MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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Representative site 4ji1:A1819, See in JSmolMgRNA representative site for type 5PO-RO-BO      Click on the image to toggle views

Site type: 5Pout·Rout·Bout

Schematic drawing for

MgRNA type 5PO-RO-BO
List of all 6 Mg2+ binding sites with the site type 5Pout·Rout·Bout in RNA crystal structures 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 #", "PDB ID" or "Mg2+ ID"
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Mg2+ ion Site type Validation parameters
PDB ID Mg2+ ID Coordination Number Qv # Qs # Qe # benchmark dataset
4dr3 A1635 5Pout·Rout·Bout 4  0.65  0.65  0.89yes
4dv1 A1627 5Pout·Rout·Bout 4  0.65  0.64  0.68yes
4dv3 A1630 5Pout·Rout·Bout 4  0.64  0.64  0.57yes
4ji1 A1791 5Pout·Rout·Bout 6  0.96  1.00  0.71yes
4ji1 A1819 5Pout·Rout·Bout 6  0.98  0.98  0.89yes
4ji7 A1963 5Pout·Rout·Bout 6  0.95  0.99  0.43no

# Validation parameters Qv, Qs, Qe are defined in the range of 0 to 1, with 0 indicating poorest reliability and higher value indicating a more reliable site
Qv measures the agreement of the inner-sphere bond valence summation with the oxidation state of Mg2+ (+2)
Qs measures the geometrical symmetry of the ligands distribution around the Mg2+ required for octahedral geometry
Qe 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
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>