MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df3:A2016, See in JSmolClick on the image to toggle views Site type: 2Pout·3Bout Schematic drawing for 2Pout·3Bout List of all 277 Mg2+ binding sites with the site type 2Pout·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 10 of 12 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3v29 A3433 2Pout·3Bout 6   0.72   0.98   0.74 yes 3df2 B3457 2Pout·3Bout 6   0.97   0.99   1.00 yes 3v2f A3460 2Pout·3Bout 5   0.61   0.79   0.87 yes 3v2d A3499 2Pout·3Bout 5   0.60   0.77   0.74 yes 4qd1 A3517 2Pout·3Bout 6   0.74   0.99   0.92 yes 4nw1 A3517 2Pout·3Bout 3   0.38   0.66   0.96 no 4nvx A3523 2Pout·3Bout 3   0.38   0.63   0.79 no 4qcx A3528 2Pout·3Bout 2   0.25   0.99   0.84 no 4qcp A3545 2Pout·3Bout 3   0.38   0.67   0.81 no 3v2d A3554 2Pout·3Bout 6   0.69   0.94   0.70 yes 3v23 A3561 2Pout·3Bout 4   0.48   0.99   0.66 no 3v29 A3574 2Pout·3Bout 6   0.74   0.98   1.00 yes 3v2f A3606 2Pout·3Bout 5   0.61   0.79   0.67 yes 4dha A3623 2Pout·3Bout 4   0.50   0.99   0.94 no 4nvx A3642 2Pout·3Bout 3   0.37   0.66   0.92 no 4qcz A3690 2Pout·3Bout 4   0.49   0.98   0.75 no 4qcr A3718 2Pout·3Bout 5   0.63   0.80   0.78 yes 4dha A3735 2Pout·3Bout 6   0.76   0.97   0.86 yes 4bpe A5018 2Pout·3Bout 6   0.75   0.99   1.00 yes 4bpo A5018 2Pout·3Bout 6   0.74   0.99   1.00 yes 4bpp A5018 2Pout·3Bout 6   0.75   0.99   1.00 yes 4bpn A5018 2Pout·3Bout 6   0.74   0.99   1.00 yes 3cma 08053 2Pout·3Bout 5   0.15   0.65   0.76 no 3cxc 08071 2Pout·3Bout 6   0.75   0.95   0.67 yes 1nji A8071 2Pout·3Bout 6   0.67   0.91   0.67 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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