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 15 of 67 | « Previous | Next » | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3ivn A101 2Ob 2   0.03   0.17   0.91 no 4qcz A3275 2Ob 2   0.11   0.08   0.91 no 3v23 A3014 2Ob 2   0.05   0.18   0.91 no 3huz A156 2Ob 2   0.04   0.18   0.91 no 1k9m A8097 2Ob 6   0.37   0.80   0.91 no 4qcn A3220 2Ob 2   0.07   0.25   0.91 no 4tp0 A1661 2Ob 2   0.07   0.28   0.91 no 3v2f A3054 2Ob 2   0.06   0.34   0.91 no 4g5t A1937 2Ob 2   0.07   0.27   0.91 no 3ohk A3088 2Ob 2   0.03   0.19   0.91 no 4qd1 A3298 2Ob 3   0.15   0.21   0.91 no 4qco A3053 2Ob 2   0.11   0.09   0.91 no 4ji2 A1768 2Ob 2   0.04   0.26   0.91 no 3cc4 08032 2Ob 6   0.18   0.86   0.91 no 4qd1 A3344 2Ob 3   0.16   0.34   0.91 no 3oh7 A3028 2Ob 2   0.07   0.18   0.91 no 4qcr A3372 2Ob 3   0.16   0.24   0.91 no 4qcr A3171 2Ob 2   0.06   0.21   0.91 no 3oi3 A3071 2Ob 2   0.13   0.09   0.91 no 3pyr A3542 2Ob 2   0.05   0.22   0.91 no 4dhc A3021 2Ob 2   0.03   0.38   0.91 no 3i56 08032 2Ob 6   0.15   0.94   0.90 no 1vqn 08042 2Ob 6   0.27   0.84   0.90 no 1vx9 A3150 2Ob 2   0.07   0.23   0.90 no 4nvz A3019 2Ob 2   0.04   0.33   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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