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 12 of 67 | « Previous | Next » | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1xnr A1632 2Ob 2   0.05   0.12   0.77 no 1y73 A25 2Ob 3   0.05   0.49   0.65 no 1yhq 08076 2Ob 6   0.44   0.85   0.84 no 1yhq 08032 2Ob 6   0.32   0.82   0.81 no 1yi2 08042 2Ob 6   0.28   0.92   0.99 no 1yi2 08097 2Ob 6   0.32   0.86   0.94 no 1yij 08042 2Ob 6   0.35   0.90   0.99 no 1yij 08043 2Ob 5   0.35   0.64   0.98 no 1yij 08097 2Ob 6   0.32   0.89   0.85 no 1yit 08042 2Ob 2   0.10   0.34   0.65 no 1yit 08097 2Ob 2   0.11   0.22   0.85 no 1yj9 08097 2Ob 6   0.32   0.75   0.74 no 1yj9 08042 2Ob 6   0.24   0.87   0.93 no 1yjn 08042 2Ob 6   0.20   0.86   0.82 no 1yjn 08097 2Ob 6   0.56   0.49   0.90 no 1yjw 78097 2Ob 6   0.58   0.71   0.82 yes 1yjw 78042 2Ob 6   0.28   0.81   0.86 no 1yjw 78043 2Ob 5   0.34   0.36   0.75 no 1yrj A101 2Ob 2   0.07   0.14   0.74 no 2f4v A1628 2Ob 2   0.06   0.28   0.78 no 2f4v A1589 2Ob 2   0.06   0.18   0.86 no 2f4v A1633 2Ob 2   0.12   0.06   0.46 no 2f4v A1634 2Ob 2   0.09   0.27   0.78 no 2j00 Z295 2Ob 2   0.09   0.10   0.46 no 2j00 Z161 2Ob 2   0.11   0.28   0.24 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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