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 14 of 67 | « Previous | Next » | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3ohd A1556 2Ob 2   0.06   0.16   0.99 no 4qcx A3007 2Ob 2   0.02   0.16   0.72 no 2wdg Z297 2Ob 2   0.03   0.16   0.88 no 4dv7 A1801 2Ob 2   0.04   0.16   0.82 no 4nvz A3069 2Ob 2   0.04   0.16   0.56 no 4dr5 A1785 2Ob 2   0.06   0.16   0.66 no 1ibm A1618 2Ob 2   0.04   0.16   0.56 no 1vw0 A3186 2Ob 2   0.04   0.16   0.54 no 2wdk Z208 2Ob 2   0.08   0.16   0.55 no 3uz3 A2200 2Ob 2   0.03   0.16   0.76 no 1vvn A1672 2Ob 2   0.06   0.16   0.73 no 4nvv A3069 2Ob 2   0.06   0.16   0.53 no 3f1f A5411 2Ob 2   0.06   0.16   0.54 no 3d5b A3532 2Ob 2   0.03   0.16   0.30 no 4lfc A1697 2Ob 2   0.05   0.16   0.65 no 3v27 A3183 2Ob 2   0.03   0.16   0.64 no 4ej9 A7108 2Ob 2   0.05   0.16   0.44 no 1hnw A1548 2Ob 2   0.05   0.16   0.75 no 3oh5 A3179 2Ob 2   0.03   0.16   0.72 no 4l6j A4942 2Ob 2   0.04   0.16   0.75 no 1vxq A3167 2Ob 2   0.04   0.16   0.87 no 2j02 Z202 2Ob 2   0.03   0.16   0.37 no 3kno A2998 2Ob 2   0.03   0.16   0.22 no 3pyo A3125 2Ob 2   0.03   0.16   0.83 no 4dr1 A1700 2Ob 2   0.05   0.16   0.89 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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