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

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Representative site 2qam:B3600, See in JSmolMgRNA representative site for type 3PO-RO-2BO     Click on the image to toggle views


Site type: 3Pout·Rout·2Bout

Schematic drawing for
3Pout·Rout·2Bout

MgRNA type 3PO-RO-2BO
List of all 78 Mg2+ binding sites with the site type 3Pout·Rout·2Bout 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 B3012 3Pout·Rout·2Bout 6  0.97  0.99  1.00yes
1vs8 B3010 3Pout·Rout·2Bout 6  0.97  1.00  0.99yes
1vt2 A3028 3Pout·Rout·2Bout 6  0.75  0.98  0.98yes
2aw4 B3012 3Pout·Rout·2Bout 6  0.97  1.00  1.00yes
2awb B3011 3Pout·Rout·2Bout 6  0.97  0.99  1.00yes
2i2p A1583 3Pout·Rout·2Bout 5  0.81  0.80  1.00yes
2i2t B3012 3Pout·Rout·2Bout 6  0.97  0.99  1.00yes
2i2v B3011 3Pout·Rout·2Bout 6  0.97  1.00  1.00yes
2qam B3600 3Pout·Rout·2Bout 6  0.97  1.00  1.00yes
2qao B3602 3Pout·Rout·2Bout 6  0.98  0.99  0.99yes
2qba B3600 3Pout·Rout·2Bout 6  0.97  1.00  1.00yes
2qbc B3602 3Pout·Rout·2Bout 6  0.97  0.99  0.99yes
2qbe B3600 3Pout·Rout·2Bout 6  0.97  1.00  1.00yes
2qbg B3012 3Pout·Rout·2Bout 6  0.97  1.00  1.00yes
2qbk B3012 3Pout·Rout·2Bout 6  0.97  1.00  0.99yes
2qov B3012 3Pout·Rout·2Bout 6  0.97  1.00  0.99yes
2qox B3011 3Pout·Rout·2Bout 6  0.97  1.00  0.99yes
2qoz B3012 3Pout·Rout·2Bout 6  0.97  0.99  1.00yes
2qp1 B3012 3Pout·Rout·2Bout 6  0.97  0.99  1.00yes
2vhm Z4052 3Pout·Rout·2Bout 4  0.17  0.39  0.13no
2xzn 010 3Pout·Rout·2Bout 6  0.11  0.99  1.00no
2z4l B3013 3Pout·Rout·2Bout 6  0.97  1.00  1.00yes
2z4n B3013 3Pout·Rout·2Bout 6  0.97  0.99  1.00yes
3cc4 08053 3Pout·Rout·2Bout 5  0.15  0.63  0.91no
3cc7 08053 3Pout·Rout·2Bout 5  0.29  0.65  0.96no

# 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>