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 12 of 24 | « Previous | Next » | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3kiu a1543 Ob·Nb 2   0.03   0.14   0.37 no 3kiu a1641 Ob·Nb 2   0.06   0.13   0.30 no 3kiu a1651 Ob·Nb 2   0.04   0.21   0.80 no 3kiw A3079 Ob·Nb 2   0.05   0.13   0.78 no 3kiw A2978 Ob·Nb 2   0.10   0.16   0.58 no 3kiw A3156 Ob·Nb 2   0.03   0.14   0.67 no 3kiw A3064 Ob·Nb 2   0.04   0.11   0.70 no 3kix a1663 Ob·Nb 2   0.12   0.27   0.83 no 3kiy A2978 Ob·Nb 2   0.07   0.16   0.64 no 3knh A1652 Ob·Nb 2   0.13   0.06   0.46 no 3kni A3288 Ob·Nb 2   0.07   0.11   0.46 no 3kni A3085 Ob·Nb 2   0.06   0.09   0.38 no 3kni A2923 Ob·Nb 2   0.34   0.07   0.23 no 3kni A3048 Ob·Nb 2   0.25   0.05   0.63 no 3kni A2995 Ob·Nb 2   0.24   0.09   0.36 no 3knj X637 Ob·Nb 2   0.11   0.53   0.49 no 3knj A1572 Ob·Nb 2   0.20   0.11   0.36 no 3knj A1582 Ob·Nb 2   0.11   0.07   0.93 no 3knk A2948 Ob·Nb 2   0.04   0.17   0.34 no 3knk A3160 Ob·Nb 2   0.11   0.20   0.70 no 3knk A2984 Ob·Nb 2   0.07   0.15   0.57 no 3knl A1614 Ob·Nb 2   0.08   0.10   0.35 no 3knm A2990 Ob·Nb 2   0.40   0.19   0.08 no 3knm A3196 Ob·Nb 2   0.03   0.14   0.77 no 3knm A2921 Ob·Nb 2   0.17   0.12   0.10 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>