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

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Representative site 2i2t:B2935, See in JSmolMgRNA representative site for type 3PO-BO         Click on the image to toggle views


Site type: 3Pout·Bout

Schematic drawing for
3Pout·Bout

MgRNA type 3PO-BO
List of all 243 Mg2+ binding sites with the site type 3Pout·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
1k8a A8090 3Pout·Bout 3  0.10  0.64  0.57no
1vs5 A1598 3Pout·Bout 6  0.97  0.99  1.00yes
1vs7 A1574 3Pout·Bout 6  0.97  1.00  0.99yes
1vs8 B2920 3Pout·Bout 6  0.97  0.99  1.00yes
1vt2 A2949 3Pout·Bout 6  0.74  0.98  0.59yes
1vt2 A2963 3Pout·Bout 6  0.74  0.99  0.38no
1w2b 38092 3Pout·Bout 4  0.19  0.46  0.52no
1yjw 78090 3Pout·Bout 3  0.29  0.22  0.82no
2avy A1597 3Pout·Bout 6  0.97  0.99  1.00yes
2aw4 B2968 3Pout·Bout 6  0.97  0.99  1.00yes
2aw4 B2931 3Pout·Bout 6  0.97  0.99  1.00yes
2aw7 A1573 3Pout·Bout 6  0.97  0.99  0.99yes
2awb B2920 3Pout·Bout 6  0.97  0.99  1.00yes
2awb B2910 3Pout·Bout 6  0.97  0.99  1.00yes
2i2p A1569 3Pout·Bout 5  0.81  0.80  1.00yes
2i2t B2935 3Pout·Bout 6  0.97  1.00  1.00yes
2qam B3369 3Pout·Bout 6  0.97  0.99  1.00yes
2qan E2155 3Pout·Bout 5  0.81  0.80  1.00yes
2qao B3092 3Pout·Bout 6  0.97  1.00  0.99yes
2qb9 A2164 3Pout·Bout 5  0.81  0.80  1.00yes
2qba B3369 3Pout·Bout 6  0.97  0.99  1.00yes
2qbc B3092 3Pout·Bout 6  0.97  0.99  1.00yes
2qbd A2129 3Pout·Bout 6  0.97  1.00  1.00yes
2qbe B3282 3Pout·Bout 6  0.97  1.00  1.00yes
2qbe B3157 3Pout·Bout 6  0.97  1.00  1.00yes

# 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>