MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3v22:A1693, See in JSmolClick on the image to toggle views Site type: Or·Ob Schematic drawing for Or·Ob List of all 283 Mg2+ binding sites with the site type 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 12 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1fjg A1588 Or·Ob 2   0.07   0.33   0.82 no 1hnw A1586 Or·Ob 2   0.06   0.35   0.74 no 1hnw A1545 Or·Ob 2   0.04   0.16   0.55 no 1hnx A1587 Or·Ob 2   0.06   0.32   0.78 no 1hnz A1587 Or·Ob 2   0.11   0.16   0.89 no 1hr0 A1586 Or·Ob 2   0.06   0.27   0.99 no 1ibl A1580 Or·Ob 2   0.07   0.38   0.55 no 1ibm A1581 Or·Ob 2   0.05   0.24   0.71 no 1k8a A8088 Or·Ob 2   0.03   0.18   0.76 no 1m1k A8066 Or·Ob 2   0.06   0.18   0.80 no 1n32 A1581 Or·Ob 2   0.06   0.39   0.56 no 1n33 A1577 Or·Ob 2   0.09   0.18   0.45 no 1vvm A3172 Or·Ob 2   0.07   0.60   0.83 no 1vvn A1614 Or·Ob 2   0.06   0.12   0.52 no 1vvo A3203 Or·Ob 2   0.04   0.42   0.73 no 1vvo A3231 Or·Ob 2   0.07   0.16   0.82 no 1vvq A3169 Or·Ob 2   0.04   0.15   0.73 no 1vvq A3175 Or·Ob 2   0.08   0.58   0.39 no 1vvq A3144 Or·Ob 2   0.08   0.36   0.96 no 1vvq A3118 Or·Ob 2   0.07   0.33   0.07 no 1vvq A3178 Or·Ob 2   0.06   0.51   0.13 no 1vvu A3172 Or·Ob 2   0.06   0.67   0.20 no 1vvu A3008 Or·Ob 2   0.15   0.05   0.07 no 1vvv X101 Or·Ob 2   0.10   0.28   0.13 no 1vvw A3230 Or·Ob 2   0.11   0.15   0.18 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>