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 11 of 67 | « Previous | Next » | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4duy A1683 2Ob 2   0.04   0.15   0.99 no 1vvn A1664 2Ob 2   0.05   0.15   0.89 no 4lf8 A1601 2Ob 2   0.03   0.15   0.78 no 4lf7 A1601 2Ob 2   0.03   0.15   0.78 no 4ji8 A1742 2Ob 2   0.03   0.15   0.88 no 3d5c A1564 2Ob 2   0.06   0.15   0.09 no 4dr5 A1849 2Ob 2   0.05   0.15   0.86 no 4b3r A2654 2Ob 2   0.05   0.15   0.98 no 3u5d 14372 2Ob 2   0.03   0.15   0.95 no 3uz6 A2261 2Ob 2   0.03   0.15   0.84 no 4qcx A3020 2Ob 2   0.17   0.15   0.77 no 4nvz A3066 2Ob 2   0.08   0.15   0.66 no 1xmo A210 2Ob 2   0.03   0.15   0.36 no 4aqy A2584 2Ob 2   0.03   0.15   0.88 no 4byc A3945 2Ob 2   0.05   0.15   0.76 no 4qco A3061 2Ob 2   0.04   0.15   0.93 no 4l6j A5594 2Ob 2   0.04   0.15   0.83 no 4dv6 A1766 2Ob 2   0.04   0.15   0.92 no 1un6 F309 2Ob 2   0.03   0.15   0.96 no 4ji6 A1969 2Ob 2   0.05   0.15   0.77 no 4dr1 A1748 2Ob 2   0.04   0.15   0.83 no 4eja A7016 2Ob 2   0.03   0.15   0.70 no 4dr2 A1813 2Ob 2   0.03   0.15   0.85 no 3ohc A1559 2Ob 2   0.05   0.15   0.74 no 1xnq A1632 2Ob 2   0.05   0.15   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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