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 8 of 14 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vvw B202 Mg2+ not bound by RNA 0  0  0   0.42 no 1vvw D302 Mg2+ not bound by RNA 1   0.35  0   0.96 no 1vvw 0101 Mg2+ not bound by RNA 0  0  0   0.13 no 1vvw A3217 Oph 1   0.21  0   0.29 no 1vvw A3221 Oph 1   0.18  0   0.64 no 1vvw A3224 Oph 1   0.05  0   0.08 no 1vvw A3241 poly-nuclear Mg2+ site 2   0.34   0.02   0.62 no 1vvw A3140 2Nb 2   0.35   0.05   0.24 no 1vvw A3131 Oph·Nb 2   0.36   0.06   0.32 no 1vvw A3154 2Or 2   0.08   0.07   0.26 no 1vvw A3176 Ob·Nb 2   0.10   0.08   0.74 no 1vvw A3035 cis-2Oph 2   0.28   0.08   0.32 no 1vvw A3233 trans-2Oph 2   0.24   0.08   0.46 no 1vvw A3096 cis-2Oph 2   0.10   0.09   0.05 no 1vvw A3093 trans-2Oph 2   0.94   0.09   0.19 no 1vvw A3098 cis-2Oph 2   0.16   0.09   0.14 no 1vvw A3061 cis-2Oph 2   0.10   0.11   0.08 no 1vvw A3162 2Or 2   0.22   0.11   0.70 no 1vvw A3214 Oph·Or 2   0.24   0.11   0.13 no 1vvw A3175 Oph·Ob 2   0.04   0.12   0.47 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/)
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