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 24 of 67 | « Previous | Next » | 20 | 21 | 22 | 23 | 24 | 25 | 26 | 27 | 28

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4dv2 A1767 2Ob 2   0.02   0.22   0.78 no 4dv3 A1767 2Ob 3   0.06   0.32   1.00 no 4dr5 A1767 2Ob 2   0.04   0.21   0.67 no 4ji2 A1768 2Ob 2   0.04   0.26   0.91 no 4duz A1768 2Ob 3   0.08   0.56   0.89 no 4ji0 A1768 2Ob 2   0.20   0.09   0.97 no 4nxn A1768 2Ob 2   0.06   0.14   0.57 no 4nxm A1769 2Ob 2   0.05   0.24   0.61 no 4nxn A1773 2Ob 2   0.15   0.25   0.73 no 4dr6 A1773 2Ob 2   0.03   0.16   0.72 no 4gkj A1773 2Ob 2   0.18   0.03   0.97 no 4dr1 A1774 2Ob 2   0.04   0.28   0.85 no 4ji2 A1774 2Ob 2   0.03   0.12   0.67 no 4dv1 A1774 2Ob 2   0.04   0.12   0.96 no 4dv4 A1775 2Ob 3   0.06   0.52   0.84 no 4dv6 A1775 2Ob 5   0.52   0.73   0.39 no 4nxm A1776 2Ob 2   0.03   0.19   0.64 no 3t1y A1776 2Ob 2   0.09   0.28   0.20 no 3t1y A1778 2Ob 2   0.08   0.12   0.14 no 4duz A1779 2Ob 2   0.03   0.12   0.99 no 4dr1 A1779 2Ob 2   0.02   0.16   0.73 no 4dv1 A1780 2Ob 2   0.04   0.12   0.78 no 4nxn A1780 2Ob 3   0.12   0.72   0.79 no 4duz A1781 2Ob 2   0.04   0.18   0.68 no 4nxn A1782 2Ob 2   0.04   0.13   0.60 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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