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

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Representative site 2qex:08096, See in JSmolMgRNA representative site for type 2OB-NB         Click on the image to toggle views


Site type: 2Ob·Nb

Schematic drawing for
2Ob·Nb

MgRNA type 2OB-NB
List of all 127 Mg2+ binding sites with the site type 2Ob·Nb 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
3oi5 A3036 2Ob·Nb 3  0.09  0.22  0.75no
4qco A3037 2Ob·Nb 3  0.11  0.25  0.96no
4qcn A3050 2Ob·Nb 3  0.08  0.36  0.80no
3kiw A3050 2Ob·Nb 3  0.31  0.26  0.88no
4qcr A3055 2Ob·Nb 3  0.06  0.45  0.99no
4qcr A3060 2Ob·Nb 3  0.07  0.24  0.69no
1vvs A3070 2Ob·Nb 3  0.40  0.27  0.67no
4kx2 A3071 2Ob·Nb 3  0.40  0.36  0.54no
3kiy A3077 2Ob·Nb 3  0.07  0.27  0.78no
3oh7 A3090 2Ob·Nb 3  0.06  0.28  0.91no
3hux A3098 2Ob·Nb 3  0.14  0.41  0.77no
4kx0 A3099 2Ob·Nb 3  0.32  0.52  0.39no
3ohz A3100 2Ob·Nb 3  0.07  0.27  0.49no
3oi5 A3102 2Ob·Nb 3  0.13  0.56  0.98no
3ohk A3104 2Ob·Nb 3  0.06  0.43  0.68no
3ohj A3105 2Ob·Nb 3  0.08  0.33  0.38no
3oh5 A3106 2Ob·Nb 3  0.07  0.26  0.30no
3oh7 A3106 2Ob·Nb 3  0.08  0.50  0.66no
3pyt A3114 2Ob·Nb 3  0.06  0.19  0.95no
1vvm A3116 2Ob·Nb 3  0.47  0.30  0.87no
3ohz A3116 2Ob·Nb 3  0.07  0.56  0.61no
1vvu A3116 2Ob·Nb 3  0.52  0.39  0.06no
3oi3 A3120 2Ob·Nb 3  0.12  0.65  0.43no
3ohj A3121 2Ob·Nb 3  0.09  0.54  0.37no
3oh5 A3122 2Ob·Nb 3  0.09  0.55  0.50no

# 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>