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 3ofd 3OFD (3.19Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to chloramphenicol. this file contains the 50s subunit of the second 70s ribosome. List of all 137 Mg2+ binding sites in the PDB structure 3ofd 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 2 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3ofd A2978 other RNA-outer types 5   0.81   0.80   0.48 no 3ofd A2919 Pout·3Bout 6   0.74   0.99   0.49 no 3ofd A3000 cis-2Oph 6   0.71   0.71   0.49 no 3ofd A2915 4Pout 6   0.75   0.99   0.50 no 3ofd A2969 Oph·Pout 5   0.70   0.68   0.51 yes 3ofd A2908 Oph·Pout 6   0.86   0.85   0.52 yes 3ofd A2960 Oph·4Pout 6   0.87   0.86   0.52 yes 3ofd A2988 Oph·Pout 6   0.83   0.81   0.52 yes 3ofd A2916 Oph·2Pout 6   0.93   0.94   0.53 yes 3ofd A2931 Oph·Pout 6   0.84   0.83   0.54 yes 3ofd A2974 Oph·Nb 6   0.73   0.67   0.55 yes 3ofd A2977 2Pout·Rout·3Bout 6   0.75   1.00   0.56 yes 3ofd A3034 Pout·2Bout 6   0.74   1.00   0.56 yes 3ofd J747 Mg2+ not bound by RNA 6   0.75   1.00   0.57 no 3ofd A2938 Oph·3Pout 6   0.85   0.84   0.57 yes 3ofd A2951 fac-3Oph 6   0.67   0.72   0.57 yes 3ofd A3025 Oph·2Pout 6   0.85   0.84   0.57 yes 3ofd A2924 2Nb 6   0.80   0.80   0.57 yes 3ofd A2982 cis-2Oph 6   0.77   0.73   0.58 yes 3ofd A3010 Or 4   0.41   0.76   0.58 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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