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 3r8s 3R8S (3Å) -- RIBOSOME : Structures of the bacterial ribosome in classical and hybrid states of trna binding List of all 190 Mg2+ binding sites in the PDB structure 3r8s 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 1 of 10 | « 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 3r8s A3004 Ob 6   0.94   0.93   0.32 no 3r8s A3071 Ob 1   0.02  0   0.04 no 3r8s B615 Ob 6   0.99   0.94  0 no 3r8s A2925 Ob 6   0.99   0.86  0 no 3r8s A2992 Ob 6   0.81   0.85   0.97 yes 3r8s A2975 Ob 6   0.97   0.88   1.00 yes 3r8s A3036 Ob 6   0.96   0.92   0.98 yes 3r8s A3043 Nb 1   0.06  0   1.00 no 3r8s A3073 2Ob 2   0.05   0.18   0.01 no 3r8s A3078 2Ob 2   0.03   0.14   0.04 no 3r8s A2923 2Nb 6   0.98   0.92  0 no 3r8s A2948 2Nb 6   0.87   0.81  0 no 3r8s A3069 Oph 1   0.02  0   0.17 no 3r8s A3054 Oph 1   0.07  0   0.06 no 3r8s A3087 Oph 1   0.05  0   1.00 no 3r8s A3066 Oph 1   0.05  0   0.01 no 3r8s A2964 Oph 5   0.68   0.67   0.91 yes 3r8s A2910 Oph 6   0.92   0.93   1.00 yes 3r8s A3097 Oph 1   0.04  0   0.49 no 3r8s A3096 Oph 1   0.06  0  0 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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>