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

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Representative site 2r8s:R1004, See in JSmolMgRNA representative site for type 2OB            Click on the image to toggle views


Site type: 2Ob

Schematic drawing for
2Ob

MgRNA type 2OB
List of all 1662 Mg2+ binding sites with the site type 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
3oh5 A3179 2Ob 2  0.03  0.16  0.72no
3oi5 A3054 2Ob 2  0.03  0.17  0.82no
1vxn A3231 2Ob 2  0.03  0.20  0.47no
4kfk A2301 2Ob 2  0.03  0.16  0.88no
3pyo A2947 2Ob 2  0.03  0.14  0.81no
4ji7 A2016 2Ob 2  0.03  0.20  0.74no
3mrz A2984 2Ob 2  0.03  0.22  0.99no
3t1y A1632 2Ob 2  0.03  0.16  0.31no
3d5b A3497 2Ob 2  0.03  0.20  0.12no
2j02 Z187 2Ob 2  0.03  0.20  0.86no
3tvf A2611 2Ob 2  0.03  0.22  0.99no
3uz6 A2285 2Ob 2  0.03  0.20  0.84no
3v2d B205 2Ob 2  0.03  0.19  0.80no
3ohk A3131 2Ob 2  0.03  0.13  0.76no
3u5d 4330 2Ob 2  0.03  0.18  0.99no
4l6j A4725 2Ob 2  0.03  0.17  0.54no
4dh9 A1811 2Ob 2  0.03  0.20  0.58no
1xmo A210 2Ob 2  0.03  0.15  0.36no
4dv4 A1821 2Ob 2  0.03  0.65  0.53no
4ji0 A1696 2Ob 2  0.03  0.18  0.73no
4dr6 A1934 2Ob 2  0.03  0.18  0.97no
4ji0 A1642 2Ob 2  0.03  0.17  0.85no
2uxc Z3 2Ob 2  0.03  0.26  0.98no
4dv4 A1742 2Ob 2  0.03  0.18  0.85no
4lf9 A1608 2Ob 2  0.03  0.18  0.85no

# 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>