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

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Representative site 2z4m:A1592, See in JSmolMgRNA representative site for type PO             Click on the image to toggle views


Site type: Pout

Schematic drawing for
Pout

MgRNA type PO
List of all 94 Mg2+ binding sites with the site type Pout in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dr4 A1944 Pout A2415, A2416, A2417, A2418 U:A294
4dr5 A1698 Pout A2134, A2135, A2136, A2137 C:A701
4dr6 A1628 Pout A2074, A2075, A2076, A2077, A2693 G:A21
4dv0 J202 Pout A2229, I201, J301, J302, J303, N201 C:A1189
4dv1 A1635 Pout A1971, A1972, A1973, A1974 U:A646
4dv2 J201 Pout A2233, J301, J302, N202, N203, N204 C:A1189
4dv6 A1841 Pout J301, J302, J303, N202, N203 C:A1189
4gar A3026 Pout A3332, A3333, A3334, A3335, A3336 A:A802
4gau A3016 Pout A3274, A3275, A3276, A3277, A3278, A3279 G:A1256
4ji1 A1790 Pout A2432, A2433, A2434, A2435, A2436, A2437 U:A5
4ji1 H202 Pout A2302, A2303, A2304, A2305, H301, H302 U:A5
4ji3 A1700 Pout A2072, A2073, A2074, A2123 A:A1204
4lf9 S101 Pout A1831, A1832, A1833, S201, S202, S203 U:A1313
4lfb A1821 Pout A1915, A1916, A1917, A1918, A1919, A1920 C:A442
4qcn A3570 Pout A4912, A4913, A4914, A4915 G:A992
4qcn A3761 Pout A5307, A5308, A5309, A5310, 03105 C:A2275
4qcq A3180 Pout A4178, A4179, E301, E302 A:A864
4qcz B3010 Pout B4008, B4009, B4010, B4011, B4012 A:B25
4tp7 A3031 Pout A3332, A3333, A3334, A3335, A3336, A3337 C:A965

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>