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 4dr6 4DR6 (3.3Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the thermus thermophilus (hb8) 30s ribosomal subunit with codon, near-cognate transfer rna anticodon stem-loop mismatched at the first codon position and streptomycin bound List of all 371 Mg2+ binding sites in the PDB structure 4dr6 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 19 | « 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 4dr6 A1752 Or 1   0.03  0   0.49 no 4dr6 A1771 Or 1   0.05  0   0.66 no 4dr6 A1691 Or 1   0.02  0   1.00 no 4dr6 A1617 Or 1   0.02  0   0.81 no 4dr6 A1729 Or 1   0.03  0   0.89 no 4dr6 A1924 Ob 1   0.02  0   0.82 no 4dr6 A1713 Ob 3   0.34   0.38   0.75 no 4dr6 A1794 Ob 2   0.05   0.14   0.72 no 4dr6 A1707 Ob 5   0.65   0.68   0.33 no 4dr6 A1709 Ob 4   0.51   0.64   0.91 yes 4dr6 A1664 Ob 3   0.33   0.34   0.63 no 4dr6 A1728 Ob 1   0.02  0   0.99 no 4dr6 A1749 Ob 1   0.02  0   0.76 no 4dr6 A1761 Ob 1   0.01  0   0.58 no 4dr6 A1805 Ob 1   0.01  0   0.89 no 4dr6 A1795 Ob 1   0.01  0   0.86 no 4dr6 A1776 Ob 1   0.01  0   0.94 no 4dr6 A1806 Ob 1   0.03  0   0.85 no 4dr6 A1652 Ob 1   0.01  0   0.79 no 4dr6 A1948 Ob 1   0.01  0   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].

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