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 4e8m 4E8M (3.5Å) -- RNA : Structure of oceanobacillus iheyensis group ii intron in a ligand-free state in the presence of k+ and mg2+ List of all 24 Mg2+ binding sites in the PDB structure 4e8m 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 2 | « Previous | Next » | 1 | 2

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4e8m A407 Ob 3   0.05   0.59   0.50 no 4e8m A423 2Or 2   0.03   0.10   0.26 no 4e8m A406 Ob·Nb 2   0.06   0.20   0.46 no 4e8m A412 Oph 1   0.42  0   0.49 no 4e8m A416 Oph 1   0.02  0   0.44 no 4e8m A419 Oph 1   0.06  0   0.58 no 4e8m A411 Oph 1   0.34  0   0.77 no 4e8m A408 Oph 1   0.15  0   0.65 no 4e8m A409 Oph 1   0.07  0   0.29 no 4e8m A401 Oph 1   0.17  0   0.39 no 4e8m A404 Oph 1   0.17  0   0.50 no 4e8m A421 Oph 1   0.04  0   0.69 no 4e8m A418 Oph·Nb 2   0.94   0.12   0.52 no 4e8m A417 Oph·Nb 2   0.11   0.14   0.53 no 4e8m A405 cis-2Oph 2   0.13   0.20   0.63 no 4e8m A414 cis-2Oph 2   0.13   0.21   0.87 no 4e8m A424 cis-2Oph 2   0.22   0.22   0.53 no 4e8m A413 trans-2Oph 2   0.04   0.62   0.35 no 4e8m A402 poly-nuclear Mg2+ site 2   0.06   0.14   0.08 no 4e8m A403 poly-nuclear Mg2+ site 4   0.54   0.79   0.79 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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