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 18 of 67 | « Previous | Next » | 14 | 15 | 16 | 17 | 18 | 19 | 20 | 21 | 22

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 2wdg Z237 2Ob 2   0.04   0.22   0.89 no 3oi1 A3187 2Ob 2   0.03   0.20   0.89 no 3v27 A3222 2Ob 2   0.04   0.37   0.89 no 3pyr A3433 2Ob 2   0.05   0.13   0.89 no 3v2d A3307 2Ob 4   0.26   0.42   0.89 no 3v2d A3638 2Ob 5   0.27   0.64   0.89 no 4gkj A1626 2Ob 2   0.03   0.20   0.89 no 1vxi A1650 2Ob 2   0.03   0.19   0.89 no 3tvf A2263 2Ob 2   0.04   0.28   0.89 no 1vx9 A3222 2Ob 2   0.08   0.28   0.89 no 4nw1 A3028 2Ob 2   0.13   0.27   0.89 no 3i8g A1600 2Ob 2   0.04   0.26   0.89 no 4kx0 A3130 2Ob 2   0.05   0.17   0.89 no 3oh5 A3213 2Ob 2   0.04   0.18   0.89 no 4dr1 A1700 2Ob 2   0.05   0.16   0.89 no 4g5v A1654 2Ob 2   0.04   0.18   0.89 no 3tvf A2589 2Ob 2   0.05   0.15   0.89 no 4qcm A1737 2Ob 3   0.15   0.19   0.89 no 1vq8 08096 2Ob 6   0.41   0.86   0.89 no 4nvx A3028 2Ob 2   0.05   0.20   0.89 no 4nvv A3359 2Ob 3   0.16   0.34   0.89 no 4qcu A3056 2Ob 2   0.09   0.36   0.89 no 4b3m A2658 2Ob 2   0.06   0.18   0.89 no 4kx2 A3152 2Ob 2   0.03   0.16   0.89 no 4duz A1768 2Ob 3   0.08   0.56   0.89 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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