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

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Representative site 2qoy:A1566, See in JSmolMgRNA representative site for type 2PO-RO-BO      Click on the image to toggle views


Site type: 2Pout·Rout·Bout

Schematic drawing for
2Pout·Rout·Bout

MgRNA type 2PO-RO-BO
List of all 70 Mg2+ binding sites with the site type 2Pout·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
1vs6 B2968 2Pout·Rout·Bout 6  0.97  0.99  1.00yes
2a43 A207 2Pout·Rout·Bout 6  0.85  0.96  0.67yes
2qan A2161 2Pout·Rout·Bout 6  0.97  1.00  1.00yes
2qbb A2189 2Pout·Rout·Bout 6  0.97  0.99  0.99yes
2qov B2908 2Pout·Rout·Bout 6  0.97  0.99  1.00yes
2qow A1591 2Pout·Rout·Bout 6  0.97  1.00  1.00yes
2qoy A1565 2Pout·Rout·Bout 6  0.97  0.99  0.50yes
2qoy A1566 2Pout·Rout·Bout 6  0.97  1.00  1.00yes
2vho Z4035 2Pout·Rout·Bout 4  0.17  0.63  0.81no
2xzm 055 2Pout·Rout·Bout 6  0.13  0.99  1.00no
2xzm 018 2Pout·Rout·Bout 6  0.12  0.99  1.00no
2xzn 031 2Pout·Rout·Bout 6  0.08  0.99  1.00no
2xzn 087 2Pout·Rout·Bout 6  0.13  1.00  1.00no
2xzn 055 2Pout·Rout·Bout 6  0.14  0.99  1.00no
2z4m A1569 2Pout·Rout·Bout 6  0.97  0.99  0.50yes
3ccr 08085 2Pout·Rout·Bout 4  0.22  0.46  0.48no
3df1 A2143 2Pout·Rout·Bout 6  0.97  0.99  1.00yes
3df3 A2168 2Pout·Rout·Bout 6  0.97  0.99  0.50no
3i1n A2960 2Pout·Rout·Bout 6  0.74  0.99  0.27no
3i1p A2933 2Pout·Rout·Bout 4  0.67  0.65  0.70yes
3i1r A2960 2Pout·Rout·Bout 6  0.74  0.99  1.00yes
3oat A2959 2Pout·Rout·Bout 6  0.75  0.99  0.29no
3ofq A2989 2Pout·Rout·Bout 5  0.82  0.79  0.78yes
3ofr A2951 2Pout·Rout·Bout 5  0.82  0.80  0.55yes
3ofz A2958 2Pout·Rout·Bout 6  0.75  0.99  0.22no

# 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
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>