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 20 of 67 | « Previous | Next » | 16 | 17 | 18 | 19 | 20 | 21 | 22 | 23 | 24

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 4qcv A3052 2Ob 2   0.03   0.17   0.65 no 4qcr A3052 2Ob 2   0.05   0.15   0.80 no 4byb A2583 2Ob 2   0.12   0.17   0.55 no 4ej9 A7059 2Ob 2   0.06   0.20   0.50 no 3knj A1586 2Ob 2   0.09   0.37   0.57 no 3oi1 A2960 2Ob 2   0.04   0.33   0.72 no 3tvf A2263 2Ob 2   0.04   0.28   0.89 no 3v28 A1654 2Ob 2   0.05   0.59   0.90 no 4tp6 A1655 2Ob 2   0.04   0.22   0.86 no 4qcu A3056 2Ob 2   0.09   0.36   0.89 no 4tpa A1655 2Ob 2   0.04   0.20   0.79 no 4nw1 A3055 2Ob 2   0.04   0.14   0.99 no 1ibk A210 2Ob 2   0.04   0.16   0.45 no 4qcw A3055 2Ob 2   0.13   0.06   0.80 no 3v25 A3056 2Ob 2   0.04   0.22   0.99 no 1vvv A1658 2Ob 2   0.04   0.18  0 no 1vy2 A1660 2Ob 2   0.14   0.12   0.41 no 4kfh A2377 2Ob 2   0.06   0.13   0.73 no 1vvq A3205 2Ob 2   0.08   0.30   0.86 no 1ibm A210 2Ob 2   0.06   0.17   0.55 no 1vxk A1661 2Ob 2   0.13   0.16   0.47 no 1vvn A1664 2Ob 2   0.05   0.15   0.89 no 4pe9 A1662 2Ob 2   0.05   0.43   0.80 no 4lf6 A1723 2Ob 2   0.03   0.15   0.72 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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