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 4dh9 4DH9 (3.2Å) -- RIBOSOME : Crystal structure of yaej bound to the 70s ribosome List of all 384 Mg2+ binding sites in the PDB structure 4dh9 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 20 | « 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 4dh9 A1717 Or 1   0.03  0   0.88 no 4dh9 A1817 Or 1   0.02  0   0.99 no 4dh9 A1605 Or 1   0.01  0   0.72 no 4dh9 A1683 Or 1   0.01  0   0.93 no 4dh9 A1724 Or 1   0.02  0   0.98 no 4dh9 A1737 Or 1   0.02  0   0.91 no 4dh9 A1781 Or 1   0.02  0   0.85 no 4dh9 A1932 Ob 4   0.39   0.75   0.75 no 4dh9 A1795 Ob 1   0.02  0   0.84 no 4dh9 A1845 Ob 5   0.53   0.69   0.86 yes 4dh9 A1733 Ob 1   0.03  0   0.89 no 4dh9 A1797 Ob 1   0.01  0   0.66 no 4dh9 A1732 Ob 1   0.01  0   0.85 no 4dh9 A1930 Ob 4   0.39   0.76   0.93 no 4dh9 A1836 Ob 1   0.02  0   0.85 no 4dh9 A1679 Ob 1   0.01  0   0.97 no 4dh9 A1629 Ob 1   0.02  0   0.80 no 4dh9 A1831 Ob 1   0.01  0   0.92 no 4dh9 A1838 Ob 2   0.15   0.08   0.85 no 4dh9 A1608 Nb 1   0.02  0   0.84 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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