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 3ms1 3MS1 (3.62Å) -- RIBOSOME : Recognition of the amber stop codon by release factor rf1. this entry 3ms1 contains 50s ribosomal subunit. the 30s ribosomal subunit can be found in pdb entry 3mr8. molecule b in the same asymmetric unit is deposited as 3mrz (50s) and 3ms0 (30s). List of all 185 Mg2+ binding sites in the PDB structure 3ms1 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 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 3ms1 A2945 cis-2Oph 2   0.06   0.12   0.54 no 3ms1 A2946 cis-2Oph 2   0.03   0.34   0.75 no 3ms1 A2967 cis-2Oph 2   0.03   0.23   0.82 no 3ms1 A2969 cis-2Oph 2   0.04   0.26   0.43 no 3ms1 A2970 cis-2Oph 2   0.05   0.11   0.28 no 3ms1 A2971 cis-2Oph 2   0.04   0.14   0.90 no 3ms1 A3041 cis-2Oph 2   0.06   0.27   0.49 no 3ms1 A3047 cis-2Oph 2   0.08   0.38   0.32 no 3ms1 A2913 cis-2Oph·Or 3   0.08   0.41   0.22 no 3ms1 A2929 fac-3Oph 3   0.06   0.14   0.82 no 3ms1 A2962 fac-3Oph 3   0.10   0.16   0.44 no 3ms1 A2920 mer-3Oph 3   0.09   0.69   0.59 no 3ms1 A5 Mg2+ not bound by RNA 0  0  0   0.39 no 3ms1 A2900 poly-nuclear Mg2+ site 1   0.03  0   0.42 no 3ms1 A2901 Mg2+ not bound by RNA 0  0  0   0.76 no 3ms1 A2903 fac-3Oph 3   0.10   0.37   0.63 no 3ms1 A2905 cis-2Oph 2   0.06   0.43   1.00 no 3ms1 A2907 cis-2Oph 2   0.06   0.61   0.59 no 3ms1 A2909 Ob 1   0.01  0   0.67 no 3ms1 A167 Or 1   0.01  0   0.79 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>