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 13 of 67 | « Previous | Next » | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2j00 Z295 2Ob 2   0.09   0.10   0.46 no 2j00 Z221 2Ob 2   0.05   0.19   0.03 no 2j00 Z218 2Ob 2   0.03   0.24   0.42 no 2j00 Z65 2Ob 2   0.07   0.20   0.15 no 2j02 Z187 2Ob 2   0.03   0.20   0.86 no 2j02 Z494 2Ob 2   0.05   0.16   0.69 no 2j02 Z206 2Ob 2   0.08   0.16   0.16 no 2j02 Z202 2Ob 2   0.03   0.16   0.37 no 2j02 Z451 2Ob 2   0.09   0.61   0.25 no 2otj 08097 2Ob 6   0.52   0.76   0.74 yes 2otj 08096 2Ob 6   0.47   0.83   0.84 no 2otj 08042 2Ob 6   0.27   0.91   0.88 no 2otl 08042 2Ob 6   0.25   0.96   1.00 no 2otl 08097 2Ob 6   0.35   0.75   1.00 no 2pn3 A2 2Ob 2   0.11   0.10   0.61 no 2qa4 03012 2Ob 2   0.04   0.21   0.93 no 2qex 08097 2Ob 6   0.30   0.72   0.89 no 2qex 08042 2Ob 6   0.26   0.88   0.99 no 2qex 08064 2Ob 4   0.23   0.38   0.72 no 2qoy A1577 2Ob 4   0.37   0.45   0.97 no 2quw B7 2Ob 2   0.06   0.42   0.88 no 2r8s R1004 2Ob 6   0.51   0.85   0.99 yes 2uu9 Z1028 2Ob 2   0.18   0.38   0.46 no 2uu9 Z1146 2Ob 2   0.04   0.16   0.70 no 2uu9 Z1018 2Ob 2   0.06   0.24   0.54 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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