MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3bo2:B2, See in JSmolClick on the image to toggle views Site type: cis-2Oph·2Or Schematic drawing for cis-2Oph·2Or List of all 37 Mg2+ binding sites with the site type cis-2Oph·2Or 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vvw A3148 cis-2Oph·2Or 4   0.18   0.61   0.64 no 1vx9 A3161 cis-2Oph·2Or 4   0.10   0.75   0.63 no 1vxj A3213 cis-2Oph·2Or 4   0.08   0.80   0.24 no 1vxn A3204 cis-2Oph·2Or 4   0.32   0.38   0.53 no 1vxt A3202 cis-2Oph·2Or 4   0.33   0.35   0.88 no 1vy3 A3147 cis-2Oph·2Or 4   0.11   0.63   0.35 no 3bo2 B2 cis-2Oph·2Or 5   0.66   0.69   0.89 yes 3bo2 B1018 cis-2Oph·2Or 4   0.26   0.54   0.88 no 3hux A3137 cis-2Oph·2Or 4   0.10   0.83   0.68 no 3huz A2998 cis-2Oph·2Or 4   0.15   0.75   0.67 no 3i8h A1676 cis-2Oph·2Or 4   0.25   0.35   0.57 no 3igi A413 cis-2Oph·2Or 4   0.35   0.60   0.59 no 3kir A3084 cis-2Oph·2Or 4   0.10   0.81   0.81 no 3oh5 A3148 cis-2Oph·2Or 4   0.10   0.66   0.83 no 3ohk A3127 cis-2Oph·2Or 4   0.10   0.80   0.90 no 3u5d 14048 cis-2Oph·2Or 4   0.09   0.69   0.66 no 3u5d 14051 cis-2Oph·2Or 4   0.06   0.79   0.93 no 3u5h 54051 cis-2Oph·2Or 4   0.12   0.73   0.66 no 3v24 A1657 cis-2Oph·2Or 6   0.35   0.68   0.89 no 3v28 A1712 cis-2Oph·2Or 6   0.35   0.64   0.86 no 3v6u A1623 cis-2Oph·2Or 5   0.51   0.23   0.02 no 4byd A2536 cis-2Oph·2Or 5   0.87   0.60   0.82 no 4dhc A3520 cis-2Oph·2Or 6   0.32   0.58   0.96 no 4dv7 A1614 cis-2Oph·2Or 5   0.25   0.52   0.75 no 4far A431 cis-2Oph·2Or 5   0.55   0.35   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/)
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