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 1vvw 1VVW (3.9Å) -- RIBOSOME : Crystal structure of frameshift suppressor trna sufa6 bound to codon ccg-g on the ribosome List of all 272 Mg2+ binding sites in the PDB structure 1vvw 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 14 | « 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 1vvw A3088 Oph 1   0.03  0   0.32 no 1vvw A3089 Oph 1   0.03  0   0.16 no 1vvw A3095 Oph 1   0.08  0   0.09 no 1vvw A3101 Oph 1   0.15  0   0.04 no 1vvw A3109 Oph 1   0.09  0   0.28 no 1vvw A3110 Oph 1   0.17  0   0.60 no 1vvw A3120 Oph 1   0.18  0   0.01 no 1vvw A3123 Oph 1   0.05  0   0.36 no 1vvw A3126 Oph 1   0.08  0   0.14 no 1vvw A3134 Oph 1   0.01  0   0.19 no 1vvw A3139 Oph 1   0.05  0   0.57 no 1vvw A3156 Oph 1   0.03  0   0.13 no 1vvw A3160 Oph 1   0.05  0   0.81 no 1vvw A3171 Oph 1   0.08  0   0.77 no 1vvw A3178 Oph 1   0.05  0   0.04 no 1vvw A3181 Oph 1   0.05  0   0.06 no 1vvw A3188 Oph 1   0.42  0   0.12 no 1vvw A3193 Oph 1   0.09  0   0.04 no 1vvw A3199 Oph 1   0.07  0   0.50 no 1vvw A3002 Oph 1   0.14  0   0.39 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>