MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qoz:B2982, See in JSmolClick on the image to toggle views Site type: Pout·3Bout Schematic drawing for Pout·3Bout List of all 472 Mg2+ binding sites with the site type Pout·3Bout 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 19 | « 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 1egk C9 Pout·3Bout 6   0.96   1.00   1.00 yes 1hr2 A16 Pout·3Bout 6   0.86   0.96   1.00 yes 2xzn 016 Pout·3Bout 6   0.12   1.00   1.00 no 2xzn 025 Pout·3Bout 6   0.12   1.00   1.00 no 1egk A25 Pout·3Bout 6   0.97   0.99   0.99 yes 2xzm 026 Pout·3Bout 6   0.13   1.00   1.00 no 2xzn 026 Pout·3Bout 6   0.12   1.00   1.00 no 4a1a 079 Pout·3Bout 6   0.76   0.99   1.00 yes 1ik5 A98 Pout·3Bout 3   0.48   0.44   0.90 no 4oji A101 Pout·3Bout 6   0.92   0.94   0.85 yes 3ivk M132 Pout·3Bout 6   0.74   0.99   1.00 yes 4a17 0204 Pout·3Bout 6   0.75   0.98   1.00 yes 4a1e 0204 Pout·3Bout 6   0.75   0.99   1.00 yes 3v27 B220 Pout·3Bout 6   0.75   0.97   0.96 yes 2z75 B304 Pout·3Bout 5   0.94   0.90   0.83 yes 4a1a 0345 Pout·3Bout 6   0.75   0.99   1.00 yes 1mms C437 Pout·3Bout 5   0.35   0.77   0.91 no 2gcs B505 Pout·3Bout 6   0.96   0.91   0.84 yes 2h0x B505 Pout·3Bout 6   0.94   0.92   0.86 yes 1ffy T1202 Pout·3Bout 6   0.71   0.98   0.99 yes 1qu2 T1202 Pout·3Bout 6   0.71   0.98   0.99 yes 3i1s A1540 Pout·3Bout 6   0.75   1.00   1.00 yes 3ofp A1543 Pout·3Bout 6   0.75   0.99   0.82 yes 3ora A1543 Pout·3Bout 6   0.75   1.00   0.78 yes 3or9 A1544 Pout·3Bout 6   0.76   1.00   0.53 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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