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 3uz7 3UZ7 (3Å) -- RIBOSOME : Crystal structure analysis of ribosomal decoding. this entry contains the 30s ribosomal subunit of the second 70s molecule in the asymmetric unit for the cognate trna-tyr complex. List of all 261 Mg2+ binding sites in the PDB structure 3uz7 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 1 of 14 | « 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 3uz7 A1656 other RNA-inner types 5   0.15   0.88   0.83 no 3uz7 G302 Mg2+ not bound by RNA 5   0.09   0.77   0.82 no 3uz7 A1622 Mg2+ bound by non-RNA 5   0.14   0.65   0.82 no 3uz7 A1608 trans,cis-4Oph 4   0.20   0.57   0.91 no 3uz7 A1657 Mg2+ bound by non-RNA 4   0.11   0.46   0.74 no 3uz7 A1960 Mg2+ bound by non-RNA 4   0.11   0.66   0.68 no 3uz7 A2197 other RNA-inner types 3   0.07   0.41   0.89 no 3uz7 A1876 Oph·2Ob 3   0.07   0.61   0.83 no 3uz7 A1799 mer-3Oph 3   0.09   0.79   0.89 no 3uz7 A1809 Oph·2Ob 3   0.08   0.53   0.85 no 3uz7 A1823 Oph·2Or 3   0.06   0.50   0.85 no 3uz7 A1623 fac-3Oph 3   0.12   0.20   0.67 no 3uz7 A1648 cis-2Oph·Ob 3   0.08   0.65   0.83 no 3uz7 A1642 fac-3Oph 3   0.15   0.50   0.99 no 3uz7 A1655 Mg2+ bound by non-RNA 3   0.08   0.63   0.74 no 3uz7 A1961 fac-3Oph 3   0.05   0.43   0.84 no 3uz7 A1617 fac-3Oph 3   0.13   0.29   0.87 no 3uz7 A1621 mer-3Oph 3   0.13   0.60   0.80 no 3uz7 A1833 mer-3Oph 3   0.05   0.68   0.82 no 3uz7 A1800 other RNA-inner types 3   0.09   0.28   0.74 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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