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

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Representative site 3df2:B3428, See in JSmolMgRNA representative site for type OP-OR          Click on the image to toggle views


Site type: Oph·Or

Schematic drawing for
Oph·Or

MgRNA type OP-OR
List of all 1185 Mg2+ binding sites with the site type Oph·Or 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
1cx0 B403 Oph·Or 3  0.11  0.31  0.88no
1fjg A1589 Oph·Or 2  0.15  0.14  0.67no
1gid B281 Oph·Or 2  0.11  0.14  0.81no
1hnw A1612 Oph·Or 2  0.05  0.11  0.53no
1hnw A1587 Oph·Or 2  0.14  0.27  0.56no
1hnw A1624 Oph·Or 2  0.25  0.45  0.55no
1hnx A1588 Oph·Or 2  0.21  0.13  0.56no
1hnz A1622 Oph·Or 2  0.25  0.16  0.52no
1hnz A1588 Oph·Or 2  0.16  0.21  0.61no
1hnz A1559 Oph·Or 2  0.16  0.04  0.54no
1hr0 A1568 Oph·Or 2  0.14  0.13  0.20no
1hr0 A1587 Oph·Or 2  0.22  0.18  0.67no
1hr0 A1558 Oph·Or 2  0.13  0.06  0.68no
1i94 A1527 Oph·Or 2  0.14  0.56  0.63no
1i95 A1528 Oph·Or 2  0.08  0.51  0.63no
1i96 A1528 Oph·Or 2  0.09  0.44  0.67no
1i97 A1528 Oph·Or 2  0.08  0.32  0.80no
1ibk A1557 Oph·Or 2  0.20  0.03  0.34no
1ibl A1581 Oph·Or 2  0.20  0.31  0.29no
1ibl A1573 Oph·Or 2  0.12  0.07  0.29no
1ibl A1558 Oph·Or 2  0.16  0.06  0.48no
1ibm A1582 Oph·Or 2  0.21  0.10  0.43no
1ibm A1557 Oph·Or 2  0.12  0.06  0.50no
1jj2 08093 Oph·Or 6  0.36  0.80  0.70no
1k73 A8093 Oph·Or 6  0.43  0.74  0.70no

# 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>