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 4 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 A1776 cis-2Oph 2   0.18   0.27   0.99 no 4gkj A1763 cis-2Oph 2   0.08   0.16   0.87 no 4gkj A1658 cis-2Oph 2   0.36   0.25   0.93 no 4gkj A1686 cis-2Oph 2   0.11   0.20   0.98 no 4gkj A1644 cis-2Oph 2   0.08   0.17   0.77 no 4gkj A1726 cis-2Oph 2   0.33   0.27   0.83 no 4gkj A1769 trans-2Oph 2   0.11   0.62   0.86 no 4gkj A1657 trans-2Oph 2   0.05   0.61   0.54 no 4gkj A1706 cis-2Oph·Ob 3   0.19   0.44   0.70 no 4gkj A1663 cis-2Oph·Ob 3   0.14   0.32   0.82 no 4gkj A1688 cis-2Oph·2Ob 4   0.43   0.65   0.90 no 4gkj A1743 fac-3Oph 3   0.30   0.44   0.93 no 4gkj A1711 mer-3Oph 3   0.38   0.38   0.96 no 4gkj A1758 mer-3Oph 3   0.44   0.57   0.93 no 4gkj A1761 other RNA-inner types 4   0.15   0.43   0.88 no 4gkj A1780 poly-nuclear Mg2+ site 1   0.01  0   0.73 no 4gkj A1738 poly-nuclear Mg2+ site 3   0.07   0.34   0.80 no 4gkj A1775 poly-nuclear Mg2+ site 1   0.02  0   0.71 no 4gkj A1614 Mg2+ not bound by RNA 0  0  0   0.67 no 4gkj A1613 Mg2+ not bound by RNA 0  0  0  0 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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