MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2r8s:R1004, See in JSmolClick on the image to toggle views Site type: 2Ob Schematic drawing for 2Ob List of all 1662 Mg2+ binding sites with the site type 2Ob 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 15 of 67 | « Previous | Next » | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2wh3 Z166 2Ob 2   0.06   0.16   0.77 no 2x9r Z181 2Ob 2   0.04   0.16   0.65 no 4ji6 A1934 2Ob 2   0.08   0.16   0.99 no 3uz6 A1906 2Ob 2   0.05   0.16   0.70 no 4dr1 A1779 2Ob 2   0.02   0.16   0.73 no 3knm A3219 2Ob 2   0.09   0.16   0.61 no 1vvz A1672 2Ob 2   0.05   0.16   0.03 no 3kis a1653 2Ob 2   0.03   0.16   0.92 no 2uuc Z1070 2Ob 2   0.03   0.16   0.86 no 4l6j A5166 2Ob 2   0.03   0.16   0.80 no 4qcu A3100 2Ob 2   0.03   0.16   0.53 no 4ji3 A1693 2Ob 2   0.04   0.16   0.98 no 1vxk A1661 2Ob 2   0.13   0.16   0.47 no 2xfz Z1684 2Ob 2   0.08   0.16   0.69 no 2x9t Z487 2Ob 2   0.03   0.16   0.76 no 3pyr A3226 2Ob 2   0.04   0.16   0.76 no 3kiu a1580 2Ob 2   0.14   0.16   0.85 no 3v27 A3041 2Ob 2   0.04   0.16   0.85 no 3i8h A1910 2Ob 2   0.07   0.16   0.95 no 3t1y A1632 2Ob 2   0.03   0.16   0.31 no 3v29 A3243 2Ob 2   0.04   0.16   0.80 no 2j02 Z206 2Ob 2   0.08   0.16   0.16 no 3huy A1575 2Ob 2   0.06   0.16   0.45 no 1ibm A1643 2Ob 2   0.03   0.16   0.78 no 4eja A7171 2Ob 2   0.02   0.16   0.80 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>