MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1hr2:A5, See in JSmolClick on the image to toggle views Site type: Ob·Nb Schematic drawing for Ob·Nb List of all 592 Mg2+ binding sites with the site type Ob·Nb 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 9 of 24 | « Previous | Next » | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vxl A3127 Ob·Nb 2   0.34   0.02   0.44 no 1vvq A3125 Ob·Nb 2   0.45   0.19   0.37 no 1vvu A3125 Ob·Nb 2   0.42   0.15   0.39 no 1vx9 A3124 Ob·Nb 2   0.40   0.21   0.95 no 1vxq A3124 Ob·Nb 2   0.41   0.20   0.76 no 1vxl A3124 Ob·Nb 2   0.45   0.22   0.49 no 4qct A3124 Ob·Nb 2   0.06   0.12   0.96 no 3v2d A3124 Ob·Nb 6   0.54   0.76   0.92 yes 1vvy A3123 Ob·Nb 2   0.42   0.19   0.30 no 1vvm A3122 Ob·Nb 2   0.49   0.21   0.87 no 1vvu A3122 Ob·Nb 2   0.46   0.24   0.10 no 1vxl A3118 Ob·Nb 2   0.43   0.14   0.70 no 4nw0 A3116 Ob·Nb 5   0.41   0.67   0.97 no 3oh7 A3116 Ob·Nb 2   0.08   0.07   0.62 no 3v23 A3114 Ob·Nb 2   0.09   0.17   0.95 no 4qcs A3114 Ob·Nb 5   0.41   0.69   0.93 no 4qcw A3113 Ob·Nb 4   0.29   0.89   0.82 no 3d5b A3109 Ob·Nb 2   0.03   0.12   0.60 no 1vy1 A3107 Ob·Nb 2   0.14   0.17   0.06 no 4nw0 A3106 Ob·Nb 4   0.28   0.86   0.67 no 1vvq A3104 Ob·Nb 2   0.37   0.17   0.12 no 1vx9 A3103 Ob·Nb 2   0.41   0.17   0.08 no 1vxl A3103 Ob·Nb 2   0.32   0.10   0.39 no 1vxq A3103 Ob·Nb 2   0.34   0.11   0.20 no 1vvm A3102 Ob·Nb 2   0.35   0.13   0.51 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>