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 12 of 67 | « Previous | Next » | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vx9 A3221 2Ob 2   0.04   0.16   0.24 no 3pyr A3542 2Ob 2   0.05   0.22   0.91 no 3u5d 14210 2Ob 2   0.05   0.24   0.94 no 3pyr A3696 2Ob 2   0.05   0.20   0.71 no 3f1f A5968 2Ob 2   0.04   0.17   0.84 no 3pyr A3708 2Ob 2   0.08   0.21   0.62 no 3f1f B6046 2Ob 2   0.05   0.68   0.33 no 4k27 U101 2Ob 2   0.16   0.28   0.68 no 3v24 A1602 2Ob 2   0.05   0.30   0.70 no 2pn3 A2 2Ob 2   0.11   0.10   0.61 no 3t1h A1602 2Ob 2   0.13   0.37   0.71 no 1vxt A3228 2Ob 2   0.04   0.19   0.84 no 3t1h A1603 2Ob 2   0.05   0.13   0.88 no 1ibk A1548 2Ob 2   0.03   0.20   0.58 no 4nvv A3004 2Ob 2   0.04   0.23   0.84 no 4qcw A3004 2Ob 2   0.07   0.13   0.83 no 4dhb A1604 2Ob 2   0.05   0.19   0.93 no 4lfa A1606 2Ob 2   0.04   0.19   0.64 no 4aqy A2549 2Ob 2   0.08   0.21   0.91 no 1vxt A3235 2Ob 2   0.07   0.23   0.58 no 2quw B7 2Ob 2   0.06   0.42   0.88 no 4lf8 A1609 2Ob 2   0.08   0.10   0.70 no 4lf9 A1608 2Ob 2   0.03   0.18   0.85 no 4lf7 A1609 2Ob 2   0.08   0.10   0.70 no 4nvz A3038 2Ob 2   0.03   0.23   0.61 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/)
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