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 3t1h A1683 Ob·Nb 2   0.07   0.13   0.39 no 4ji2 A1685 Ob·Nb 6   0.65   0.72   0.57 yes 4nxm A1685 Ob·Nb 6   0.68   0.71   0.63 yes 4ox9 A1686 Ob·Nb 2   0.39   0.05   0.44 no 3t1y A1693 Ob·Nb 2   0.17   0.23   0.13 no 3i9d A1693 Ob·Nb 2   0.21   0.42   0.91 no 3t1y A1696 Ob·Nb 2   0.09   0.17   0.30 no 3v26 A1697 Ob·Nb 4   0.28   0.41   0.97 no 3v22 A1697 Ob·Nb 4   0.29   0.50   0.88 no 4kfh A1698 Ob·Nb 2   0.07   0.32   0.57 no 3t1h A1699 Ob·Nb 2   0.04   0.14   0.28 no 3t1y A1700 Ob·Nb 2   0.06   0.11   0.25 no 3wqy C1703 Ob·Nb 2   0.07   0.09   0.56 no 4ji4 A1706 Ob·Nb 5   0.52   0.74   0.79 yes 4qcm A1708 Ob·Nb 2   0.05   0.21   0.93 no 4duy A1709 Ob·Nb 5   0.51   0.49   0.53 no 4ji0 A1710 Ob·Nb 3   0.18   0.14   0.64 no 4g5t A1715 Ob·Nb 2   0.09   0.16   0.97 no 4g5v A1715 Ob·Nb 2   0.22   0.26   0.90 no 4nxm A1720 Ob·Nb 2   0.04   0.13   0.79 no 4ji6 A1720 Ob·Nb 2   0.08   0.13   0.81 no 3t1y A1721 Ob·Nb 2   0.05   0.12   0.46 no 4ji0 A1721 Ob·Nb 2   0.04   0.15   0.90 no 4dr1 A1728 Ob·Nb 2   0.03   0.13   0.90 no 4ji5 A1730 Ob·Nb 2   0.07   0.10   0.84 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/)
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