MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3q1r:B349, See in JSmolClick on the image to toggle views Site type: cis-2Oph·Or·Ob Schematic drawing for cis-2Oph·Or·Ob List of all 24 Mg2+ binding sites with the site type cis-2Oph·Or·Ob in RNA crystal structures 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 #", "PDB ID" or "Mg2+ ID" Page 1 of 1

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1hnw A1563 cis-2Oph·Or·Ob 4   0.13   0.68   0.54 no 1hnz A1563 cis-2Oph·Or·Ob 4   0.12   0.80   0.60 no 1hr0 A1562 cis-2Oph·Or·Ob 4   0.11   0.68   0.68 no 1ibk A1561 cis-2Oph·Or·Ob 4   0.15   0.65   0.48 no 1xnr A1561 cis-2Oph·Or·Ob 4   0.13   0.63   0.90 no 2f4v A1549 cis-2Oph·Or·Ob 4   0.17   0.63   0.41 no 2v46 Z170 cis-2Oph·Or·Ob 4   0.29   0.42   0.52 no 3eoh A436 cis-2Oph·Or·Ob 4   0.07   0.76   0.80 no 3huy A1561 cis-2Oph·Or·Ob 4   0.24   0.51   0.43 no 3kis a1584 cis-2Oph·Or·Ob 4   0.19   0.36   0.73 no 3kno A3007 cis-2Oph·Or·Ob 4   0.18   0.73   0.68 no 3oi0 A1553 cis-2Oph·Or·Ob 4   0.16   0.60   0.77 no 3oi2 A1554 cis-2Oph·Or·Ob 4   0.14   0.61   0.93 no 3q1q B903 cis-2Oph·Or·Ob 4   0.60   0.83   1.00 yes 3q1r B349 cis-2Oph·Or·Ob 4   0.60   0.83   1.00 yes 3t1y A1665 cis-2Oph·Or·Ob 4   0.51   0.60   0.54 no 4b3s A2569 cis-2Oph·Or·Ob 4   0.14   0.59   0.69 no 4b3t A2570 cis-2Oph·Or·Ob 4   0.15   0.73   0.69 no 4dv1 A1629 cis-2Oph·Or·Ob 6   0.39   0.43   0.99 no 4eja A7056 cis-2Oph·Or·Ob 4   0.18   0.82   0.41 no 4khp A1623 cis-2Oph·Or·Ob 4   0.15   0.53   0.80 no 4lf5 A1624 cis-2Oph·Or·Ob 4   0.19   0.63   0.64 no 4nvu A3006 cis-2Oph·Or·Ob 4   0.14   0.43   0.97 no 4qcm A1743 cis-2Oph·Or·Ob 5   0.21   0.57   0.87 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>