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 12 of 24 | « 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 4bye A4096 Ob·Nb 2   0.09   0.12   0.86 no 4g5t A1715 Ob·Nb 2   0.09   0.16   0.97 no 3i9b A1770 Ob·Nb 2   0.10   0.23   0.72 no 4qcn A3143 Ob·Nb 2   0.10   0.31   0.96 no 4ji2 A1808 Ob·Nb 2   0.10   0.28   0.79 no 1cx0 B402 Ob·Nb 2   0.10   0.12   0.95 no 3oi5 A3041 Ob·Nb 2   0.10   0.09   0.56 no 4kvb A1663 Ob·Nb 2   0.10   0.18   0.63 no 3kiw A2978 Ob·Nb 2   0.10   0.16   0.58 no 3i9b A1851 Ob·Nb 2   0.10   0.18   0.65 no 3cma 08080 Ob·Nb 5   0.10   0.51   0.68 no 3i8h A1971 Ob·Nb 2   0.10   0.37   0.53 no 1vvw A3176 Ob·Nb 2   0.10   0.08   0.74 no 3i8g A2028 Ob·Nb 2   0.10   0.39   0.78 no 2wdk Z311 Ob·Nb 2   0.10   0.12   0.60 no 1hnw A1610 Ob·Nb 3   0.10   0.39   0.48 no 3i9b A1861 Ob·Nb 2   0.11   0.06   0.94 no 3knj X637 Ob·Nb 2   0.11   0.53   0.49 no 4fb0 A409 Ob·Nb 3   0.11   0.24   0.60 no 3knj A1582 Ob·Nb 2   0.11   0.07   0.93 no 3v27 A3163 Ob·Nb 2   0.11   0.18   0.79 no 3huz A3000 Ob·Nb 2   0.11   0.17   0.62 no 3g71 08080 Ob·Nb 5   0.11   0.71   0.69 no 2j02 Z192 Ob·Nb 2   0.11   0.08   0.48 no 4pe9 A1665 Ob·Nb 2   0.11   0.42   0.86 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>