MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2z4n:B3007, See in JSmolClick on the image to toggle views Site type: cis-2Oph·Or Schematic drawing for cis-2Oph·Or List of all 279 Mg2+ binding sites with the site type cis-2Oph·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 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 1hnx A1578 cis-2Oph·Or 3   0.22   0.24   0.42 no 1hnz A1578 cis-2Oph·Or 3   0.15   0.32   0.49 no 1hr0 A1577 cis-2Oph·Or 3   0.15   0.25   0.50 no 1hr0 A1605 cis-2Oph·Or 3   0.12   0.40   0.78 no 1hr2 A57 cis-2Oph·Or 3   0.30   0.32   0.88 no 1ibk A1575 cis-2Oph·Or 3   0.23   0.21   0.30 no 1ibl A1574 cis-2Oph·Or 4   0.39   0.44   0.30 no 1n32 A1575 cis-2Oph·Or 3   0.60   0.21   0.30 no 1n33 A1631 cis-2Oph·Or 3   0.44   0.38   0.47 no 1n33 A1592 cis-2Oph·Or 3   0.28   0.30   0.59 no 1n33 A1570 cis-2Oph·Or 3   0.25   0.23   0.30 no 1q7y A8057 cis-2Oph·Or 5   0.65   0.32   0.67 no 1vq8 08057 cis-2Oph·Or 5   0.26   0.72   0.64 no 1vq9 08057 cis-2Oph·Or 3   0.09   0.60   0.67 no 1vqk 08057 cis-2Oph·Or 5   0.15   0.60   0.67 no 1vql 08057 cis-2Oph·Or 5   0.21   0.79   0.75 no 1vqn 08057 cis-2Oph·Or 5   0.24   0.68   0.74 no 1vqo 08057 cis-2Oph·Or 3   0.11   0.63   0.58 no 1vs6 B3006 cis-2Oph·Or 6   0.71   0.76   0.85 yes 1vs7 A1556 cis-2Oph·Or 6   0.99   0.75   0.71 yes 1vs8 B3004 cis-2Oph·Or 6   0.70   0.76   0.57 yes 1vvz A1644 cis-2Oph·Or 3   0.40   0.07   0.09 no 1vxi A1619 cis-2Oph·Or 3   0.06   0.67   0.52 no 1vxi A1623 cis-2Oph·Or 3   0.25   0.22   0.40 no 1vxm A1623 cis-2Oph·Or 3   0.22   0.39   0.35 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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