MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs8:B2991, See in JSmolClick on the image to toggle views Site type: trans,cis-4Oph Schematic drawing for trans,cis-4Oph List of all 107 Mg2+ binding sites with the site type trans,cis-4Oph 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 3 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 4pec A3040 trans,cis-4Oph 4   0.11   0.69   0.70 no 4bye A3940 trans,cis-4Oph 4   0.74   0.64   0.74 yes 4qct A3464 trans,cis-4Oph 5   0.22   0.45   0.92 no 2vhn Z4076 trans,cis-4Oph 5   0.12   0.63   0.95 no 4qcp A3457 trans,cis-4Oph 5   0.22   0.44   0.90 no 4dhc A3404 trans,cis-4Oph 5   0.26   0.39   0.95 no 3v2d A3426 trans,cis-4Oph 5   0.33   0.72   0.84 no 4kj1 A3040 trans,cis-4Oph 5   0.36   0.41   0.84 no 4kiz A3109 trans,cis-4Oph 5   0.59   0.52   0.47 no 4kj5 A3106 trans,cis-4Oph 5   0.76   0.61   0.63 yes 4kix A3107 trans,cis-4Oph 5   0.91   0.63   0.78 yes 3i1n A3013 trans,cis-4Oph 6   0.54   0.66   0.24 no 3orb A3011 trans,cis-4Oph 6   0.60   0.63   0.24 no 2qbk B2993 trans,cis-4Oph 6   0.88   0.72   0.48 no 2qp1 B2993 trans,cis-4Oph 6   0.63   0.45   0.36 no 4kj3 A3040 trans,cis-4Oph 6   0.36   0.59   0.60 no 2vhn Z4073 trans,cis-4Oph 6   0.24   0.65   0.48 no 2qao B3512 trans,cis-4Oph 6   0.94   0.84   0.69 yes 2z4l B2992 trans,cis-4Oph 6   0.79   0.87   0.50 no 3df4 B3512 trans,cis-4Oph 6   0.83   0.89   0.72 yes 2qox B2955 trans,cis-4Oph 6   0.99   0.69   0.52 yes 2qox B2992 trans,cis-4Oph 6   0.82   0.67   0.39 no 4tpd A3110 trans,cis-4Oph 6   0.82   0.91   0.09 no 4dha A3733 trans,cis-4Oph 6   0.45   0.60   0.85 no 3v2f A3495 trans,cis-4Oph 6   0.38   0.67   0.93 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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