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 3i1p 3I1P (3.19Å) -- RIBOSOME : Crystal structure of the e. coli 70s ribosome in an intermediate state of ratcheting List of all 137 Mg2+ binding sites in the PDB structure 3i1p 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 7 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 3i1p A3022 cis-2Oph·Nb 6   0.62   0.58   0.73 no 3i1p A3023 4Pout 4   0.67   0.99   0.84 yes 3i1p A3024 cis-2Oph·Nb 6   0.66   0.74   0.92 yes 3i1p A3025 fac-3Oph 6   0.49   0.72   0.98 no 3i1p A3026 Oph·2Pout 6   0.84   0.86   0.85 yes 3i1p A3027 cis-2Oph·Nb 6   0.58   0.57   0.79 no 3i1p A3028 3Pout·Rout·2Bout 6   0.75   0.98   0.93 yes 3i1p A3029 Oph·Pout 5   0.69   0.68   0.75 yes 3i1p A3030 cis-2Oph 5   0.44   0.74   0.97 no 3i1p A3031 Mg2+ bound by non-RNA 6   0.73   0.74   0.74 yes 3i1p A3032 Pout·3Bout 6   0.74   1.00   0.42 no 3i1p A3033 Ob 6   0.82   0.83   0.84 yes 3i1p A3034 2Pout·3Bout 6   0.73   0.98   0.44 no 3i1p A3035 Pout·2Bout 6   0.74   0.99   0.58 yes 3i1p A3036 Oph·Pout 6   0.90   0.93   0.88 yes 3i1p A3037 Pout·Bout 6   0.74   0.99   0.45 no 3i1p A3038 3Pout 6   0.74   0.99   0.70 yes

^# 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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