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

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Representative site 4kj6:A1630, See in JSmolMgRNA representative site for type OP-2OB         Click on the image to toggle views


Site type: Oph·2Ob

Schematic drawing for
Oph·2Ob

MgRNA type OP-2OB
List of all 199 Mg2+ binding sites with the site type Oph·2Ob 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
1n32 A1666 Oph·2Ob 3  0.11  0.51  0.57no
1vvm A3217 Oph·2Ob 3  0.13  0.39  0.88no
1vvo A3144 Oph·2Ob 3  0.20  0.48  0.87no
1vvo A3236 Oph·2Ob 3  0.18  0.59  0.84no
1vvo A3202 Oph·2Ob 3  0.13  0.26  0.90no
1vvq A3219 Oph·2Ob 3  0.19  0.23  0.79no
1vvr A1671 Oph·2Ob 3  0.16  0.52  0.78no
1vvs A3232 Oph·2Ob 3  0.14  0.50  0.57no
1vvt A1640 Oph·2Ob 3  0.18  0.50  0.56no
1vvv A1668 Oph·2Ob 3  0.15  0.56  0.47no
1vvy A3215 Oph·2Ob 3  0.08  0.29  0.99no
1vw0 A3144 Oph·2Ob 3  0.20  0.54  0.42no
1vw0 A3225 Oph·2Ob 3  0.06  0.66  0.25no
1vx9 A3217 Oph·2Ob 3  0.10  0.36  0.46no
1vxi A1671 Oph·2Ob 3  0.13  0.59  0.84no
1vxj A3143 Oph·2Ob 3  0.14  0.37  0.17no
1vxj A3233 Oph·2Ob 3  0.10  0.57  0.56no
1vxl A3218 Oph·2Ob 3  0.17  0.40  0.78no
1vxn A3235 Oph·2Ob 3  0.12  0.68  0.82no
1vxn A3202 Oph·2Ob 3  0.11  0.28  0.76no
1vxq A3118 Oph·2Ob 3  0.35  0.53  0.90no
1vxq A3217 Oph·2Ob 3  0.17  0.39  0.61no
1vxt A3200 Oph·2Ob 3  0.17  0.37  0.94no
1vxt A3234 Oph·2Ob 3  0.18  0.48  0.72no
1vxt A3143 Oph·2Ob 3  0.26  0.26  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>