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 6 of 67 | « Previous | Next » | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4b3m A2749 2Ob 2   0.12   0.17   0.87 no 3uz6 A2268 2Ob 2   0.04   0.17   0.80 no 1vw0 A3212 2Ob 2   0.05   0.17   0.43 no 4nxn A1817 2Ob 2   0.07   0.16   0.61 no 3kir A3104 2Ob 2   0.07   0.27   0.82 no 4qcx A3217 2Ob 2   0.04   0.18   0.72 no 4dh9 A1827 2Ob 2   0.03   0.19   0.79 no 3pyt A2986 2Ob 2   0.06   0.19   0.70 no 4qcn A3217 2Ob 2   0.05   0.20   0.96 no 1vvm A3220 2Ob 2   0.08   0.23   0.72 no 1vx9 A3220 2Ob 2   0.04   0.21   0.46 no 1vx9 A3221 2Ob 2   0.04   0.16   0.24 no 1vxq A3221 2Ob 2   0.07   0.35   0.99 no 1vvy A3220 2Ob 2   0.05   0.12   0.62 no 1vx9 A3222 2Ob 2   0.08   0.28   0.89 no 3uyf A2276 2Ob 2   0.04   0.14   0.80 no 4dr3 A1836 2Ob 2   0.03   0.14   0.88 no 1vxt A3228 2Ob 2   0.04   0.19   0.84 no 1vxj A3234 2Ob 2   0.04   0.23   0.18 no 3ohj A3124 2Ob 2   0.06   0.25   0.65 no 1vvs A3233 2Ob 2   0.05   0.16   0.15 no 1vxt A3235 2Ob 2   0.07   0.23   0.58 no 4dr5 A1849 2Ob 2   0.05   0.15   0.86 no 3sgf A3153 2Ob 2   0.03   0.53   0.98 no 3i9d A1815 2Ob 2   0.04   0.20   0.78 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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