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 7 of 24 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4gd1 A1660 Ob·Nb 2   0.03   0.14   0.37 no 3knj X637 Ob·Nb 2   0.11   0.53   0.49 no 1vvx A1661 Ob·Nb 2   0.33   0.09   0.95 no 4ox9 A1667 Ob·Nb 2   0.37   0.04   0.93 no 4qcw A3062 Ob·Nb 2   0.05   0.68   0.71 no 4g5v A1715 Ob·Nb 2   0.22   0.26   0.90 no 2x9r Z151 Ob·Nb 2   0.07   0.13   0.60 no 4ji8 A1666 Ob·Nb 2   0.03   0.14   0.84 no 4tp4 A1663 Ob·Nb 2   0.03   0.37   0.96 no 4qcx A3064 Ob·Nb 2   0.03   0.13   0.93 no 1vvt A1664 Ob·Nb 2   0.39   0.13   0.42 no 4pe9 A1665 Ob·Nb 2   0.11   0.42   0.86 no 2uuc Z1068 Ob·Nb 2   0.03   0.13   0.81 no 3d5c V64 Ob·Nb 2   0.14   0.17   0.26 no 4tou A1666 Ob·Nb 2   0.07   0.45   0.80 no 4tpc A1666 Ob·Nb 2   0.05   0.30   0.81 no 2vhn Z4065 Ob·Nb 5   0.21   0.61   0.72 no 4b3r A2611 Ob·Nb 2   0.06   0.47   0.73 no 1xnr A1610 Ob·Nb 2   0.04   0.14   0.65 no 2uu9 Z1071 Ob·Nb 2   0.04   0.13   0.89 no 4byd A2600 Ob·Nb 2   0.04   0.30   0.77 no 2qa4 02988 Ob·Nb 2   0.07   0.14   0.53 no 4kfh A1698 Ob·Nb 2   0.07   0.32   0.57 no 3ccu 08080 Ob·Nb 6   0.26   0.71   0.64 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>