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 1vq5 1VQ5 (2.6Å) -- RIBOSOME : The structure of the transition state analogue "raa" bound to the large ribosomal subunit of haloarcula marismortui List of all 118 Mg2+ binding sites in the PDB structure 1vq5 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 3 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vq5 08067 Mg2+ bound by non-RNA 5   0.40   0.86   0.71 no 1vq5 08088 poly-nuclear Mg2+ site 6   0.28   0.89   0.90 no 1vq5 08119 poly-nuclear Mg2+ site 5   0.73   0.59   0.80 no 1vq5 A8066 Mg2+ bound by non-RNA 5   0.48   0.61   0.84 no 1vq5 28076 Rout·2Bout 5   0.33   0.63   0.75 no 1vq5 38078 Mg2+ bound by non-RNA 6   0.49   0.91   0.93 no 1vq5 08050 Oph 2   0.27   0.23   0.69 no 1vq5 08082 Oph·Pout 4   0.28   0.41   0.75 no 1vq5 T8073 Mg2+ not bound by RNA 5   0.13   0.70   0.68 no 1vq5 Y8109 Mg2+ not bound by RNA 5   0.20   0.46   0.94 no 1vq5 08024 Nb 4   0.35   0.49   0.66 no 1vq5 08008 mer-3Oph 6   0.90   0.92   0.97 yes 1vq5 08081 mer-3Oph 5   0.58   0.70   1.00 yes 1vq5 08001 fac-3Oph 6   0.85   0.95   0.99 yes 1vq5 08010 Mg2+ bound by non-RNA 6   0.95   0.91   0.86 yes 1vq5 08031 poly-nuclear Mg2+ site 6   0.97   0.82   0.89 yes 1vq5 08038 6Bout 6   0.88   0.86   0.98 yes 1vq5 08045 Oph·2Pout 5   0.59   0.70   0.75 yes 1vq5 08063 2Bout 5   0.57   0.75   0.76 yes 1vq5 08091 Oph·5Pout 6   0.67   0.89   0.59 yes

^# 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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