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 3pyr A3296 2Ob 2   0.05   0.38   0.72 no 4qcn A3623 2Ob 3   0.15   0.23   0.72 no 4ji4 A1757 2Ob 2   0.06   0.22   0.72 no 3v27 B206 2Ob 2   0.03   0.17   0.72 no 4qcx A3007 2Ob 2   0.02   0.16   0.72 no 4nvz A3044 2Ob 3   0.07   0.46   0.72 no 4ji6 A1724 2Ob 2   0.06   0.15   0.72 no 4dr7 A1885 2Ob 3   0.07   0.60   0.72 no 4nxn A1789 2Ob 2   0.04   0.16   0.72 no 3v27 A3168 2Ob 2   0.03   0.17   0.72 no 3uz7 A2046 2Ob 2   0.04   0.41   0.72 no 4ji2 A1733 2Ob 2   0.11   0.12   0.72 no 4lf9 A1708 2Ob 2   0.05   0.19   0.72 no 3f1f A5440 2Ob 2   0.05   0.19   0.72 no 3ccv 08033 2Ob 5   0.19   0.65   0.72 no 4qcr A3513 2Ob 4   0.28   0.91   0.72 no 4ji6 A1741 2Ob 2   0.12   0.21   0.72 no 4qcv A3471 2Ob 4   0.29   0.92   0.72 no 4dr6 A1773 2Ob 2   0.03   0.16   0.72 no 1vvm A3220 2Ob 2   0.08   0.23   0.72 no 2wdk Z221 2Ob 2   0.09   0.41   0.72 no 1hnw A1613 2Ob 2   0.06   0.23   0.72 no 4kx0 A3139 2Ob 2   0.08   0.22   0.72 no 2uxc Z130 2Ob 2   0.09   0.34   0.72 no 1vvm A3184 2Ob 2   0.08   0.27   0.73 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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