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

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Representative site 2avy:A1578, See in JSmolMgRNA representative site for type PO-RO          Click on the image to toggle views


Site type: Pout·Rout

Schematic drawing for
Pout·Rout

MgRNA type PO-RO
List of all 142 Mg2+ binding sites with the site type Pout·Rout 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
1dno B23 Pout·Rout 6  0.96  0.99  0.77yes
1jj2 A8065 Pout·Rout 6  0.85  0.92  0.91yes
1k73 C8065 Pout·Rout 6  0.88  0.83  0.90yes
1k9m C8065 Pout·Rout 6  0.73  0.79  0.84yes
1m90 C8065 Pout·Rout 6  0.96  0.80  0.86yes
1nji C8065 Pout·Rout 6  0.69  0.71  0.78yes
1q7y A8099 Pout·Rout 3  0.11  0.58  0.65no
1s72 A8065 Pout·Rout 6  0.82  0.90  0.86yes
1vq5 A8065 Pout·Rout 6  0.70  0.82  0.98yes
1vq7 A8065 Pout·Rout 6  0.66  0.89  0.91yes
1yij A8065 Pout·Rout 6  0.87  0.78  0.75yes
2avy A1578 Pout·Rout 6  0.97  0.99  1.00yes
2otl A8065 Pout·Rout 6  0.82  0.82  0.84yes
2vhm Z4058 Pout·Rout 3  0.14  0.42  0.52no
2vhn Z4097 Pout·Rout 3  0.15  0.61  0.29no
2xzm 090 Pout·Rout 6  0.13  1.00  1.00no
2xzm 042 Pout·Rout 6  0.12  1.00  1.00no
2xzn 042 Pout·Rout 6  0.13  0.99  1.00no
2xzn 090 Pout·Rout 6  0.13  1.00  1.00no
3cc2 A8065 Pout·Rout 6  0.79  0.90  0.86yes
3cc7 A8050 Pout·Rout 6  0.54  0.95  0.59yes
3ccr 08050 Pout·Rout 4  0.13  0.33  0.70no
3ccs 08030 Pout·Rout 2  0.08  0.19  0.67no
3ccs A8050 Pout·Rout 6  0.35  0.83  0.82no
3ccu A8050 Pout·Rout 6  0.49  0.92  0.79no

# 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>