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 7 of 17 | « Previous | Next » | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4g5k A1684 poly-nuclear Mg2+ site 3   0.42   0.49   0.83 no 4g5k A1984 Mg2+ not bound by RNA 0  0  0   0.83 no 4g5k A1892 poly-nuclear Mg2+ site 2   0.05   0.15   0.83 no 4g5k A1633 Mg2+ not bound by RNA 0  0  0   0.83 no 4g5k A1612 Oph 1   0.16  0   0.83 no 4g5k A1698 Mg2+ not bound by RNA 0  0  0   0.83 no 4g5k R103 Mg2+ not bound by RNA 0  0  0   0.83 no 4g5k A1988 Ob 1   0.06  0   0.84 no 4g5k A2001 poly-nuclear Mg2+ site 2   0.09   0.32   0.84 no 4g5k A1928 Mg2+ not bound by RNA 0  0  0   0.84 no 4g5k A1799 Mg2+ not bound by RNA 0  0  0   0.84 no 4g5k A2029 Mg2+ not bound by RNA 0  0  0   0.84 no 4g5k A1868 Mg2+ not bound by RNA 0  0  0   0.84 no 4g5k A1870 Mg2+ not bound by RNA 0  0  0   0.84 no 4g5k A1784 Ob 1   0.02  0   0.84 no 4g5k A2039 poly-nuclear Mg2+ site 1   0.10  0   0.85 no 4g5k A2060 Or 1   0.02  0   0.85 no 4g5k A1774 Oph 1   0.03  0   0.85 no 4g5k A1960 Mg2+ not bound by RNA 0  0  0   0.85 no 4g5k A1845 Mg2+ not bound by RNA 0  0  0   0.85 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>