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 4g5k 4G5K (3.3Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the 70s ribosome with tetracycline. this entry contains the 30s subunit of molecule a. List of all 324 Mg2+ binding sites in the PDB structure 4g5k 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 17 | « 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 4g5k A1793 other RNA-inner types 4   0.36   0.74   0.88 no 4g5k A2046 trans-2Oph 2   0.03   0.74   0.81 no 4g5k A1610 2Nb 2   0.49   0.72   0.92 no 4g5k A1992 other RNA-inner types 5   0.78   0.72   0.89 no 4g5k A1613 2Or 2   0.20   0.69   0.89 no 4g5k A1914 other RNA-inner types 4   0.28   0.69   0.93 no 4g5k A1986 other RNA-inner types 4   0.63   0.67   0.94 no 4g5k A1637 Oph·Or 2   0.11   0.67   0.93 no 4g5k A1769 other RNA-inner types 4   0.19   0.66   0.95 no 4g5k A1644 mer-3Oph 3   0.53   0.64   0.80 no 4g5k A1796 other RNA-inner types 4   0.47   0.64   0.93 no 4g5k A1996 other RNA-inner types 2   0.25   0.62   0.90 no 4g5k A1938 2Ob·Nb 3   0.97   0.59   0.96 no 4g5k A1730 other RNA-inner types 5   0.78   0.59   0.81 no 4g5k A1604 mer-3Oph 3   0.21   0.57   0.82 no 4g5k A1942 Mg2+ bound by non-RNA 2   0.08   0.56   0.87 no 4g5k A1850 Ob·2Nb 3   0.29   0.56   0.93 no 4g5k A1823 poly-nuclear Mg2+ site 2   0.45   0.53   0.93 no 4g5k A1839 Oph·Or 2   0.21   0.52   0.94 no 4g5k A1621 trans-2Oph 2   0.06   0.52   0.66 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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>