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 3cc4 08080 Ob·Nb 6   0.16   0.76   0.78 no 3cc7 08080 Ob·Nb 6   0.23   0.88   0.69 no 3cce 08080 Ob·Nb 6   0.27   0.64   0.66 no 3ccm 08080 Ob·Nb 6   0.22   0.67   0.70 no 3ccq 08080 Ob·Nb 6   0.23   0.74   0.65 no 3ccu 08080 Ob·Nb 6   0.26   0.71   0.64 no 3ccv 08080 Ob·Nb 5   0.26   0.61   0.68 no 3cma 08080 Ob·Nb 5   0.10   0.51   0.68 no 3cme 08080 Ob·Nb 4   0.08   0.36   0.87 no 3cpw 08080 Ob·Nb 6   0.30   0.89   0.73 no 3cxc 08102 Ob·Nb 6   0.45   0.83   0.70 no 3d5b A3068 Ob·Nb 2   0.02   0.42   0.11 no 3d5b A3204 Ob·Nb 2   0.04   0.14   0.18 no 3d5b A3357 Ob·Nb 2   0.04   0.14   0.18 no 3d5b A2980 Ob·Nb 2   0.09   0.19   0.07 no 3d5b A3109 Ob·Nb 2   0.03   0.12   0.60 no 3d5c V64 Ob·Nb 2   0.14   0.17   0.26 no 3d5c A1638 Ob·Nb 2   0.05   0.52   0.33 no 3d5c A1846 Ob·Nb 2   0.05   0.16   0.22 no 3d5d A3465 Ob·Nb 2   0.06   0.17   0.18 no 3d5d A3550 Ob·Nb 2   0.04   0.13   0.21 no 3d5d A3548 Ob·Nb 2   0.03   0.16   0.99 no 3dll Z124 Ob·Nb 2   0.04   0.12   0.21 no 3f1f A5795 Ob·Nb 2   0.06   0.23   0.45 no 3f1f A5546 Ob·Nb 2   0.03   0.13   0.95 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>