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 4tpf 4TPF (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to flopristin and linopristin. this file contains the 50s subunit of the second 70s ribosome with flopristin and linopristin bound. List of all 169 Mg2+ binding sites in the PDB structure 4tpf 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 5 of 9 | « 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 4tpf A3075 trans-2Oph 6   0.83   0.87   0.81 yes 4tpf A3082 Oph·Pout 6   0.84   0.82   0.81 yes 4tpf A3042 trans,cis-4Oph 4   0.19   0.72   0.81 no 4tpf A3008 Oph 6   0.82   0.82   0.82 yes 4tpf A3060 Oph·2Pout 6   0.85   0.84   0.82 yes 4tpf A3089 cis-2Oph 6   0.76   0.76   0.82 yes 4tpf A3018 3Pout·Rout·3Bout 6   0.75   0.99   0.82 yes 4tpf A3038 Oph·2Pout 6   0.84   0.84   0.82 yes 4tpf A3165 Nb 1   0.01  0   0.82 no 4tpf A3059 4Pout 4   0.67   0.65   0.82 yes 4tpf A3139 Ob 1   0.07  0   0.83 no 4tpf A3160 Oph·Or 2   0.12   0.45   0.83 no 4tpf A3159 2Ob 2   0.09   0.25   0.83 no 4tpf A3164 Oph 1   0.01  0   0.83 no 4tpf A3146 Oph·Nb 2   0.47   0.80   0.83 no 4tpf A3108 fac-3Oph 6   0.54   0.85   0.83 yes 4tpf A3078 Oph·Pout 5   0.70   0.72   0.83 yes 4tpf A3043 4Pout 5   0.81   0.80   0.84 yes 4tpf A3091 Oph·Pout 6   0.85   0.84   0.85 yes 4tpf A3047 cis-2Oph 6   0.79   0.75   0.85 yes

^# 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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