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 4kja 4KJA (2.9Å) -- RIBOSOME/ANTIBIOTIC : Control of ribosomal subunit rotation by elongation factor g List of all 43 Mg2+ binding sites in the PDB structure 4kja 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 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Validation parameters PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset 4kja A1604 Oph·2Ob 4   0.26   0.26   0.98 no 4kja A1627 Oph·Ob·Nb 4   0.15   0.32   0.76 no 4kja A1626 cis-2Oph 5   0.82   0.70   0.92 yes 4kja A1608 cis-2Oph 4   0.65   0.43   0.97 no 4kja A1618 cis-2Oph 3   0.28   0.23   0.92 no 4kja A1617 cis-2Oph·Nb 4   0.41   0.35   0.51 no 4kja A1635 fac-3Oph 5   0.61   0.48   0.50 no 4kja A1620 fac-3Oph 5   0.54   0.51   0.42 no 4kja A1639 mer-3Oph 3   0.34   0.66   0.91 no 4kja A1629 other RNA-inner types 5   0.51   0.37   0.71 no 4kja U101 Bout 2   0.06   0.57   0.64 no 4kja A1621 Bout 2   0.38   0.06   0.59 no 4kja A1611 Pout 2   0.30   0.19   0.14 no 4kja A1616 Pout·2Bout 2   0.34   0.05   0.63 no 4kja A1619 Pout·2Bout 2   0.10   0.09   0.52 no 4kja A1641 2Pout 4   0.24   0.24   0.95 no 4kja A1614 2Pout·Rout 5   0.42   0.62   0.46 no 4kja A1622 2Pout·Bout 3   0.32   0.15   0.64 no 4kja A1638 4Pout·Rout 3   0.16   0.38   0.50 no 4kja E201 Mg2+ not bound by RNA 0  0  0   0.58 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>