MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs6:B2970, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout·Bout Schematic drawing for 3Pout·Rout·Bout List of all 48 Mg2+ binding sites with the site type 3Pout·Rout·Bout 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vs6 B2970 3Pout·Rout·Bout 6   0.97   1.00   1.00 yes 2i2v B2938 3Pout·Rout·Bout 5   0.81   0.80   0.99 yes 2qbk B2938 3Pout·Rout·Bout 5   0.81   0.80   0.99 yes 2qox B2963 3Pout·Rout·Bout 5   0.81   0.80   1.00 yes 2qp1 B2964 3Pout·Rout·Bout 5   0.81   0.80   1.00 yes 2z4n B2939 3Pout·Rout·Bout 5   0.81   0.80   0.99 yes 3df4 B3201 3Pout·Rout·Bout 5   0.81   0.80   0.99 yes 3i1p A2963 3Pout·Rout·Bout 6   0.74   0.99   0.38 no 3i1t A2979 3Pout·Rout·Bout 5   0.81   0.82   1.00 yes 3i1z A1540 3Pout·Rout·Bout 5   0.82   0.81   1.00 yes 3i20 A3032 3Pout·Rout·Bout 6   0.76   0.98   1.00 yes 3i22 A2955 3Pout·Rout·Bout 6   0.75   0.99   1.00 yes 3i22 A3027 3Pout·Rout·Bout 6   0.75   0.99   1.00 yes 3la5 A2 3Pout·Rout·Bout 6   0.68   0.97   0.96 yes 3oas A2983 3Pout·Rout·Bout 5   0.81   0.80   0.58 yes 3oat A2950 3Pout·Rout·Bout 5   0.82   0.80   0.50 no 3ofd A2983 3Pout·Rout·Bout 5   0.82   0.80   0.58 yes 3ofq A2979 3Pout·Rout·Bout 5   0.81   0.81   0.59 yes 3ofr A2960 3Pout·Rout·Bout 6   0.75   0.99   0.32 no 3og0 A2982 3Pout·Rout·Bout 5   0.81   0.81   0.57 yes 3v29 A3575 3Pout·Rout·Bout 4   0.53   0.97   0.78 yes 3v2d A3512 3Pout·Rout·Bout 5   0.61   0.81   0.50 yes 4bpe A5015 3Pout·Rout·Bout 6   0.75   0.99   0.99 yes 4bpn A5015 3Pout·Rout·Bout 6   0.77   0.99   0.98 yes 4bpn A5002 3Pout·Rout·Bout 6   0.75   0.98   1.00 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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