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 3v2e 3V2E (2.7Å) -- RIBOSOME/INHIBITOR : Crystal structure of yfia bound to the 70s ribosome. this pdb entry contains coordinates for the 30s subunit with bound yfia of the 2nd ribosome in the asu List of all 206 Mg2+ binding sites in the PDB structure 3v2e 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 5 of 11 | « 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 3v2e A1675 Oph·Ob·Nb 5   0.36   0.63   0.97 no 3v2e A1662 cis-2Oph 4   0.38   0.36   0.94 no 3v2e A1656 cis-2Oph 4   0.32   0.35   0.91 no 3v2e A1692 cis-2Oph 5   0.43   0.46   0.79 no 3v2e A1672 cis-2Oph 5   0.45   0.77   0.87 no 3v2e A1667 cis-2Oph 6   0.57   0.92   0.90 yes 3v2e A1621 cis-2Oph 2   0.05   0.14   0.73 no 3v2e A1663 trans-2Oph 4   0.30   0.35   0.95 no 3v2e A1712 trans-2Oph 5   0.49   0.73   0.98 no 3v2e A1665 fac-3Oph 4   0.18   0.50   0.92 no 3v2e A1680 mer-3Oph·Or 6   0.39   0.66   0.86 no 3v2e A1639 other RNA-inner types 3   0.06   0.60   0.81 no 3v2e A1699 other RNA-inner types 4   0.17   0.29   0.97 no 3v2e A1689 other RNA-inner types 6   0.21   0.63   0.92 no 3v2e A1618 other RNA-inner types 4   0.11   0.51   0.89 no 3v2e A1619 other RNA-inner types 3   0.06   0.26   0.67 no 3v2e A1615 other RNA-inner types 4   0.07   0.51   0.88 no 3v2e A1631 other RNA-inner types 5   0.07   0.53   0.96 no 3v2e A1713 other RNA-inner types 5   0.19   0.43   0.98 no 3v2e A1791 other RNA-inner types 5   0.31   0.65   0.97 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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