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 1 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 2wdg Z230 2Ob 2   0.02   0.18   0.99 no 4dha A3387 2Ob 2   0.02   0.12   0.93 no 3v29 A3100 2Ob 2   0.02   0.20   0.87 no 4dv2 A1767 2Ob 2   0.02   0.22   0.78 no 3hux A3081 2Ob 2   0.02   0.16   0.60 no 4dhc A3032 2Ob 2   0.02   0.26   0.93 no 3v27 A3158 2Ob 2   0.02   0.20   0.84 no 2uub Z1114 2Ob 2   0.02   0.17   0.79 no 4dr1 A1779 2Ob 2   0.02   0.16   0.73 no 4l6j A5190 2Ob 2   0.02   0.13   0.70 no 3uz7 A1853 2Ob 2   0.02   0.18   0.80 no 4khp A1702 2Ob 2   0.02   0.17   0.95 no 4qcx A3007 2Ob 2   0.02   0.16   0.72 no 3tvg A2035 2Ob 2   0.02   0.18   0.59 no 3tvf A2745 2Ob 2   0.02   0.15   0.76 no 3gx2 A203 2Ob 2   0.02   0.94   0.98 no 4eja A7171 2Ob 2   0.02   0.16   0.80 no 3i8h A1642 2Ob 2   0.02   0.16   0.72 no 3v26 A1671 2Ob 2   0.03   0.21   0.80 no 4kvb A1735 2Ob 2   0.03   0.19   0.88 no 3uz7 C136 2Ob 2   0.03   0.15   0.77 no 4ji0 A1674 2Ob 2   0.03   0.21   0.93 no 4ji2 A1861 2Ob 2   0.03   0.49   0.81 no 3kiy A3169 2Ob 2   0.03   0.21   0.91 no 3pyt A3086 2Ob 2   0.03   0.25   0.85 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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