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 4qcy A3037 2Ob 2   0.07   0.18   0.65 no 4qcr B215 2Ob 3   0.15   0.14   0.65 no 1yit 08042 2Ob 2   0.10   0.34   0.65 no 1vxm A1608 2Ob 2   0.10   0.42   0.65 no 1vxm A1666 2Ob 2   0.09   0.11   0.65 no 4qcv A3052 2Ob 2   0.03   0.17   0.65 no 3pyt A3005 2Ob 2   0.07   0.19   0.65 no 4dv1 A1732 2Ob 2   0.05   0.10   0.66 no 4dr5 A1785 2Ob 2   0.06   0.16   0.66 no 4qcx A3263 2Ob 2   0.06   0.23   0.66 no 3f1e A5110 2Ob 2   0.05   0.10   0.66 no 4qcz A3189 2Ob 2   0.07   0.19   0.66 no 1ibm A1612 2Ob 2   0.05   0.15   0.66 no 4qcz B3017 2Ob 3   0.16   0.31   0.66 no 3kit A2995 2Ob 2   0.07   0.19   0.66 no 4dv2 A1734 2Ob 2   0.03   0.21   0.66 no 1vxl A3160 2Ob 2   0.12   0.24   0.66 no 4dv0 A1730 2Ob 2   0.03   0.17   0.66 no 4qcp A3284 2Ob 4   0.29   0.49   0.66 no 4byc A3933 2Ob 2   0.04   0.19   0.66 no 3i8g A1586 2Ob 2   0.03   0.19   0.66 no 2wdg Z234 2Ob 2   0.08   0.16   0.66 no 4nvz A3066 2Ob 2   0.08   0.15   0.66 no 4dv5 A1791 2Ob 2   0.04   0.14   0.67 no 3i9b A1554 2Ob 2   0.10   0.13   0.67 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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