MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df2:B3428, See in JSmolClick on the image to toggle views Site type: Oph·Or Schematic drawing for Oph·Or List of all 1185 Mg2+ binding sites with the site type Oph·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 7 of 48 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4ej9 A7068 Oph·Or 2   0.03   0.12   0.40 no 1n33 A1578 Oph·Or 2   0.28   0.12   0.35 no 1vxl A3093 Oph·Or 2   0.16   0.12   0.20 no 4dv1 A1654 Oph·Or 3   0.19   0.12   0.75 no 2j00 Z502 Oph·Or 2   0.14   0.13   0.03 no 3oi5 A2988 Oph·Or 2   0.09   0.13   0.72 no 2vqe Z46 Oph·Or 2   0.16   0.13   0.56 no 3ohj A2989 Oph·Or 2   0.08   0.13   0.53 no 3f1e A5220 Oph·Or 2   0.12   0.13   0.13 no 4ox9 A1633 Oph·Or 2   0.11   0.13   0.47 no 4qcq A3105 Oph·Or 2   0.13   0.13   0.87 no 3t1y A1782 Oph·Or 2   0.10   0.13   0.31 no 3v2d A3041 Oph·Or 2   0.05   0.13   0.85 no 3sgf A2920 Oph·Or 2   0.12   0.13   0.50 no 4mgn D104 Oph·Or 2   0.17   0.13   0.99 no 3oi0 A1560 Oph·Or 2   0.08   0.13   0.77 no 4g5v C107 Oph·Or 2   0.08   0.13   0.88 no 4qcv A3227 Oph·Or 2   0.08   0.13   0.72 no 1hnx A1588 Oph·Or 2   0.21   0.13   0.56 no 1vy3 A3087 Oph·Or 2   0.09   0.13   0.20 no 3v26 A1624 Oph·Or 2   0.08   0.13   0.82 no 3kiu a1534 Oph·Or 2   0.37   0.13   0.38 no 2uxc Z172 Oph·Or 2   0.05   0.13   0.85 no 4lfb A1667 Oph·Or 2   0.13   0.13   0.82 no 2uub Z1099 Oph·Or 2   0.22   0.13   0.55 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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