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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 2qbg:B2930, See in JSmolMgRNA representative site for type PO-4BO Click on the image to toggle views


Site type: Pout·4Bout

Schematic drawing for
Pout·4Bout
MgRNA type PO-4BO
List of all 135 Mg2+ binding sites with the site type Pout·4Bout 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
2qoy A1548 Pout·4Bout A1924, A1925, A1926, A1927, A1928, A1929 U:A644 G:A645, U:A593, U:A644, G:A646
2qp1 B2939 Pout·4Bout B3691, B3692, B3693, B3694, B3695, B3696 A:B447 G:B473, U:B29, C:B31, G:B474
2z4k A1562 Pout·4Bout A1689, A1690, A1691, A1692, A1693 A:A1201 G:A1050, G:A1207, C:A1208, U:A1205
2z4k A1549 Pout·4Bout A1629, A1630, A1631, A1632, A1633, A1634 U:A644 G:A645, U:A593, U:A644, G:A646
2z4m A1563 Pout·4Bout A1692, A1693, A1694, A1695, A1696, A1697 U:A644 G:A592, U:A593, G:A646, G:A645
2z4n B2924 Pout·4Bout B3106, B3107, B3108, B3109, B3110, B3111 U:B1267 A:B2009, U:B2011, G:B2012, G:B2010
3df4 B3110 Pout·4Bout B4111, B4112, B4113, B4114, B4115, B4116 U:B1267 A:B2009, U:B2011, G:B2012, G:B2010
3i1m A1549 Pout·4Bout A1653, A1654, N121, N123, N124, N125 A:A1360 A:A1360, G:A1361, C:A979, C:A980
3i1p A2943 Pout·4Bout A3223, A3224, A3225, A3226, A3227, A3228 U:A1267 A:A2009, G:A2010, U:A2011, G:A2012
3i1p A2919 Pout·4Bout A3118, A3119, A3120, A3121, A3122, A3123 C:A1257 U:A580, C:A581, G:A1259, U:A1258
3i1q A1543 Pout·4Bout A1618, A1619, A1620, A1621, A1622, A1623 G:A645 G:A646, G:A592, U:A593, G:A645
3i1s A1558 Pout·4Bout A1708, A1709, A1710, A1711, A1712 A:A1349 A:A1350, G:A1371, U:A1372, G:A1370
3i1t A2925 Pout·4Bout A3148, A3149, A3150, A3151, A3152, A3153 U:A755 U:A755, G:A757, A:A739, A:A756
3i20 A2941 Pout·4Bout A3215, A3216, A3217, A3218, A3219, A3220 U:A1267 G:A2010, U:A2011, G:A2012, A:A2009
3i21 A1540 Pout·4Bout A1616, A1617, A1618, A1619, A1620, A1621 G:A645 C:A647, G:A645, G:A592, U:A593
3i22 A2979 Pout·4Bout A3399, A3400, A3401, A3402, A3403, A3404 G:A2454 C:A2496, G:A2454, G:A2455, A:A2453
3ivk C132 Pout·4Bout C177, C178, C179, C180, C181, C182 A:C-4 A:C-4, A:C14, G:C-3, U:C-2
3oar A1543 Pout·4Bout A1616, A1617, A1618, A1619, A1620, A1621 G:A645 G:A646, G:A645, G:A592, U:A593
3oas A2942 Pout·4Bout A3223, A3224, A3225, A3226, A3227, A3228 U:A1267 A:A2009, G:A2010, U:A2011, G:A2012
3oat A2984 Pout·4Bout A3409, A3410, A3411, A3412, A3413, A3414 A:A933 G:A841, U:A842, G:A843, A:A936
3ofa A1537 Pout·4Bout A1592, A1593, A1594, A1595, A1596, A1597 A:A415 G:A417, C:A418, G:A416, U:A426
3ofb A1543 Pout·4Bout A1617, A1618, A1619, A1620, A1621, A1622 G:A645 G:A646, G:A645, G:A592, U:A593
3ofc A2939 Pout·4Bout A3208, A3209, A3210, A3211, A3212, A3213 U:A1267 G:A2010, U:A2011, G:A2012, A:A2009
3ofd A2942 Pout·4Bout A3222, A3223, A3224, A3225, A3226, A3227 U:A1267 G:A2010, U:A2011, G:A2012, A:A2009
3ofo A1537 Pout·4Bout A1591, A1592, A1593, A1594, A1595, A1596 A:A415 G:A417, C:A418, G:A416, U:A426

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>