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 3oi5 3OI5 (3.1Å) -- RIBOSOME/ANTIBIOTIC : Structure of the thermus thermophilus 70s ribosome complexed with telithromycin. this file contains the 50s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes. List of all 328 Mg2+ binding sites in the PDB structure 3oi5 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 10 of 17 | « Previous | Next » | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3oi5 A3020 Oph 1   0.07  0   0.89 no 3oi5 A3019 cis-2Oph 2   0.15   0.13   0.71 no 3oi5 A3018 Mg2+ not bound by RNA 0  0  0   0.97 no 3oi5 A3017 poly-nuclear Mg2+ site 1   0.03  0   0.97 no 3oi5 A3016 other RNA-inner types 3   0.20   0.51   0.93 no 3oi5 A3015 Ob 1   0.01  0   0.71 no 3oi5 A3014 Oph 1   0.06  0   0.74 no 3oi5 A3013 other RNA-inner types 3   0.06   0.57   0.91 no 3oi5 A3012 Oph·2Ob 3   0.09   0.61   0.84 no 3oi5 A3011 Mg2+ bound by non-RNA 2   0.15   0.41   0.61 no 3oi5 A3010 Mg2+ not bound by RNA 0  0  0   0.73 no 3oi5 A3009 Oph 1   0.03  0   0.76 no 3oi5 A3008 Ob 1   0.03  0   0.78 no 3oi5 A3007 poly-nuclear Mg2+ site 2   0.12   0.16   0.90 no 3oi5 A3006 Mg2+ not bound by RNA 0  0  0   1.00 no 3oi5 A3005 other RNA-inner types 2   0.05   0.29   0.86 no 3oi5 A3004 cis-2Oph 2   0.11   0.13   0.95 no 3oi5 A3003 Oph 1   0.04  0   0.63 no 3oi5 A3002 trans-2Oph 2   0.27   0.70   0.76 no 3oi5 A3001 Oph 1   0.15  0   0.60 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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