MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3428, See in JSmolClick on the image to toggle views Site type: Oph·Or Schematic drawing for Oph·Or List of all 1185 Mg2+ binding sites with the site type Oph·Or 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 7 of 48 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dr4 A1846 Oph·Or 2   0.04   0.56   0.60 no 3ohk A2996 Oph·Or 2   0.04   0.36   0.82 no 4dr7 A1694 Oph·Or 2   0.04   0.39   0.82 no 4kfh A2039 Oph·Or 2   0.04   0.23   0.38 no 4ji1 A1692 Oph·Or 2   0.04   0.40   0.83 no 4l6j A6053 Oph·Or 2   0.04   0.22   0.79 no 4dv3 A1815 Oph·Or 2   0.04   0.30   0.85 no 3i9d C1411 Oph·Or 2   0.04   0.46   0.95 no 4dv5 A1800 Oph·Or 2   0.04   0.70   0.64 no 4kfh A2559 Oph·Or 2   0.04   0.26   0.70 no 3ohk A3155 Oph·Or 2   0.04   0.16   0.80 no 4dv2 A1776 Oph·Or 2   0.04   0.36   0.91 no 3uzg A1699 Oph·Or 2   0.04   0.42   0.79 no 3f1h A5219 Oph·Or 2   0.04   0.79   0.07 no 3pyo A3654 Oph·Or 2   0.04   0.39   0.99 no 4qcn A3181 Oph·Or 2   0.04   0.63   0.62 no 3d5d A3144 Oph·Or 2   0.04   0.33   0.19 no 3oh7 A3133 Oph·Or 2   0.04   0.30   0.92 no 3u5h 54432 Oph·Or 2   0.04   0.56   0.48 no 4qcr A3139 Oph·Or 2   0.04   0.28   0.69 no 3huw A1588 Oph·Or 2   0.04   0.40   0.71 no 4btd A3965 Oph·Or 2   0.04   0.71   0.64 no 4l6j A4100 Oph·Or 2   0.04   0.43   0.62 no 4duz A1738 Oph·Or 2   0.04   0.55   0.76 no 3pio X2956 Oph·Or 2   0.04   0.30   0.74 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].

---

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>