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 4gkj 4GKJ (3.3Å) -- RIBOSOME/ANTIBIOTIC : Structure of the thermus thermophilus 30s ribosomal subunit complexed with a human mitochondrial anticodon stem loop (asl) of transfer rna methionine (trnamet) bound to an mrna with an aug-codon in the a-site and paromomycin. List of all 166 Mg2+ binding sites in the PDB structure 4gkj 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 7 of 9 | « 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 4gkj A1754 Mg2+ not bound by RNA 0  0  0   0.85 no 4gkj A1755 Mg2+ not bound by RNA 0  0  0   0.70 no 4gkj A1756 Mg2+ not bound by RNA 0  0  0   0.83 no 4gkj A1762 Mg2+ not bound by RNA 0  0  0   0.71 no 4gkj A1764 Mg2+ not bound by RNA 0  0  0   0.88 no 4gkj A1783 Mg2+ not bound by RNA 0  0  0   0.94 no 4gkj A1620 Mg2+ not bound by RNA 0  0  0   0.81 no 4gkj A1784 Mg2+ not bound by RNA 0  0  0   0.96 no 4gkj A1778 Mg2+ not bound by RNA 0  0  0   0.48 no 4gkj B301 Mg2+ not bound by RNA 0  0  0   0.93 no 4gkj N101 Mg2+ not bound by RNA 0  0  0   0.79 no 4gkj A1668 Mg2+ not bound by RNA 0  0  0   0.99 no 4gkj A1670 Mg2+ not bound by RNA 0  0  0   0.97 no 4gkj A1692 Mg2+ not bound by RNA 0  0  0   0.63 no 4gkj A1621 Mg2+ not bound by RNA 0  0  0   0.73 no 4gkj A1699 Mg2+ not bound by RNA 0  0  0   0.93 no 4gkj A1652 Mg2+ not bound by RNA 0  0  0   0.94 no 4gkj A1729 Mg2+ not bound by RNA 0  0  0   0.75 no 4gkj A1744 Mg2+ not bound by RNA 0  0  0   0.83 no 4gkj A1656 Mg2+ not bound by RNA 0  0  0   0.80 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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