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 5 of 24 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4l81 A111 Ob·Nb 2   0.04   0.12   0.92 no 1vxs A1616 Ob·Nb 2   0.14   0.18   0.38 no 4kvb A1663 Ob·Nb 2   0.10   0.18   0.63 no 2x9t Z24 Ob·Nb 2   0.05   0.15   0.73 no 2x9r Z24 Ob·Nb 2   0.15   0.08   0.63 no 3kiu a1543 Ob·Nb 2   0.03   0.14   0.37 no 4g5k A1636 Ob·Nb 2   0.05   0.11   0.59 no 4l6j A4032 Ob·Nb 2   0.04   0.13   0.61 no 3i9b A1553 Ob·Nb 2   0.13   0.05   0.58 no 2v46 Z28 Ob·Nb 2   0.04   0.14   0.31 no 1gid B271 Ob·Nb 2   0.18   0.13   0.93 no 4qcr A3018 Ob·Nb 2   0.06   0.20   0.85 no 2wdh Z33 Ob·Nb 2   0.06   0.13   0.60 no 4g5v A1645 Ob·Nb 2   0.22   0.19   0.99 no 2uuc Z1024 Ob·Nb 2   0.06   0.16   0.98 no 4kvb A1669 Ob·Nb 2   0.14   0.15   0.48 no 3ohd A1570 Ob·Nb 2   0.03   0.13   0.59 no 2uub Z1024 Ob·Nb 2   0.12   0.21   0.87 no 1i97 A1547 Ob·Nb 2   0.06   0.31   0.65 no 2vhm Z4028 Ob·Nb 4   0.21   0.44   0.21 no 3dll Z124 Ob·Nb 2   0.04   0.12   0.21 no 4dr7 A1630 Ob·Nb 5   0.52   0.56   0.64 no 4l6j A4065 Ob·Nb 2   0.03   0.61   0.95 no 4kwz A1631 Ob·Nb 2   0.44   0.15   0.81 no 4nyg A103 Ob·Nb 2   0.08   0.11   0.85 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>