MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob 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 8 of 67 | « 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 4qcn A3347 2Ob 4   0.28   0.45   0.92 no 3v2d A3175 2Ob 4   0.28   0.47   0.97 no 3cpw 08032 2Ob 6   0.28   0.83   0.79 no 1yjw 78042 2Ob 6   0.28   0.81   0.86 no 4bye A4014 2Ob 2   0.27   0.06   0.62 no 2otj 08042 2Ob 6   0.27   0.91   0.88 no 4qcv A3321 2Ob 4   0.27   0.38   0.93 no 4dha A3634 2Ob 5   0.27   0.48   0.82 no 4nvv A3491 2Ob 4   0.27   0.48   0.76 no 1vq5 08042 2Ob 6   0.27   0.72   0.94 no 3ccl 08076 2Ob 6   0.27   0.80   0.98 no 3v2d A3638 2Ob 5   0.27   0.64   0.89 no 3v2d A3343 2Ob 4   0.27   0.44   0.93 no 4ji5 A1746 2Ob 2   0.27   0.14   0.79 no 1vq6 08042 2Ob 6   0.27   0.80   0.97 no 3v2f A3531 2Ob 4   0.27   0.51   0.90 no 1vqn 08042 2Ob 6   0.27   0.84   0.90 no 1m90 A8042 2Ob 6   0.27   0.88   0.88 no 4kiz A3102 2Ob 5   0.27   0.39   0.59 no 4qcv A3359 2Ob 4   0.27   0.40   0.99 no 1vq8 08042 2Ob 6   0.27   0.85   0.71 no 4dhc A3617 2Ob 4   0.27   0.54   0.97 no 4nw1 A3612 2Ob 4   0.26   0.40   0.83 no 3v2d A3307 2Ob 4   0.26   0.42   0.89 no 1vq6 08097 2Ob 6   0.26   0.78   0.87 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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