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 11 of 67 | « Previous | Next » | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3u5d 13948 2Ob 2   0.03   0.14   0.78 no 3v29 B202 2Ob 2   0.03   0.17   0.94 no 3d5d A3456 2Ob 2   0.05   0.29   0.37 no 4qcz A3607 2Ob 4   0.29   0.93   0.96 no 3pyt A2986 2Ob 2   0.06   0.19   0.70 no 4dh9 A1827 2Ob 2   0.03   0.19   0.79 no 4nvx B3008 2Ob 2   0.04   0.35   0.73 no 4qcx A3217 2Ob 2   0.04   0.18   0.72 no 3ohk A3027 2Ob 2   0.06   0.17   0.86 no 3cce 08075 2Ob 5   0.16   0.56   0.97 no 4nw1 B3008 2Ob 2   0.03   0.34   0.88 no 3pyo A3485 2Ob 2   0.07   0.11   0.80 no 3kir A3104 2Ob 2   0.07   0.27   0.82 no 3f1f A5703 2Ob 2   0.03   0.21   0.68 no 3d5b A3532 2Ob 2   0.03   0.16   0.30 no 4qcz A3678 2Ob 3   0.15   0.26   0.81 no 4qcn A3673 2Ob 5   0.18   0.42   0.80 no 3f1f A5710 2Ob 2   0.08   0.31   0.25 no 3u5d 14055 2Ob 2   0.05   0.19   0.97 no 3f1f A5741 2Ob 2   0.05   0.19   0.50 no 3u5h 54136 2Ob 2   0.05   0.25   0.98 no 3pyo A3557 2Ob 2   0.03   0.23   0.61 no 4qcz B3015 2Ob 3   0.16   0.19   0.96 no 4nvz B3003 2Ob 2   0.03   0.20   0.61 no 3v2d A3638 2Ob 5   0.27   0.64   0.89 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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