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 10 of 67 | « Previous | Next » | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1vvq A3167 2Ob 2   0.09   0.14   0.59 no 4dv5 A1784 2Ob 2   0.05   0.14   0.89 no 4fax A402 2Ob 2   0.07   0.14   0.69 no 3uz7 A2251 2Ob 2   0.04   0.14   0.98 no 3ms1 A2948 2Ob 2   0.05   0.14   0.60 no 3oi1 A3115 2Ob 2   0.04   0.15   0.91 no 4ej9 A7072 2Ob 2   0.05   0.15   0.52 no 3kiw A3067 2Ob 2   0.03   0.15   0.95 no 1vvv A1624 2Ob 2   0.15   0.15   0.35 no 4qcm A1631 2Ob 2   0.08   0.15   0.83 no 4duy A1747 2Ob 2   0.03   0.15   0.75 no 3f1e A5319 2Ob 2   0.06   0.15   0.68 no 1vvs A3226 2Ob 2   0.09   0.15   0.63 no 4l6j A5025 2Ob 2   0.04   0.15   0.82 no 4aqy A2642 2Ob 2   0.13   0.15   0.94 no 1ibm A1612 2Ob 2   0.05   0.15   0.66 no 1ibl A1638 2Ob 2   0.05   0.15   0.53 no 3knh A1575 2Ob 2   0.06   0.15   0.62 no 4lf6 A1723 2Ob 2   0.03   0.15   0.72 no 3oto A1623 2Ob 2   0.04   0.15   0.63 no 4nvz B3006 2Ob 2   0.03   0.15   0.84 no 4g5v A1617 2Ob 2   0.05   0.15   0.79 no 2uxc Z58 2Ob 2   0.03   0.15   0.83 no 1vxi A1660 2Ob 2   0.05   0.15   0.20 no 4dv4 A1637 2Ob 2   0.03   0.15   0.86 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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