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 3v6u 3V6U (3.9Å) -- RIBOSOME : Crystal structure of the bacterial ribosome ram mutation g347u. this entry contains the 30s ribosomal subunit of the first 70s molecule in the asymmetric unit List of all 94 Mg2+ binding sites in the PDB structure 3v6u 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 4 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 3v6u A1626 fac-3Oph 3   0.32   0.15   0.07 no 3v6u A1703 Oph·Or 2   0.31   0.18   0.01 no 3v6u A1620 Ob·Nb 2   0.09   0.18   0.04 no 3v6u A1670 cis-2Oph 2   0.58   0.21  0 no 3v6u A1623 cis-2Oph·2Or 5   0.51   0.23   0.02 no 3v6u A1702 cis-2Oph·Or 3   0.14   0.23   0.01 no 3v6u X102 cis-2Oph 3   0.35   0.27   0.62 no 3v6u A1646 2Or 2   0.45   0.27   0.62 no 3v6u A1680 other RNA-inner types 3   0.07   0.27   0.03 no 3v6u A1609 Oph·Ob 2   0.08   0.29  0 no 3v6u A1711 Oph·Nb 2   0.09   0.30   0.42 no 3v6u A1616 cis-2Oph 2   0.39   0.32   0.04 no 3v6u A1659 cis-2Oph 2   0.30   0.32  0 no 3v6u A1666 trans-2Oph 2   0.09   0.33   0.57 no 3v6u A1634 Ob·2Nb 3   0.41   0.33   0.84 no 3v6u A1636 cis-2Oph 2   0.06   0.37   0.09 no 3v6u X101 other RNA-inner types 3   0.14   0.40   0.09 no 3v6u A1641 cis-2Oph 3   0.33   0.41   0.48 no 3v6u A1603 cis-2Oph·Or 3   0.39   0.42   0.01 no 3v6u A1714 other RNA-inner types 3   0.12   0.42   0.09 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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