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 4nw0 4NW0 (3.1Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of antibiotic ge82832 bound to 70s ribosome List of all 179 Mg2+ binding sites in the PDB structure 4nw0 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 2 of 9 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4nw0 A3022 Oph 1   0.09  0   0.77 no 4nw0 A3121 Oph 3   0.26   0.37   0.95 no 4nw0 A3120 Oph 2   0.14   0.25   0.79 no 4nw0 A3117 Oph 2   0.14   0.04   0.93 no 4nw0 A3061 Oph 1   0.17  0   0.57 no 4nw0 A3128 Oph 3   0.28   0.44   0.62 no 4nw0 A3114 Oph 3   0.27   0.29   0.85 no 4nw0 A3161 Oph 2   0.14   0.18   0.87 no 4nw0 A3111 Oph 2   0.15   0.16   0.89 no 4nw0 A3164 Oph 3   0.28   0.85   0.98 no 4nw0 A3107 Oph 2   0.16   0.34   0.60 no 4nw0 A3084 Oph 4   0.41   0.61   0.74 no 4nw0 A3076 Oph 2   0.14   0.05   0.63 no 4nw0 A3048 Oph 1   0.03  0   0.88 no 4nw0 A3038 Oph 1   0.03  0   0.97 no 4nw0 A3011 Oph 1   0.07  0   0.63 no 4nw0 A3046 Oph 1   0.01  0   0.67 no 4nw0 A3003 Oph 1   0.15  0   0.77 no 4nw0 A3028 Oph 1   0.05  0   0.58 no 4nw0 A3056 Oph 1   0.03  0   0.87 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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