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

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Representative site 3r8s:A3000, See in JSmolMgRNA representative site for type OP-5PO         Click on the image to toggle views


Site type: Oph·5Pout

Schematic drawing for
Oph·5Pout

MgRNA type OP-5PO
List of all 81 Mg2+ binding sites with the site type Oph·5Pout 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
1jj2 08091 Oph·5Pout 6  0.44  0.82  0.72no
1jj2 08060 Oph·5Pout 5  0.78  0.62  0.94yes
1k73 A8091 Oph·5Pout 6  0.47  0.91  0.72no
1k73 A8060 Oph·5Pout 5  0.74  0.57  0.80no
1k9m A8060 Oph·5Pout 5  0.50  0.61  0.71yes
1kc8 A8060 Oph·5Pout 5  0.42  0.43  0.99no
1kd1 A8060 Oph·5Pout 5  0.43  0.55  0.89no
1kqs 08060 Oph·5Pout 4  0.40  0.38  0.98no
1m90 A8060 Oph·5Pout 5  0.78  0.60  0.66yes
1n8r A8060 Oph·5Pout 4  0.23  0.45  0.75no
1nji A8060 Oph·5Pout 5  0.88  0.61  0.97yes
1nji A8091 Oph·5Pout 6  0.64  0.85  0.77yes
1q82 A8060 Oph·5Pout 4  0.30  0.42  0.86no
1q86 A8060 Oph·5Pout 5  0.65  0.47  0.50no
1qvf 08060 Oph·5Pout 5  0.80  0.54  0.83no
1s72 08060 Oph·5Pout 5  0.78  0.61  0.96yes
1vq4 08091 Oph·5Pout 6  0.58  0.81  0.77yes
1vq4 08060 Oph·5Pout 5  0.52  0.56  0.90no
1vq5 08060 Oph·5Pout 5  0.69  0.66  0.92yes
1vq5 08091 Oph·5Pout 6  0.67  0.89  0.59yes
1vq6 08091 Oph·5Pout 6  0.63  0.78  0.60yes
1vq6 08060 Oph·5Pout 5  0.49  0.57  0.92no
1vq7 08060 Oph·5Pout 5  0.70  0.64  0.97yes
1vq7 08091 Oph·5Pout 6  0.61  0.88  0.59yes
1vqk 08091 Oph·5Pout 6  0.41  0.80  0.90no

# 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>