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 1hnw 1HNW (3.4Å) -- RIBOSOME : Structure of the thermus thermophilus 30s ribosomal subunit in complex with tetracycline List of all 92 Mg2+ binding sites in the PDB structure 1hnw 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 5 | « Previous | Next » | 1 | 2 | 3 | 4 | 5

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1hnw A212 Mg2+ not bound by RNA 0  0  0   0.15 no 1hnw A1614 Mg2+ not bound by RNA 0  0  0   0.17 no 1hnw A1620 poly-nuclear Mg2+ site 3   0.35   0.43   0.18 no 1hnw A1626 poly-nuclear Mg2+ site 3   0.29   0.27   0.19 no 1hnw A1623 poly-nuclear Mg2+ site 1   0.02  0   0.21 no 1hnw A1569 Oph·2Or 3   0.31   0.41   0.21 no 1hnw A1630 poly-nuclear Mg2+ site 2   0.59   0.02   0.28 no 1hnw A1571 Ob 1   0.05  0   0.31 no 1hnw A1627 other RNA-inner types 4   0.79   0.29   0.31 no 1hnw A1584 Ob 1   0.03  0   0.32 no 1hnw A1607 Ob 1   0.02  0   0.33 no 1hnw A1576 Mg2+ not bound by RNA 0  0  0   0.34 no 1hnw A1621 trans-2Oph 2   0.11   0.27   0.35 no 1hnw A1547 Oph 1   0.24  0   0.36 no 1hnw A1585 Oph 1   0.24  0   0.38 no 1hnw A1629 poly-nuclear Mg2+ site 5   0.48   0.46   0.44 no 1hnw A1599 Oph 1   0.19  0   0.44 no 1hnw A1606 Mg2+ not bound by RNA 0  0  0   0.45 no 1hnw A1550 Oph·Ob 2   0.05   0.13   0.46 no 1hnw A1577 cis-2Oph 2   0.17   0.16   0.46 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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