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 2 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 3kiu a1651 Ob·Nb 2   0.04   0.21   0.80 no 4nxm A1720 Ob·Nb 2   0.04   0.13   0.79 no 2uxc Z128 Ob·Nb 2   0.08   0.12   0.69 no 3t1h A1732 Ob·Nb 2   0.06   0.17   0.05 no 4dr1 A1733 Ob·Nb 5   0.50   0.50   0.63 no 3i9d A1669 Ob·Nb 2   0.25   0.08   0.51 no 2uub Z1141 Ob·Nb 2   0.05   0.43   0.64 no 3v27 A3163 Ob·Nb 2   0.11   0.18   0.79 no 4tpb A3163 Ob·Nb 2   0.04   0.16   0.67 no 3oi3 A163 Ob·Nb 2   0.03   0.13   0.65 no 4qcn A3171 Ob·Nb 2   0.05   0.36   0.76 no 2wdk Z311 Ob·Nb 2   0.10   0.12   0.60 no 4nxn A1783 Ob·Nb 2   0.06   0.10   0.48 no 2wdk Z491 Ob·Nb 2   0.04   0.14   0.81 no 2wdk Z493 Ob·Nb 2   0.03   0.32   0.59 no 4ji2 A1813 Ob·Nb 2   0.09   0.24   0.93 no 1vvw A3210 Ob·Nb 2   0.40   0.13   0.82 no 4duz A1832 Ob·Nb 2   0.03   0.39   0.92 no 3v2f A3240 Ob·Nb 5   0.40   0.51   0.74 no 4kfk A2191 Ob·Nb 2   0.05   0.12   0.70 no 3uz7 C124 Ob·Nb 2   0.03   0.23   0.97 no 4ji1 A1868 Ob·Nb 2   0.04   0.13   0.81 no 4qcr A3259 Ob·Nb 2   0.05   0.22   0.86 no 4dv4 A1868 Ob·Nb 2   0.04   0.15   0.95 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>