MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qao:B3525, See in JSmolClick on the image to toggle views Site type: mer-3Oph·Or Schematic drawing for mer-3Oph·Or List of all 93 Mg2+ binding sites with the site type mer-3Oph·Or 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 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1fjg A1607 mer-3Oph·Or 4   0.11   0.58   0.71 no 1hnw A1605 mer-3Oph·Or 4   0.11   0.60   0.64 no 1hnx A1606 mer-3Oph·Or 4   0.10   0.62   0.66 no 1hnz A1606 mer-3Oph·Or 4   0.11   0.64   0.79 no 1ibk A1600 mer-3Oph·Or 4   0.15   0.53   0.50 no 1ibl A1599 mer-3Oph·Or 4   0.16   0.63   0.43 no 1n32 A1600 mer-3Oph·Or 4   0.13   0.65   0.47 no 1vs6 B2994 mer-3Oph·Or 6   0.68   0.73   0.84 yes 1vs8 B2994 mer-3Oph·Or 6   0.92   0.85   0.63 yes 1vvz A1620 mer-3Oph·Or 4   0.11   0.62   0.06 no 1xmo A1592 mer-3Oph·Or 4   0.13   0.64   0.47 no 1xmq A1592 mer-3Oph·Or 4   0.15   0.70   0.59 no 1xnq A1592 mer-3Oph·Or 4   0.08   0.66   0.64 no 1xnr A1592 mer-3Oph·Or 4   0.09   0.62   0.61 no 2aw4 B2994 mer-3Oph·Or 6   0.63   0.70   0.76 yes 2awb B2995 mer-3Oph·Or 6   0.89   0.88   0.65 yes 2i2v B2995 mer-3Oph·Or 6   0.67   0.87   0.97 yes 2j00 Z178 mer-3Oph·Or 4   0.33   0.43   0.25 no 2qam B3509 mer-3Oph·Or 6   0.73   0.76   0.85 yes 2qao B3525 mer-3Oph·Or 6   0.86   0.88   0.87 yes 2qba B3509 mer-3Oph·Or 6   0.66   0.76   0.93 yes 2qbc B3525 mer-3Oph·Or 6   0.90   0.88   0.79 yes 2qbe B3509 mer-3Oph·Or 6   0.86   0.76   0.83 yes 2qbg B2996 mer-3Oph·Or 6   0.77   0.76   0.70 yes 2qbi B2994 mer-3Oph·Or 6   0.77   0.74   0.79 yes

^# 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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