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

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Representative site 1vs8:B2932, See in JSmolMgRNA representative site for type 3PO            Click on the image to toggle views

Site type: 3Pout

Schematic drawing for

MgRNA type 3PO
List of all 207 Mg2+ binding sites with the site type 3Pout 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
1vs5 A1589 3Pout A1824, A1825, A1826, A1827, A1828, A1829 C:A25, U:A552, A:A553
1vs8 B2932 3Pout B3150, B3151, B3152, B3153, B3154, B3155 A:B947, G:B822, C:B965
1vt2 A2984 3Pout A3422, A3423, A3424, A3425, C477 A:A2587, G:A2588, A:A2600
1vt2 A3037 3Pout A3645, A3646, A3647, A3648, A3649, N780 C:A2874, G:A2819, G:A2838
2avy A1588 3Pout A1820, A1821, A1822, A1823, A1824, A1825 C:A25, U:A552, A:A553
2avy A1555 3Pout A1659, A1660, A1661, A1662, A1663, A1664 A:A1204, G:A1048, U:A1049
2aw4 B2908 3Pout B3028, B3029, B3030, B3031, B3032, B3033 C:B560, A:B1008, G:B559
2awb B2932 3Pout B3151, B3152, B3153, B3154, B3155, B3156 A:B947, G:B822, C:B965
2i2p A1555 3Pout A1660, A1661, A1662, A1663, A1664, A1665 A:A1204, G:A1048, U:A1049
2i2p A1594 3Pout A1853, A1854, A1855, A1856, A1857 C:A536, G:A537, A:A523
2i2u N340 3Pout A1783, A1784, A1785, A1786, A1787, N192 A:A1204, G:A1048, U:A1049
2i2v B2932 3Pout B3161, B3162, B3163, B3164, B3165, B3166 G:B822, C:B965, A:B947
2i2v B2986 3Pout B3414, B3415, B3416, B3417, B3418, B3419 C:B2050, A:B2051, A:B2614
2qam B3021 3Pout B3630, B3631, B3632, B3633, B3634, B3635 C:B560, A:B1008, G:B559
2qam B3561 3Pout B4067, B4068, B4069, B4070, B4071, B4072 G:B205, C:B383, C:B385
2qb9 A2070 3Pout A2416, A2417, A2418, A2419, A2420, A2421 A:A1204, G:A1048, U:A1049
2qbd A2070 3Pout A2071, A2072, A2074, A2075, A2076, N2073 G:A1048, A:A1204, U:A1049
2qbe B3021 3Pout B3630, B3631, B3632, B3633, B3634, B3635 C:B560, A:B1008, G:B2038
2qbf A1548 3Pout A1627, A1628, A1629, A1630, A1631, A1632 G:A15, U:A13, U:A14
2qbf A1550 3Pout A1638, A1639, A1640, A1641, A1642, A1643 U:A333, G:A350, C:A334
2qbg B2932 3Pout B3153, B3154, B3155, B3156, B3157, B3158 C:B965, G:B822, A:B947
2qbi B2921 3Pout B3090, B3091, B3092, B3093, B3094, B3095 G:B822, C:B965, A:B947
2qou A1555 3Pout A1662, A1954, A1955, A1956, A1957, N101 U:A1049, A:A1204, G:A1048
2qou A1598 3Pout A2162, A2163, A2164, A2165, A2166, A2167 A:A1394, G:A917, A:A918
2qou A1594 3Pout A2145, A2146, A2147, A2148, L308 C:A504, C:A536, C:A503

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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/)
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