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 5 of 67 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4nxm A1776 2Ob 2   0.03   0.19   0.64 no 2uub Z1176 2Ob 2   0.08   0.17   0.64 no 1vvo A3177 2Ob 2   0.04   0.17   0.80 no 4nxn A1782 2Ob 2   0.04   0.13   0.60 no 3tvf A2589 2Ob 2   0.05   0.15   0.89 no 3v27 A3183 2Ob 2   0.03   0.16   0.64 no 4dr5 A1788 2Ob 2   0.04   0.29   0.82 no 4ji4 A1786 2Ob 2   0.06   0.17   0.87 no 4nvu A3181 2Ob 3   0.16   0.37   0.63 no 1vvm A3184 2Ob 2   0.08   0.27   0.73 no 4dv5 A1786 2Ob 2   0.03   0.49   0.75 no 4b3t A2728 2Ob 2   0.29   0.15   0.86 no 4duz A1788 2Ob 2   0.04   0.18   0.82 no 4dv5 A1791 2Ob 2   0.04   0.14   0.67 no 4hub 08195 2Ob 2   0.09   0.12   0.77 no 4dr2 A1813 2Ob 2   0.03   0.15   0.85 no 4dv3 A1796 2Ob 2   0.03   0.14   0.81 no 4hub 08196 2Ob 2   0.09   0.18   0.84 no 1vy1 A3196 2Ob 2   0.08   0.22   0.76 no 3kiw A3093 2Ob 2   0.04   0.26   0.68 no 1vxl A3204 2Ob 2   0.09   0.31   0.95 no 4qd1 A3212 2Ob 2   0.07   0.22   0.79 no 1vvq A3205 2Ob 2   0.08   0.30   0.86 no 4kx2 A3210 2Ob 2   0.08   0.22   0.87 no 3ivn A101 2Ob 2   0.03   0.17   0.91 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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