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

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Representative site 1vs6:B2983, See in JSmolMgRNA representative site for type 3PO-3BO        Click on the image to toggle views


Site type: 3Pout·3Bout

Schematic drawing for
3Pout·3Bout

MgRNA type 3PO-3BO
List of all 47 Mg2+ binding sites with the site type 3Pout·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
1dul B801 3Pout·3Bout 6  0.97  0.95  0.91yes
1hq1 B1801 3Pout·3Bout 6  0.94  0.99  0.99yes
1vs6 B2983 3Pout·3Bout 6  0.97  1.00  1.00yes
1vs8 B2958 3Pout·3Bout 6  0.97  1.00  1.00yes
1vs8 B2917 3Pout·3Bout 6  0.97  1.00  1.00yes
1vt2 A2906 3Pout·3Bout 6  0.75  1.00  0.74yes
2awb B2917 3Pout·3Bout 6  0.97  0.99  1.00yes
2i2t B2957 3Pout·3Bout 6  0.97  1.00  1.00yes
2i2v B2939 3Pout·3Bout 6  0.97  0.99  1.00yes
2i2v B2927 3Pout·3Bout 6  0.97  1.00  1.00yes
2qou A1584 3Pout·3Bout 5  0.81  0.80  1.00yes
2qov B2923 3Pout·3Bout 6  0.97  1.00  1.00yes
2vhm Z4019 3Pout·3Bout 5  0.23  0.42  0.73no
2xzm 010 3Pout·3Bout 6  0.12  1.00  1.00no
2xzm 066 3Pout·3Bout 6  0.12  1.00  1.00no
3df2 B3110 3Pout·3Bout 6  0.97  0.99  1.00yes
3df4 B3207 3Pout·3Bout 6  0.97  0.99  1.00yes
3i1o A2 3Pout·3Bout 6  0.75  0.99  0.94yes
3i1r A2974 3Pout·3Bout 6  0.74  0.99  1.00yes
3i1t A2905 3Pout·3Bout 6  0.75  1.00  1.00yes
3i20 A3036 3Pout·3Bout 6  0.74  0.99  1.00yes
3i55 08053 3Pout·3Bout 6  0.16  0.68  0.73no
3i56 08053 3Pout·3Bout 5  0.17  0.74  0.95no
3oar A1535 3Pout·3Bout 6  0.75  0.99  0.92yes
3ofb A1535 3Pout·3Bout 6  0.75  1.00  0.85yes

# 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>