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 4tp4 4TP4 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 30s subunit of the first 70s ribosome. List of all 72 Mg2+ binding sites in the PDB structure 4tp4 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 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4tp4 A1662 Or 1   0.02  0   0.98 no 4tp4 A1631 Ob 5   0.73   0.65   0.96 yes 4tp4 A1661 Ob 1   0.04  0   0.57 no 4tp4 A1620 Ob 6   0.90   0.91   0.71 yes 4tp4 A1654 Ob 1   0.33  0   0.57 no 4tp4 A1669 Ob 1   0.03  0   0.86 no 4tp4 A1630 Nb 6   0.87   0.87   0.82 yes 4tp4 A1603 Nb 6   0.84   0.85   0.79 yes 4tp4 A1668 Nb 1   0.03  0   0.78 no 4tp4 A1663 Ob·Nb 2   0.03   0.37   0.96 no 4tp4 A1656 Ob·Nb 2   0.79   0.32   0.91 no 4tp4 A1665 Ob·Nb 2   0.05   0.27   0.85 no 4tp4 A1625 2Nb 6   0.84   0.85   0.59 yes 4tp4 A1615 Oph 6   0.89   0.89   0.88 yes 4tp4 A1671 Oph 1   0.01  0   0.43 no 4tp4 A1666 Oph 1   0.04  0   0.69 no 4tp4 A1624 Oph 6   0.88   0.88   0.92 yes 4tp4 A1660 Oph 1   0.08  0   0.69 no 4tp4 A1649 Oph 1   0.02  0   0.97 no 4tp4 A1655 Oph 1   0.25  0   0.95 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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Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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