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 3oi3 3OI3 (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 372 Mg2+ binding sites in the PDB structure 3oi3 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 8 of 19 | « Previous | Next » | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3oi3 A3006 Oph 1   0.13  0   0.87 no 3oi3 A3007 cis-2Oph 2   0.19   0.15   0.58 no 3oi3 A3008 poly-nuclear Mg2+ site 2   0.06   0.21   0.92 no 3oi3 A3009 Oph 1   0.09  0   0.63 no 3oi3 A3010 Mg2+ not bound by RNA 0  0  0   0.77 no 3oi3 A3011 poly-nuclear Mg2+ site 2   0.22   0.19   0.43 no 3oi3 A3012 poly-nuclear Mg2+ site 2   0.05   0.14   0.66 no 3oi3 A3013 Mg2+ not bound by RNA 0  0  0   0.74 no 3oi3 A3014 Mg2+ not bound by RNA 0  0  0   0.40 no 3oi3 A3015 Oph·2Ob 3   0.10   0.71   0.53 no 3oi3 A3016 2Or 2   0.11   0.46   0.68 no 3oi3 A3017 Oph 1   0.17  0   0.52 no 3oi3 A3018 Ob 1   0.01  0   0.69 no 3oi3 A3019 Oph·Or 2   0.06   0.11   0.73 no 3oi3 A3020 poly-nuclear Mg2+ site 1   0.07  0   0.90 no 3oi3 A3021 poly-nuclear Mg2+ site 1   0.04  0   0.86 no 3oi3 A3022 cis-2Oph 2   0.11   0.10   0.58 no 3oi3 A3023 Oph 1   0.10  0   0.61 no 3oi3 A3024 cis-2Oph 2   0.18   0.45   0.76 no 3oi3 A3025 Oph·Ob 2   0.06   0.57   0.69 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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