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

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Representative site 2qbb:A2049, See in JSmolMgRNA representative site for type 2PO-BO         Click on the image to toggle views


Site type: 2Pout·Bout

Schematic drawing for
2Pout·Bout

MgRNA type 2PO-BO
List of all 169 Mg2+ binding sites with the site type 2Pout·Bout 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
2qow A1555 2Pout·Bout A1942, A1943, A1944, A1945, A1946, A1947 A:A315, A:A329 G:A319
2qoz B2968 2Pout·Bout B3805, B3806, B3807, B3808, B3809, B3810 C:B1376, C:B1351 G:B1377
2qp0 A1580 2Pout·Bout A2065, A2066, A2067, A2068, A2069, A2070 G:A259, G:A258 G:A259
2qp1 B2920 2Pout·Bout B3596, B3597, B3598, B3599, B3600, B3601 C:B1376, C:B1351 G:B1377
2z4k A1567 2Pout·Bout A1718, A1719, A1720, A1721, A1722, A1723 A:A1357, G:A1356 C:A1359
2z4k A1582 2Pout·Bout A1791, A1792, A1793, T233, T236 U:A323, G:A324 G:A324
3df1 A2231 2Pout·Bout A4232, A4234, A4235, T4233, T4236 U:A323, G:A324 G:A324
3df1 A2014 2Pout·Bout A4015, A4016, A4017, A4018, A4019, A4020 U:A804, G:A803 G:A771
3df3 A2084 2Pout·Bout A4085, A4086, A4087, A4088, A4089, A4090 U:A1049, A:A1201 U:A1205
3df3 A2353 2Pout·Bout A4354, A4355, A4356, A4357, A4358, A4359 G:A259, G:A258 G:A259
3df3 E2155 2Pout·Bout A4156, A4157, A4158, A4160, E4159 U:A20, U:A561 G:A21
3df4 B3262 2Pout·Bout B4263, B4264, B4265, B4266, B4267 G:B297, G:B338 G:B298
3df4 B3074 2Pout·Bout B4075, B4076, B4077, B4078, B4079, B4080 A:B2033, U:B2026 U:B2028
3gx5 A800 2Pout·Bout A801, A802, A803, A804, A805, A806 G:A1, A:A33 G:A32
3i1p A2916 2Pout·Bout A3101, A3102, A3103, A3104, A3105, A3106 U:A568, C:A944 A:A945
3i1q A1552 2Pout·Bout A1661, A1662, A1663, A1664, A1665, E167 G:A1077, U:A1076 G:A1077
3i1q A1563 2Pout·Bout A1711, A1712, A1713, A1714, A1715 A:A1433, A:A1434 G:A1435
3i1r A2951 2Pout·Bout A3257, A3258, A3259, A3260, A3261 G:A1455, A:A1453 U:A1457
3i1t A2916 2Pout·Bout A3100, A3101, A3102, A3103, A3104, A3105 U:A568, C:A944 A:A945
3i1z A1563 2Pout·Bout A1713, A1714, A1715, A1716, A1717 A:A1433, A:A1434 G:A1435
3i21 A1562 2Pout·Bout A1726, A1727, A1728, A1729, A1730 U:A323, G:A324 G:A324
3i22 A2916 2Pout·Bout A3099, A3100, A3101, A3102, A3103, L203 A:A943, C:A944 A:A945
3oaq A1563 2Pout·Bout A1715, A1716, A1717, A1718, A1719 A:A1433, A:A1434 G:A1435
3oar E159 2Pout·Bout A1686, A1687, A1688, A1689, A1690, A1691 U:A20, G:A21 G:A21
3ofb A1557 2Pout·Bout A1686, A1687, A1688, A1689, A1690, A1691 U:A20, G:A21 G:A21

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>