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

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Representative site 2qbc:B3207, See in JSmolMgRNA representative site for type 3PO-RO-3BO     Click on the image to toggle views


Site type: 3Pout·Rout·3Bout

Schematic drawing for
3Pout·Rout·3Bout

MgRNA type 3PO-RO-3BO
List of all 40 Mg2+ binding sites with the site type 3Pout·Rout·3Bout 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
1vq8 08014 3Pout·Rout·3Bout 5  0.18  0.90  0.80no
2aw4 B2956 3Pout·Rout·3Bout 6  0.97  0.99  1.00yes
2awb B2939 3Pout·Rout·3Bout 6  0.97  0.99  1.00yes
2qam B3302 3Pout·Rout·3Bout 6  0.97  1.00  1.00yes
2qao B3207 3Pout·Rout·3Bout 6  0.97  1.00  1.00yes
2qbc B3320 3Pout·Rout·3Bout 6  0.97  0.99  1.00yes
2qbc B3207 3Pout·Rout·3Bout 6  0.97  1.00  1.00yes
2qox B2959 3Pout·Rout·3Bout 6  0.97  1.00  1.00yes
2xzn 03 3Pout·Rout·3Bout 6  0.12  0.99  1.00no
3i1t A2920 3Pout·Rout·3Bout 6  0.75  1.00  1.00yes
3i20 A2905 3Pout·Rout·3Bout 6  0.75  0.99  1.00yes
3ofq A2921 3Pout·Rout·3Bout 6  0.75  0.99  0.79yes
3ofq A2906 3Pout·Rout·3Bout 6  0.75  0.99  0.69yes
3og0 A3026 3Pout·Rout·3Bout 6  0.75  0.99  0.91yes
3v25 A3289 3Pout·Rout·3Bout 4  0.53  0.98  0.94yes
3v27 A3627 3Pout·Rout·3Bout 6  0.88  0.93  0.71yes
3v2d A3693 3Pout·Rout·3Bout 6  0.80  0.97  0.89yes
4bpe A5046 3Pout·Rout·3Bout 6  0.75  0.99  1.00yes
4bpn A5046 3Pout·Rout·3Bout 6  0.75  1.00  1.00yes
4bpn A5069 3Pout·Rout·3Bout 6  0.75  0.99  1.00yes
4bpo A5046 3Pout·Rout·3Bout 6  0.75  0.99  1.00yes
4bpp A5046 3Pout·Rout·3Bout 6  0.75  1.00  1.00yes
4dha A3646 3Pout·Rout·3Bout 5  0.64  0.74  0.75yes
4gar A3016 3Pout·Rout·3Bout 6  0.75  1.00  0.94yes
4ji8 A1876 3Pout·Rout·3Bout 6  0.91  0.94  0.42no

# 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>