MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbg:B2955, See in JSmolClick on the image to toggle views Site type: trans,trans-4Oph Schematic drawing for trans,trans-4Oph List of all 74 Mg2+ binding sites with the site type trans,trans-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 1 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vs6 B2944 trans,trans-4Oph 6   0.98   0.82   0.52 yes 1vs8 B2954 trans,trans-4Oph 6   0.94   0.88   0.81 yes 1vvm A3054 trans,trans-4Oph 4   0.58   0.77   0.57 yes 1vvo A3080 trans,trans-4Oph 4   0.51   0.50   0.67 no 1vvq A3056 trans,trans-4Oph 4   0.66   0.73   0.03 no 1vvs A3078 trans,trans-4Oph 4   0.45   0.38   0.44 no 1vvw A3080 trans,trans-4Oph 4   0.31   0.40   0.18 no 1vw0 A3079 trans,trans-4Oph 4   0.56   0.68   0.38 no 1vxj A3079 trans,trans-4Oph 4   0.49   0.67   0.17 no 1vxl A3055 trans,trans-4Oph 4   0.38   0.58   0.40 no 1vxn A3080 trans,trans-4Oph 4   0.42   0.69   0.24 no 1vxq A3055 trans,trans-4Oph 4   0.65   0.63   0.27 no 1vxt A3079 trans,trans-4Oph 4   0.41   0.63   0.49 no 1vy1 A3059 trans,trans-4Oph 4   0.58   0.50   0.20 no 1x8w D4 trans,trans-4Oph 4   0.36   0.76   0.62 no 1x8w B2 trans,trans-4Oph 4   0.77   0.65   0.87 yes 1x8w C1 trans,trans-4Oph 4   0.55   0.92   0.47 no 2aw4 B2944 trans,trans-4Oph 6   0.99   0.80   0.67 yes 2awb B2955 trans,trans-4Oph 6   0.97   0.87   0.67 yes 2i2t B2944 trans,trans-4Oph 6   0.97   0.85   0.90 yes 2i2v B2955 trans,trans-4Oph 6   0.95   0.79   0.80 yes 2qam B3232 trans,trans-4Oph 6   0.99   0.93   0.80 yes 2qao B3298 trans,trans-4Oph 6   0.95   0.79   1.00 yes 2qba B3232 trans,trans-4Oph 6   0.90   0.77   0.96 yes 2qbc B3298 trans,trans-4Oph 6   0.98   0.91   0.55 yes

^# 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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