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 16 of 67 | « Previous | Next » | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dr3 A1653 2Ob 2   0.05   0.20   0.73 no 3kis a1653 2Ob 2   0.03   0.16   0.92 no 4ji7 A1654 2Ob 5   0.51   0.70   0.63 yes 3v28 A1654 2Ob 2   0.05   0.59   0.90 no 4g5v A1654 2Ob 2   0.04   0.18   0.89 no 4tpa A1655 2Ob 2   0.04   0.20   0.79 no 4ox9 A1655 2Ob 2   0.07   0.20   0.89 no 4tp2 A1655 2Ob 2   0.03   0.21   0.90 no 4tp6 A1655 2Ob 2   0.04   0.22   0.86 no 3kix a1656 2Ob 2   0.03   0.45   0.93 no 4dr4 A1656 2Ob 4   0.35   0.44   0.98 no 3kiq a1656 2Ob 2   0.10   0.22   0.94 no 1ibm A1656 2Ob 2   0.06   0.16   0.71 no 3v6v A1657 2Ob 2   0.18   0.14   0.10 no 3kiu a1657 2Ob 2   0.03   0.19   0.95 no 1vvv A1658 2Ob 2   0.04   0.18  0 no 1vvt A1658 2Ob 2   0.23   0.27   0.81 no 3kiu a1658 2Ob 2   0.03   0.86   0.54 no 1vvl A1658 2Ob 2   0.09   0.29   0.85 no 4g5k A1659 2Ob 2   0.26   0.19   0.98 no 4dr7 A1660 2Ob 4   0.38   0.53   0.46 no 1vy2 A1660 2Ob 2   0.14   0.12   0.41 no 1vxi A1660 2Ob 2   0.05   0.15   0.20 no 1vxk A1661 2Ob 2   0.13   0.16   0.47 no 4tp0 A1661 2Ob 2   0.07   0.28   0.91 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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