MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1hr2:A5, See in JSmolClick on the image to toggle views Site type: Ob·Nb Schematic drawing for Ob·Nb List of all 592 Mg2+ binding sites with the site type Ob·Nb 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 5 of 24 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4nvx A3508 Ob·Nb 4   0.28   0.59   0.77 no 4qcn A3783 Ob·Nb 4   0.28   0.39   0.92 no 4qcx A3460 Ob·Nb 4   0.29   0.37   0.74 no 4qd1 A3474 Ob·Nb 4   0.31   0.38   0.87 no 4kj8 A1631 Ob·Nb 4   0.67   0.60   0.99 yes 4kj5 A3044 Ob·Nb 4   0.37   0.42   0.56 no 4far A407 Ob·Nb 4   0.18   0.29   0.84 no 4dha A3598 Ob·Nb 4   0.26   0.46   0.92 no 3v2d A3213 Ob·Nb 4   0.28   0.57   0.76 no 4qcw A3113 Ob·Nb 4   0.29   0.89   0.82 no 4kj3 A3095 Ob·Nb 4   0.15   0.62   0.30 no 4nw0 A3106 Ob·Nb 4   0.28   0.86   0.67 no 4dha A3517 Ob·Nb 4   0.32   0.36   0.90 no 3v2d A3151 Ob·Nb 4   0.33   0.36   0.87 no 2vhn Z4093 Ob·Nb 4   0.15   0.58   0.31 no 3v2c A1678 Ob·Nb 4   0.26   0.37   0.94 no 3g4s 08090 Ob·Nb 4   0.07   0.66   0.98 no 4qcn A3566 Ob·Nb 4   0.28   0.42   0.63 no 4kj3 A3071 Ob·Nb 4   0.41   0.51   0.93 no 4qct A3546 Ob·Nb 4   0.28   0.46   0.71 no 4dha A3523 Ob·Nb 4   0.28   0.38   0.84 no 4qct A3465 Ob·Nb 4   0.18   0.23   0.76 no 4nw1 A3428 Ob·Nb 4   0.34   0.75   0.81 no 4qcp A3359 Ob·Nb 4   0.30   0.38   0.97 no 4nvx A3434 Ob·Nb 4   0.36   0.70   0.90 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/)
For any help please contact <dust@iwonka.med.virginia.edu>