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 4kj1 A3040 trans,cis-4Oph 5   0.36   0.41   0.84 no 4kj3 A3040 trans,cis-4Oph 6   0.36   0.59   0.60 no 4pec A3040 trans,cis-4Oph 4   0.11   0.69   0.70 no 4tpb A3041 trans,cis-4Oph 4   0.10   0.58   0.72 no 4tp3 A3041 trans,cis-4Oph 4   0.11   0.64   0.79 no 4tp7 A3042 trans,cis-4Oph 4   0.16   0.63   0.74 no 4tpf A3042 trans,cis-4Oph 4   0.19   0.72   0.81 no 4qco A3044 trans,cis-4Oph 4   0.41   0.55   0.89 no 4kx0 A3044 trans,cis-4Oph 4   0.62   0.34   0.56 no 1vvu A3054 trans,cis-4Oph 4   0.61   0.63   0.76 yes 1vvy A3054 trans,cis-4Oph 4   0.69   0.49   0.20 no 1vx9 A3055 trans,cis-4Oph 4   0.74   0.73   0.59 yes 4kx0 A3088 trans,cis-4Oph 4   0.34   0.38   0.52 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 4tom A3109 trans,cis-4Oph 6   0.72   0.94   0.58 yes 4kiz A3109 trans,cis-4Oph 5   0.59   0.52   0.47 no 1vvs A3110 trans,cis-4Oph 4   0.60   0.55   0.51 no 4tp5 A3110 trans,cis-4Oph 6   0.75   0.81   0.53 yes 4tpd A3110 trans,cis-4Oph 6   0.82   0.91   0.09 no 1vy1 A3110 trans,cis-4Oph 4   0.45   0.32   0.63 no 4kx2 A3112 trans,cis-4Oph 4   0.60   0.72   0.89 yes 1vw0 A3112 trans,cis-4Oph 4   0.87   0.68   0.28 no 3d5b A3132 trans,cis-4Oph 4   0.16   0.55   0.33 no 3d5d A3147 trans,cis-4Oph 4   0.18   0.36   0.31 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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