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 3ofd A2945 trans,cis-4Oph 6   0.48   0.84   0.73 no 3ofq A2946 trans,cis-4Oph 6   0.49   0.84   0.96 no 3ofr A3012 trans,cis-4Oph 6   0.67   0.72   0.87 yes 3og0 A2944 trans,cis-4Oph 6   0.46   0.90   0.75 no 3ohj A2993 trans,cis-4Oph 4   0.33   0.55   0.45 no 3ohz A2967 trans,cis-4Oph 4   0.26   0.40   0.65 no 3oi1 A2966 trans,cis-4Oph 4   0.17   0.36   0.73 no 3oi3 A2993 trans,cis-4Oph 4   0.31   0.56   0.33 no 3oi3 A2968 trans,cis-4Oph 4   0.46   0.50   0.82 no 3oi5 A2992 trans,cis-4Oph 4   0.31   0.32   0.99 no 3orb A3011 trans,cis-4Oph 6   0.60   0.63   0.24 no 3pio X2944 trans,cis-4Oph 4   0.11   0.42   0.98 no 3pip X2951 trans,cis-4Oph 4   0.17   0.29   0.50 no 3pyt A2920 trans,cis-4Oph 4   0.34   0.45   0.64 no 3r8s A3013 trans,cis-4Oph 6   0.95   0.90  0 no 3r8t A3012 trans,cis-4Oph 6   0.69   0.85   0.70 yes 3sgf A2973 trans,cis-4Oph 4   0.32   0.59   0.97 no 3u5h 53945 trans,cis-4Oph 4   0.28   0.54   0.74 no 3uz7 A1608 trans,cis-4Oph 4   0.20   0.57   0.91 no 3v23 A3189 trans,cis-4Oph 4   0.19   0.57   0.73 no 3v23 A3236 trans,cis-4Oph 4   0.20   0.45   0.89 no 3v27 A3259 trans,cis-4Oph 4   0.17   0.37   0.77 no 3v27 A3281 trans,cis-4Oph 4   0.15   0.43   0.64 no 3v2d A3426 trans,cis-4Oph 5   0.33   0.72   0.84 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].

---

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>