MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qox:B2986, See in JSmolClick on the image to toggle views Site type: 5Pout Schematic drawing for 5Pout List of all 24 Mg2+ binding sites with the site type 5Pout 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 1

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vt2 A2998 5Pout 6   0.75   0.99   0.87 yes 2qox B2986 5Pout 6   0.97   1.00   1.00 yes 3df4 B3485 5Pout 6   0.97   1.00   1.00 yes 3i22 A2997 5Pout 6   0.75   1.00   1.00 yes 3r8t A2958 5Pout 5   0.80   0.79   0.97 yes 3v29 A3385 5Pout 6   0.72   0.98   0.96 yes 3v2d A3650 5Pout 6   0.71   0.96   0.60 yes 4dv1 A1798 5Pout 6   0.93   0.98   0.40 no 4dv7 A1834 5Pout 6   0.95   1.00   0.61 yes 4gar A3134 5Pout 6   0.75   1.00   0.89 yes 4ji1 A1800 5Pout 6   0.96   0.99   0.37 no 4peb A3107 5Pout 3   0.53   0.39   0.65 no 4pec A3101 5Pout 4   0.66   0.65   0.85 yes 4qcn A3299 5Pout 4   0.49   0.63   0.85 no 4tol A1640 5Pout 6   0.74   0.99   0.74 yes 4too A3056 5Pout 5   0.80   0.81   0.69 yes 4tox A3057 5Pout 5   0.79   0.81   0.73 yes 4tp3 A3025 5Pout 4   0.67   0.64   0.73 yes 4tp3 A3086 5Pout 5   0.82   0.80   0.82 yes 4tp3 A3120 5Pout 4   0.67   0.65   0.81 yes 4tp7 A3121 5Pout 4   0.67   0.64   0.72 yes 4tpb A3025 5Pout 4   0.67   0.65   0.72 yes 4tpb A3086 5Pout 5   0.82   0.80   0.82 yes 4tpf A3026 5Pout 4   0.67   0.64   0.70 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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