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 4ji1 4JI1 (3.14Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of 30s ribosomal subunit from thermus thermophilus List of all 304 Mg2+ binding sites in the PDB structure 4ji1 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 16 | « 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 4ji1 A1667 Or 1   0.02  0   0.95 no 4ji1 A1678 Or 1   0.15  0   0.45 no 4ji1 A1861 Or 1   0.01  0   0.73 no 4ji1 A1700 Or 1   0.01  0   0.63 no 4ji1 A1677 Or 2   0.07   0.45   0.82 no 4ji1 A1888 Or 1   0.02  0   0.92 no 4ji1 A1850 Ob 1   0.01  0   0.90 no 4ji1 A1694 Ob 1   0.02  0   0.89 no 4ji1 A1843 Ob 1   0.01  0   0.72 no 4ji1 A1679 Ob 1   0.03  0   0.84 no 4ji1 A1657 Ob 4   0.50   0.65   0.79 no 4ji1 A1698 Ob 1   0.02  0   0.99 no 4ji1 A1708 Ob 1   0.01  0   0.91 no 4ji1 A1712 Ob 4   0.49   0.71   0.48 no 4ji1 A1640 Ob 4   0.48   0.65   0.57 no 4ji1 A1895 Ob 2   0.06   0.30   1.00 no 4ji1 A1634 Ob 1   0.01  0   0.70 no 4ji1 A1654 Ob 4   0.49   0.67   0.86 no 4ji1 A1713 Ob 5   0.67   0.67   0.56 yes 4ji1 A1824 Ob 1   0.01  0   0.65 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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