MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 4g5m:A1746, See in JSmolClick on the image to toggle views Site type: Ob·2Nb Schematic drawing for Ob·2Nb List of all 105 Mg2+ binding sites with the site type Ob·2Nb 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 1 of 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1fjg A1612 Ob·2Nb 4   0.22   0.47   0.66 no 1hnz A1611 Ob·2Nb 4   0.23   0.39   0.64 no 1i94 A1555 Ob·2Nb 3   0.14   0.24   0.85 no 1i95 A1558 Ob·2Nb 3   0.10   0.30   0.86 no 1i96 A1557 Ob·2Nb 3   0.10   0.26   0.87 no 1i97 A1557 Ob·2Nb 3   0.10   0.28   0.69 no 1ibk A1605 Ob·2Nb 3   0.12   0.24   0.44 no 1vvm A3100 Ob·2Nb 3   0.43   0.71   0.58 no 1vvm A3118 Ob·2Nb 3   0.51   0.30   0.80 no 1vvq A3102 Ob·2Nb 3   0.47   0.72   0.46 no 1vvy A3119 Ob·2Nb 3   0.49   0.28   0.40 no 1vvy A3100 Ob·2Nb 3   0.39   0.63   0.39 no 1vvz A1670 Ob·2Nb 3   0.52   0.27   0.86 no 1vx9 A3120 Ob·2Nb 3   0.54   0.42   0.22 no 1vxl A3120 Ob·2Nb 3   0.62   0.40   0.58 no 1vxn A3238 Ob·2Nb 3   0.44   0.15   0.49 no 1vy1 A3228 Ob·2Nb 3   0.13   0.16   0.26 no 1vy1 A3105 Ob·2Nb 3   0.13   0.67   0.58 no 2j00 Z493 Ob·2Nb 3   0.10   0.31   0.21 no 2j02 Z186 Ob·2Nb 3   0.12   0.31   0.02 no 2qus B73 Ob·2Nb 3   0.72   0.51   0.97 no 2uu9 Z1051 Ob·2Nb 3   0.86   0.28   0.03 no 2uua Z53 Ob·2Nb 3   0.67   0.30   0.04 no 2uuc Z1048 Ob·2Nb 3   0.66   0.32   0.02 no 2v48 G2521 Ob·2Nb 3   0.42   0.33   0.09 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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