trans,cis-4Oph 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 4 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2qam B3496 trans,cis-4Oph 6   0.80   0.83   0.80 yes 3oas A2945 trans,cis-4Oph 6   0.49   0.88   0.80 no 1l8v A307 trans,cis-4Oph 4   0.52   0.54   0.80 no 4tpf A3042 trans,cis-4Oph 4   0.19   0.72   0.81 no 3oi3 A2968 trans,cis-4Oph 4   0.46   0.50   0.82 no 4qd1 A3258 trans,cis-4Oph 4   0.23   0.33   0.83 no 4kj1 A3040 trans,cis-4Oph 5   0.36   0.41   0.84 no 3v2d A3426 trans,cis-4Oph 5   0.33   0.72   0.84 no 4dha A3733 trans,cis-4Oph 6   0.45   0.60   0.85 no 1l8v B305 trans,cis-4Oph 4   0.52   0.65   0.85 yes 2vhn Z4043 trans,cis-4Oph 4   0.14   0.35   0.86 no 4qd1 A3167 trans,cis-4Oph 4   0.22   0.40   0.87 no 3ofr A3012 trans,cis-4Oph 6   0.67   0.72   0.87 yes 3v23 A3236 trans,cis-4Oph 4   0.20   0.45   0.89 no 3hux A2972 trans,cis-4Oph 4   0.22   0.41   0.89 no 4qco A3044 trans,cis-4Oph 4   0.41   0.55   0.89 no 4kx2 A3112 trans,cis-4Oph 4   0.60   0.72   0.89 yes 3hux A2998 trans,cis-4Oph 4   0.19   0.39   0.90 no 4qcp A3457 trans,cis-4Oph 5   0.22   0.44   0.90 no 4gar A3039 trans,cis-4Oph 6   0.57   0.81   0.90 yes 3uz7 A1608 trans,cis-4Oph 4   0.20   0.57   0.91 no 3i1p A2946 trans,cis-4Oph 6   0.53   0.87   0.92 yes 4qct A3464 trans,cis-4Oph 5   0.22   0.45   0.92 no 3v2f A3495 trans,cis-4Oph 6   0.38   0.67   0.93 no 2vhn Z4076 trans,cis-4Oph 5   0.12   0.63   0.95 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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