MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 1vq8 1VQ8 (2.2Å) -- RIBOSOME : The structure of ccda-phe-cap-bio and the antibiotic sparsomycin bound to the large ribosomal subunit of haloarcula marismortui List of all 94 Mg2+ binding sites in the PDB structure 1vq8 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 #", "Site type" 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 1vq8 08050 Oph 1   0.10  0   0.61 no 1vq8 08082 Pout·2Bout 2   0.10   0.19   0.64 no 1vq8 08103 Oph·Pout 2   0.09   0.77   0.78 no 1vq8 A8066 Mg2+ not bound by RNA 2   0.37   0.07   0.95 no 1vq8 08024 Pout 2   0.05   0.17   0.73 no 1vq8 08072 Oph·2Pout 3   0.14   0.70   0.77 no 1vq8 08099 Or 3   0.20   0.47   0.74 no 1vq8 08055 2Pout 3   0.22   0.38   0.73 no 1vq8 08040 2Pout 3   0.23   0.30   0.82 no 1vq8 08065 Mg2+ not bound by RNA 3   0.19   0.33   0.51 no 1vq8 08047 2Pout·Bout 3   0.11   0.58   0.50 no 1vq8 08061 cis-2Oph 3   0.38   0.70   0.65 no 1vq8 08090 Oph·Pout 3   0.08   0.56   0.65 no 1vq8 08104 cis-2Oph 3   0.15   0.56   0.98 no 1vq8 08025 poly-nuclear Mg2+ site 4   0.35   0.38   0.49 no 1vq8 08108 Pout·2Bout 4   0.20   0.58   0.77 no 1vq8 08092 poly-nuclear Mg2+ site 4   0.18   0.72   0.59 no 1vq8 08107 cis-2Oph 4   0.19   0.59   0.61 no 1vq8 98095 cis-2Oph 4   0.20   0.29   0.88 no 1vq8 08046 Nb 4   0.32   0.66   0.76 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].

---

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>