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 3f1h A5260 2Ob 2   0.04   0.15   0.05 no 2wh1 Z174 2Ob 2   0.04   0.20   0.50 no 1ibm A1618 2Ob 2   0.04   0.16   0.56 no 3kis a1618 2Ob 2   0.04   0.20   0.83 no 4nvw A3009 2Ob 2   0.04   0.15   0.73 no 3kit A3007 2Ob 2   0.04   0.15   0.85 no 4ji3 A1693 2Ob 2   0.04   0.16   0.98 no 3f1h A5414 2Ob 2   0.04   0.18   0.02 no 3u5h 53998 2Ob 2   0.04   0.22   0.76 no 4qcp A3109 2Ob 2   0.04   0.15   0.80 no 4dv7 A1751 2Ob 2   0.04   0.17   0.98 no 3pyr A141 2Ob 2   0.04   0.16   0.55 no 4dha A3118 2Ob 2   0.04   0.17   0.79 no 4byc A3933 2Ob 2   0.04   0.19   0.66 no 4nvx A3039 2Ob 2   0.04   0.15   0.90 no 1vy0 A1628 2Ob 2   0.04   0.11   0.18 no 3i8g A1600 2Ob 2   0.04   0.26   0.89 no 4lf8 A1697 2Ob 2   0.04   0.15   0.80 no 4lf7 A1697 2Ob 2   0.04   0.15   0.80 no 2wdk Z519 2Ob 2   0.04   0.48   0.77 no 4dr3 A1847 2Ob 2   0.04   0.16   0.75 no 4dv1 A1774 2Ob 2   0.04   0.12   0.96 no 4dhc A3025 2Ob 2   0.04   0.14   0.82 no 2qa4 03012 2Ob 2   0.04   0.21   0.93 no 2x9r Z223 2Ob 2   0.04   0.16   0.70 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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