MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2aw4:B2955, See in JSmolClick on the image to toggle views Site type: 4Pout·Rout Schematic drawing for 4Pout·Rout List of all 62 Mg2+ binding sites with the site type 4Pout·Rout 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 1hr2 A14 4Pout·Rout 6   0.86   0.96   0.99 yes 1vs8 B2966 4Pout·Rout 6   0.97   0.99   1.00 yes 1vs8 B2935 4Pout·Rout 6   0.97   1.00   1.00 yes 2aw4 B2955 4Pout·Rout 6   0.98   1.00   1.00 yes 2awb B2936 4Pout·Rout 6   0.97   0.99   1.00 yes 2qam B3295 4Pout·Rout 6   0.97   1.00   1.00 yes 2qao B3189 4Pout·Rout 6   0.97   1.00   1.00 yes 2qba B3295 4Pout·Rout 6   0.97   1.00   1.00 yes 2qbc B3189 4Pout·Rout 6   0.97   1.00   1.00 yes 2qbe B3295 4Pout·Rout 6   0.97   1.00   1.00 yes 2qbf A1596 4Pout·Rout 5   0.81   0.80   1.00 yes 2qbg B2968 4Pout·Rout 6   0.97   0.99   1.00 yes 2qbg B2936 4Pout·Rout 6   0.97   1.00   1.00 yes 2qbi B2955 4Pout·Rout 6   0.97   0.99   1.00 yes 2qov B2955 4Pout·Rout 6   0.97   1.00   1.00 yes 2qox B2936 4Pout·Rout 6   0.97   1.00   1.00 yes 2qoz B2955 4Pout·Rout 6   0.97   0.99   1.00 yes 2qp1 B2936 4Pout·Rout 6   0.97   0.99   1.00 yes 2z4l B2909 4Pout·Rout 6   0.97   0.99   1.00 yes 2z4n B2969 4Pout·Rout 6   0.97   0.99   1.00 yes 2z4n B2937 4Pout·Rout 6   0.97   0.99   1.00 yes 3df4 B3189 4Pout·Rout 6   0.97   1.00   1.00 yes 3df4 B3375 4Pout·Rout 6   0.97   0.99   1.00 yes 3i1p A2998 4Pout·Rout 6   0.75   1.00   0.98 yes 3i1t A2914 4Pout·Rout 6   0.74   1.00   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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