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 2 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 3pyt A2910 2Ob 2   0.04   0.15   0.08 no 3f1h A5270 2Ob 2   0.05   0.20   0.08 no 3d5c A1564 2Ob 2   0.06   0.15   0.09 no 1vvy A3132 2Ob 2   0.07   0.11   0.09 no 3v6v A1657 2Ob 2   0.18   0.14   0.10 no 4kx0 A3165 2Ob 2   0.19   0.29   0.10 no 2v46 Z30 2Ob 2   0.10   0.18   0.11 no 1vvt A1645 2Ob 2   0.06   0.13   0.11 no 3d5b A3497 2Ob 2   0.03   0.20   0.12 no 3t1y A1707 2Ob 2   0.10   0.32   0.13 no 3t1y A1778 2Ob 2   0.08   0.12   0.14 no 1vvy A3178 2Ob 2   0.06   0.19   0.14 no 1vvr A1672 2Ob 2   0.10   0.16   0.14 no 3d5b A3258 2Ob 2   0.03   0.22   0.14 no 1vvs A3233 2Ob 2   0.05   0.16   0.15 no 2j00 Z65 2Ob 2   0.07   0.20   0.15 no 3d5a A1753 2Ob 2   0.05   0.23   0.15 no 3f1h A5330 2Ob 2   0.06   0.24   0.15 no 1vx9 A3162 2Ob 2   0.05   0.34   0.16 no 3d5d A2989 2Ob 2   0.05   0.38   0.16 no 2j02 Z206 2Ob 2   0.08   0.16   0.16 no 1vy0 A1628 2Ob 2   0.04   0.11   0.18 no 1vxj A3234 2Ob 2   0.04   0.23   0.18 no 1vxj A3218 2Ob 2   0.09   0.19   0.18 no 1vvs A3168 2Ob 2   0.09   0.12   0.18 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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