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 4g5v 4G5V (3.1Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the 70s ribosome with tigecycline. this entry contains the 30s subunit of molecule b. List of all 243 Mg2+ binding sites in the PDB structure 4g5v 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 13 | « 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 4g5v A1709 Or 1   0.03  0   0.93 no 4g5v A1836 Or 1   0.05  0   0.84 no 4g5v A1743 Or 1   0.01  0   0.98 no 4g5v A1630 Ob 1   0.02  0   0.76 no 4g5v A1823 Ob 1   0.03  0   0.98 no 4g5v A1790 Ob 1   0.12  0   0.86 no 4g5v A1705 Ob 1   0.01  0   0.99 no 4g5v A1941 Ob 1   0.07  0   0.72 no 4g5v A1886 Ob 1   0.01  0   0.96 no 4g5v A1660 Ob 1   0.05  0   0.92 no 4g5v A1879 Ob 1   0.02  0   0.66 no 4g5v A1707 Ob 1   0.06  0   0.82 no 4g5v A1833 Nb 1   0.18  0   0.97 no 4g5v A1957 Nb 1   0.03  0   0.87 no 4g5v A1916 Nb 1   0.07  0   0.77 no 4g5v A1968 Nb 1   0.03  0   0.94 no 4g5v A1807 Nb 1   0.04  0   0.89 no 4g5v A1649 Nb 3   0.44   0.70   0.94 no 4g5v A1885 Nb 1   0.12  0   0.98 no 4g5v G301 Nb 2   0.14   0.15   0.99 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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