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 14 of 67 | « Previous | Next » | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dr6 A1782 2Ob 3   0.06   0.68   0.87 no 4qcs A3161 2Ob 3   0.15   0.18   0.94 no 3v2d A3192 2Ob 3   0.18   0.33   0.94 no 4nvx A3297 2Ob 3   0.15   0.28   0.88 no 4qcn A3349 2Ob 3   0.15   0.21   0.90 no 4qcp A3316 2Ob 3   0.17   0.31   0.89 no 4qct A3320 2Ob 3   0.17   0.35   0.74 no 4qcm A1737 2Ob 3   0.15   0.19   0.89 no 4qd1 A3344 2Ob 3   0.16   0.34   0.91 no 4qcq A3134 2Ob 3   0.15   0.20   0.98 no 4qcy A3152 2Ob 3   0.15   0.19   0.68 no 4dr7 A1885 2Ob 3   0.07   0.60   0.72 no 3v25 A3102 2Ob 3   0.05   0.60   0.96 no 4dv7 A1698 2Ob 3   0.19   0.13   0.97 no 4nxn A1708 2Ob 3   0.20   0.14   0.96 no 4nvz A3354 2Ob 3   0.15   0.32   0.67 no 4nvx A3509 2Ob 3   0.19   0.38   0.62 no 4ji1 A1695 2Ob 3   0.06   0.71   0.88 no 4dv3 A1693 2Ob 3   0.19   0.18   0.77 no 4dv4 A1639 2Ob 3   0.22   0.21   0.48 no 1y73 A25 2Ob 3   0.05   0.49   0.65 no 4qcm A1758 2Ob 3   0.16   0.26   0.79 no 3v2f A3134 2Ob 3   0.06   0.40   0.81 no 4nvw A3006 2Ob 3   0.10   0.33   0.96 no 4qcz A3051 2Ob 3   0.12   0.32   0.77 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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