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 1vvp 1VVP (3.9Å) -- RIBOSOME : Crystal structure of frameshift suppressor trna sufa6 bound to codon ccc-a on the ribosome List of all 68 Mg2+ binding sites in the PDB structure 1vvp 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 1 of 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vvp A1656 Or 3   0.28   0.20   0.46 no 1vvp A1664 Or 1   0.03  0   0.18 no 1vvp A1648 Ob 1   0.06  0   0.25 no 1vvp A1603 Ob 1   0.02  0   0.21 no 1vvp A1650 Ob 1   0.02  0   0.16 no 1vvp A1655 Ob 1   0.11  0   0.96 no 1vvp A1646 Ob 1   0.04  0   0.15 no 1vvp A1665 Nb 1   0.03  0   0.64 no 1vvp A1628 Nb 1   0.28  0   0.41 no 1vvp A1647 2Or 3   0.23   0.33   0.85 no 1vvp A1645 2Or 2   0.10   0.28   0.55 no 1vvp A1627 2Ob 2   0.03   0.18   0.02 no 1vvp A1636 Ob·Nb 2   0.40   0.04   0.22 no 1vvp A1625 2Nb 2   0.67   0.39   0.85 no 1vvp A1608 2Ob·Nb 3   0.40   0.18   0.92 no 1vvp A1661 2Ob·Nb 3   0.42   0.21   0.59 no 1vvp A1638 Oph 1   0.02  0   0.09 no 1vvp A1614 Oph 1   0.08  0   0.51 no 1vvp A1618 Oph 1   0.08  0   0.08 no 1vvp A1624 Oph 1   0.11  0   0.25 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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