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 3g71 3G71 (2.85Å) -- RIBOSOME : Co-crystal structure of bruceantin bound to the large ribosomal subunit List of all 93 Mg2+ binding sites in the PDB structure 3g71 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 3g71 08023 cis-2Oph 6   0.33   0.71   0.51 no 3g71 08084 cis-2Oph 6   0.25   0.56   0.63 no 3g71 08039 trans-2Oph 5   0.17   0.50   0.84 no 3g71 08002 trans-2Oph·Ob 6   0.40   0.65   0.60 no 3g71 08011 cis-2Oph·Nb 6   0.28   0.56   0.93 no 3g71 08001 fac-3Oph 6   0.28   0.54   0.59 no 3g71 08019 fac-3Oph 6   0.35   0.55   0.81 no 3g71 08003 fac-3Oph 6   0.41   0.69   0.94 no 3g71 08005 mer-3Oph 6   0.41   0.75   0.86 no 3g71 08006 mer-3Oph 6   0.36   0.65   0.68 no 3g71 08049 2Bout 5   0.14   0.55   0.62 no 3g71 08028 6Bout 6   0.37   0.83   0.63 no 3g71 28060 Pout·Rout·2Bout 3   0.10   0.43   0.96 no 3g71 B8042 2Pout 5   0.19   0.50   0.94 no 3g71 08085 2Pout·Rout·2Bout 5   0.18   0.62   0.84 no 3g71 08052 Mg2+ bound by non-RNA 5   0.32   0.91   0.72 no 3g71 08034 Mg2+ bound by non-RNA 5   0.26   0.89   0.94 no 3g71 08043 Mg2+ bound by non-RNA 5   0.25   0.45   0.92 no 3g71 A8051 Mg2+ bound by non-RNA 4   0.08   0.40   0.71 no 3g71 K8054 Mg2+ bound by non-RNA 6   0.22   0.73   0.81 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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