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 1n8r 1N8R (3Å) -- RIBOSOME : Structure of large ribosomal subunit in complex with virginiamycin m List of all 117 Mg2+ binding sites in the PDB structure 1n8r 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 5 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 1n8r A8036 Oph·2Pout 6   0.33   0.74   0.81 no 1n8r A8112 Nb 5   0.68   0.57   0.81 no 1n8r A8103 cis-2Oph 3   0.13   0.47   0.82 no 1n8r A8100 Ob 6   0.57   0.46   0.83 no 1n8r B8095 cis-2Oph 3   0.43   0.16   0.83 no 1n8r C8065 Rout 6   0.75   0.86   0.83 yes 1n8r A8045 Oph·3Pout 5   0.53   0.61   0.83 yes 1n8r C8105 Mg2+ not bound by RNA 1   0.01  0   0.84 no 1n8r A8088 poly-nuclear Mg2+ site 6   0.42   0.76   0.84 no 1n8r A8032 Oph·3Pout 6   0.99   0.69   0.84 yes 1n8r A8067 Mg2+ bound by non-RNA 5   0.33   0.88   0.84 no 1n8r A8068 Oph·2Pout 6   0.89   0.75   0.86 yes 1n8r A8087 cis-2Oph 4   0.48   0.53   0.86 no 1n8r A8079 cis-2Oph·Nb 6   0.80   0.81   0.86 yes 1n8r A8053 Ob 6   0.39   0.78   0.86 no 1n8r A8056 Mg2+ bound by non-RNA 6   0.99   0.82   0.87 yes 1n8r A8001 fac-3Oph 6   0.80   0.68   0.87 yes 1n8r A8043 poly-nuclear Mg2+ site 5   0.56   0.41   0.88 no 1n8r A8025 poly-nuclear Mg2+ site 6   0.37   0.71   0.90 no 1n8r A8082 Oph·Pout 5   0.42   0.40   0.91 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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