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 24 of 67 | « Previous | Next » | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vxt A3228 2Ob 2   0.04   0.19   0.84 no 3uyf A1918 2Ob 2   0.05   0.16   0.85 no 1ibl A1622 2Ob 2   0.03   0.21   0.28 no 4dhb A1685 2Ob 2   0.03   0.23   0.85 no 4b3r A2626 2Ob 2   0.06   0.21   0.79 no 3kiq a1620 2Ob 2   0.20   0.06   0.42 no 4dv6 A1685 2Ob 2   0.03   0.14   0.95 no 4qcp A3085 2Ob 2   0.03   0.18   0.94 no 3d5b A2987 2Ob 2   0.04   0.26   0.02 no 3kix a1618 2Ob 2   0.04   0.14   0.21 no 3kiq a1621 2Ob 2   0.07   0.25   0.80 no 4lf8 A1697 2Ob 2   0.04   0.15   0.80 no 3knj A1615 2Ob 2   0.05   0.24   0.80 no 3oto A1623 2Ob 2   0.04   0.15   0.63 no 2uub Z1086 2Ob 2   0.14   0.16   0.37 no 3knl A1615 2Ob 2   0.05   0.17   0.68 no 3kis a1618 2Ob 2   0.04   0.20   0.83 no 2quw B7 2Ob 2   0.06   0.42   0.88 no 4aqy A2630 2Ob 2   0.08   0.10   0.75 no 4ji6 A1689 2Ob 2   0.06   0.36   0.81 no 1xmq A1632 2Ob 2   0.06   0.17   0.55 no 4lf9 A1608 2Ob 2   0.03   0.18   0.85 no 2x9r Z181 2Ob 2   0.04   0.16   0.65 no 3t1y A1699 2Ob 2   0.05   0.14   0.27 no 1vvs A3142 2Ob 2   0.12   0.23   0.34 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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