MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 3v2d 3V2D (2.7Å) -- RIBOSOME : Crystal structure of yfia bound to the 70s ribosome. this pdb entry contains coordinates for the 50s subunit of the 1st ribosome in the asu List of all 803 Mg2+ binding sites in the PDB structure 3v2d 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 #", "Site type" or "Mg2+ ID" Page 3 of 41 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3v2d A3201 Ob 6   0.67   0.96   0.65 yes 3v2d A3060 Ob 1   0.02  0   0.82 no 3v2d B213 Ob 4   0.38   0.73   0.88 no 3v2d A3640 Ob 2   0.17   0.19   0.82 no 3v2d A3057 Nb 1   0.03  0   0.96 no 3v2d A3525 Nb 3   0.26   0.45   0.78 no 3v2d A3462 Nb 3   0.24   0.36   0.93 no 3v2d A3162 Nb 4   0.37   0.71   0.66 no 3v2d A3273 Nb 2   0.13   0.15   0.92 no 3v2d A3429 Nb 4   0.41   0.61   0.81 no 3v2d A3228 Nb 3   0.27   0.42   0.92 no 3v2d A3207 Nb 6   0.66   0.87   0.98 yes 3v2d A3096 Nb 1   0.03  0   0.95 no 3v2d A3255 Nb 4   0.42   0.76   0.71 no 3v2d A3496 Nb 4   0.38   0.75   0.70 no 3v2d A3407 Nb 6   0.75   0.94   0.81 yes 3v2d A3120 Nb 6   0.71   0.96   0.75 yes 3v2d A3034 2Or 2   0.02   0.18   0.89 no 3v2d A3081 2Or 2   0.06   0.12   0.79 no 3v2d A3606 2Or 5   0.37   0.50   0.89 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>