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

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Representative site 2qba:B3573, See in JSmolMgRNA representative site for type OP-2OR         Click on the image to toggle views


Site type: Oph·2Or

Schematic drawing for
Oph·2Or

MgRNA type OP-2OR
List of all 294 Mg2+ binding sites with the site type Oph·2Or 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
1fjg A1570 Oph·2Or 3  0.24  0.24  0.26no
1hnw A1569 Oph·2Or 3  0.31  0.41  0.21no
1hnx A1569 Oph·2Or 3  0.19  0.44  0.11no
1jj2 08041 Oph·2Or 6  0.39  0.75  0.88no
1k73 A8041 Oph·2Or 6  0.45  0.65  0.91no
1k8a A8041 Oph·2Or 6  0.43  0.67  0.80no
1k9m A8041 Oph·2Or 6  0.31  0.79  0.77no
1k9m A8119 Oph·2Or 3  0.16  0.32  0.67no
1kc8 A8041 Oph·2Or 5  0.32  0.75  0.76no
1kd1 A8041 Oph·2Or 6  0.41  0.68  0.84no
1kqs 08041 Oph·2Or 6  0.33  0.70  0.88no
1m1k A8041 Oph·2Or 6  0.38  0.67  0.77no
1m90 A8041 Oph·2Or 6  0.36  0.69  0.74no
1n8r A8041 Oph·2Or 5  0.36  0.61  0.73no
1nji A8041 Oph·2Or 6  0.46  0.64  0.54no
1q7y A8041 Oph·2Or 4  0.59  0.49  0.60no
1q81 A8041 Oph·2Or 4  0.19  0.51  0.70no
1q82 A8041 Oph·2Or 5  0.33  0.62  0.88no
1q86 A8041 Oph·2Or 6  0.33  0.86  0.64no
1qvf 08041 Oph·2Or 6  0.41  0.68  0.99no
1qvg 08057 Oph·2Or 5  0.43  0.55  0.84no
1qvg 08041 Oph·2Or 5  0.44  0.57  0.92no
1s72 08041 Oph·2Or 6  0.38  0.75  0.89no
1vq4 08041 Oph·2Or 6  0.36  0.69  0.87no
1vq5 08041 Oph·2Or 6  0.33  0.59  0.68no

# 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>