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 16 of 67 | « Previous | Next » | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dv0 A1679 2Ob 2   0.04   0.16   0.98 no 4dv7 A1739 2Ob 2   0.03   0.16   0.92 no 4kfk A2100 2Ob 2   0.07   0.16   0.75 no 3pyo A2929 2Ob 2   0.03   0.16   0.53 no 4qcv A3344 2Ob 3   0.15   0.16   0.75 no 4nxn A1715 2Ob 2   0.05   0.16   0.76 no 1vx9 A3221 2Ob 2   0.04   0.16   0.24 no 4ji7 A1676 2Ob 2   0.03   0.16   0.77 no 3v23 B202 2Ob 2   0.03   0.16   0.90 no 4dv2 A1730 2Ob 2   0.03   0.16   0.85 no 4ji7 A1678 2Ob 2   0.03   0.16   0.68 no 3pyr A141 2Ob 2   0.04   0.16   0.55 no 4qcv A3262 2Ob 2   0.05   0.16   0.87 no 4dr6 A1773 2Ob 2   0.03   0.16   0.72 no 3i8h A1642 2Ob 2   0.02   0.16   0.72 no 3d5b A3080 2Ob 2   0.07   0.16   0.51 no 3uz4 A1764 2Ob 2   0.04   0.16   0.76 no 3oto A1628 2Ob 2   0.05   0.16   0.76 no 4kfk A2301 2Ob 2   0.03   0.16   0.88 no 3oi3 A3208 2Ob 2   0.09   0.16   0.77 no 1ibm A1656 2Ob 2   0.06   0.16   0.71 no 4nxn A1789 2Ob 2   0.04   0.16   0.72 no 2uxc Z174 2Ob 2   0.05   0.16   0.86 no 3hux A3280 2Ob 2   0.04   0.16   0.57 no 1vvz A1628 2Ob 2   0.09   0.16   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].

---

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>