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 4jya 4JYA (3.1Å) -- RIBOSOME : Crystal structures of pseudouridinilated stop codons with asls List of all 13 Mg2+ binding sites in the PDB structure 4jya 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 1

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4jya A1613 2Ob 2   0.03   0.19   0.57 no 4jya A1610 Oph 1   0.14  0   0.82 no 4jya A1604 cis-2Oph 2   0.35   0.11   0.74 no 4jya A1602 cis-2Oph 2   0.37   0.21   0.69 no 4jya A1603 fac-3Oph 3   0.26   0.25   0.79 no 4jya A1609 mer-3Oph 3   0.31   0.35   0.90 no 4jya A1606 other RNA-inner types 4   0.18   0.35   0.82 no 4jya A1605 other RNA-inner types 3   0.06   0.23   0.55 no 4jya A1601 other RNA-inner types 3   0.07   0.36   0.53 no 4jya A1608 Mg2+ not bound by RNA 0  0  0   0.82 no 4jya A1612 Mg2+ not bound by RNA 0  0  0   0.88 no 4jya X101 Mg2+ not bound by RNA 1   0.02  0   0.71 no 4jya A1607 Mg2+ not bound by RNA 0  0  0   0.83 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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