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 1vvq A3201 2Ob 2   0.08   0.22   0.86 no 4ji1 A1823 2Ob 2   0.15   0.26   0.86 no 1vvq A3205 2Ob 2   0.08   0.30   0.86 no 4dr5 A1849 2Ob 2   0.05   0.15   0.86 no 4qcv A3129 2Ob 2   0.05   0.21   0.86 no 3skw A305 2Ob 2   0.07   0.10   0.86 no 4dr2 A1914 2Ob 2   0.03   0.18   0.86 no 4ox9 A1607 2Ob 2   0.14   0.27   0.86 no 2uuc Z1098 2Ob 2   0.09   0.27   0.86 no 2uu9 Z1100 2Ob 2   0.04   0.19   0.86 no 4g5t C151 2Ob 2   0.07   0.19   0.86 no 3ohk A3027 2Ob 2   0.06   0.17   0.86 no 3oi2 A1571 2Ob 2   0.05   0.11   0.86 no 3v29 A3043 2Ob 2   0.03   0.15   0.86 no 1nji A8042 2Ob 6   0.35   0.81   0.86 no 4qcn A3373 2Ob 5   0.19   0.36   0.85 no 4b3t A2557 2Ob 2   0.14   0.32   0.85 no 3g71 08075 2Ob 6   0.24   0.89   0.85 no 4dv2 A1730 2Ob 2   0.03   0.16   0.85 no 4nvv A3293 2Ob 2   0.04   0.63   0.85 no 4qcz A3356 2Ob 3   0.16   0.23   0.85 no 3v2c A1651 2Ob 4   0.29   0.84   0.85 no 4dhb A1608 2Ob 2   0.04   0.23   0.85 no 1kd1 A8097 2Ob 6   0.46   0.75   0.85 no 3kix a1650 2Ob 2   0.04   0.14   0.85 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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