MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qal:A2335, See in JSmolClick on the image to toggle views Site type: Rout·3Bout Schematic drawing for Rout·3Bout List of all 23 Mg2+ binding sites with the site type Rout·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 1

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2avy A1598 Rout·3Bout 6   0.97   0.99   1.00 yes 2i2u A1583 Rout·3Bout 6   0.98   0.99   1.00 yes 2qal A2335 Rout·3Bout 6   0.97   1.00   1.00 yes 2qox B2939 Rout·3Bout 6   0.97   1.00   1.00 yes 2qoy A1557 Rout·3Bout 6   0.97   0.99   1.00 yes 2xzm 017 Rout·3Bout 6   0.13   1.00   1.00 no 3cd6 08060 Rout·3Bout 4   0.12   0.34   0.72 no 3df1 A2335 Rout·3Bout 6   0.97   1.00   1.00 yes 3nkb B206 Rout·3Bout 6   0.40   0.97   0.84 no 3oas A2991 Rout·3Bout 6   0.75   1.00   0.60 yes 3ofc A2983 Rout·3Bout 6   0.76   0.99   0.91 yes 3orb A2983 Rout·3Bout 6   0.77   0.97   0.82 yes 3v23 A3546 Rout·3Bout 2   0.25   0.43   0.88 no 3v25 A3377 Rout·3Bout 3   0.37   0.64   0.77 no 3v27 A3503 Rout·3Bout 6   0.73   0.96   0.99 yes 3v27 A3495 Rout·3Bout 5   0.62   0.81   0.77 yes 3v2d A3167 Rout·3Bout 5   0.60   0.77   0.74 yes 4duy A1845 Rout·3Bout 4   0.63   0.65   0.46 no 4ji4 A1790 Rout·3Bout 3   0.47   0.66   0.42 no 4nxm A1790 Rout·3Bout 3   0.48   0.66   0.64 no 4qcn A3294 Rout·3Bout 3   0.37   0.43   0.66 no 4qcp A3604 Rout·3Bout 6   0.75   1.00   0.91 yes 4qcx A3473 Rout·3Bout 4   0.50   0.99   0.81 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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