MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 4g5m:A1746, See in JSmolClick on the image to toggle views Site type: Ob·2Nb Schematic drawing for Ob·2Nb List of all 105 Mg2+ binding sites with the site type Ob·2Nb 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 1 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2j02 Z186 Ob·2Nb 3   0.12   0.31   0.02 no 2uuc Z1048 Ob·2Nb 3   0.66   0.32   0.02 no 4lfc A1628 Ob·2Nb 3   0.58   0.33   0.03 no 2uu9 Z1051 Ob·2Nb 3   0.86   0.28   0.03 no 2uua Z53 Ob·2Nb 3   0.67   0.30   0.04 no 2vhp Z4033 Ob·2Nb 6   0.38   0.58   0.06 no 2v48 G2521 Ob·2Nb 3   0.42   0.33   0.09 no 4lfc A1605 Ob·2Nb 3   0.43   0.29   0.11 no 3d5a A1676 Ob·2Nb 3   0.06   0.34   0.12 no 2vhm Z4055 Ob·2Nb 6   0.33   0.83   0.13 no 3oto A1568 Ob·2Nb 3   0.11   0.23   0.21 no 2j00 Z493 Ob·2Nb 3   0.10   0.31   0.21 no 1vx9 A3120 Ob·2Nb 3   0.54   0.42   0.22 no 1vy1 A3228 Ob·2Nb 3   0.13   0.16   0.26 no 4aqy A2685 Ob·2Nb 3   0.25   0.26   0.26 no 4kx0 A3085 Ob·2Nb 3   0.51   0.20   0.28 no 4b3s A2547 Ob·2Nb 3   0.23   0.28   0.28 no 3knk A2934 Ob·2Nb 3   0.16   0.31   0.29 no 4kvb A1609 Ob·2Nb 3   0.10   0.25   0.31 no 4lfa A1624 Ob·2Nb 3   0.50   0.28   0.32 no 3huy A1570 Ob·2Nb 3   0.06   0.26   0.32 no 4kvb A1645 Ob·2Nb 3   0.36   0.32   0.32 no 3knm A2997 Ob·2Nb 3   0.08   0.31   0.34 no 3i8h A2130 Ob·2Nb 3   0.22   0.27   0.34 no 3d5a A1801 Ob·2Nb 3   0.06   0.59   0.35 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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