MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3df1:A2096, See in JSmolClick on the image to toggle views Site type: 4Pout Schematic drawing for 4Pout List of all 174 Mg2+ binding sites with the site type 4Pout 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" Page 3 of 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3df3 A2042 4Pout A4043, A4044, A4045, A4046, A4047, A4048 U:A333, G:A350, C:A334, A:A349 3df3 A2077 4Pout A4079, A4080, A4082, A4083, N4078, N4081 C:A1203, A:A1204, G:A1048, U:A1049 3df4 B3344 4Pout B4345, B4346, B4347, B4348, B4349, B4350 U:B1915, A:B1912, A:B1913, C:B1914 3hhn C151 4Pout C150, C152, C153, C154, C155, C156 A:C95, A:C96, U:C94, G:C118 3hhn E191 4Pout E190, E192, E193, E194, E195, E196 A:E102, C:E101, C:E83, U:E84 3i1m N1550 4Pout A1655, A1656, A1657, A1658, A1659, N132 U:A1049, C:A1203, A:A1204, G:A1048 3i1o A1547 4Pout A1652, A1653, A1654, A1655, A1656, N130 A:A1204, G:A1048, U:A1049, C:A1203 3i1p A3023 4Pout A3573, A3574, A3575, A3576 C:A787, C:A791, C:A786, U:A790 3i1r A3039 4Pout A3650, A3651, A3652, A3653, A3654, N797 C:A2874, G:A2819, G:A2838, A:A2820 3i1t A2998 4Pout A3485, A3486, A3487, A3488, A3489, A3490 U:A1636, G:A1300, A:A1635, G:A1299 3i1t A3023 4Pout A3576, A3577, A3578, A3579 C:A787, C:A791, C:A786, U:A790 3i1z A1550 4Pout A1655, A1656, A1657, A1658, N128, N132 U:A1049, C:A1203, A:A1204, G:A1048 3i20 A3039 4Pout A3650, A3651, A3652, A3653, N797, N798 G:A2819, G:A2838, C:A2874, A:A2820 3l0u A77 4Pout A80, A81, A82, A83, A84, A85 U:A8, A:A9, C:A11, U:A12 3oaq A1550 4Pout A1655, A1656, A1657, A1658, A1659, N106 U:A1049, C:A1203, A:A1204, G:A1048 3oar A1550 4Pout A1651, A1652, A1653, A1654, A1655, N105 A:A1204, G:A1048, U:A1049, C:A1203 3oas A2997 4Pout A3481, A3482, A3483, A3484, A3485, A3486 U:A1636, G:A1300, A:A1637, A:A1635 3ofa N101 4Pout A1654, A1655, A1656, A1657, A1658, N106 U:A1049, C:A1203, A:A1204, G:A1048 3ofb A1550 4Pout A1651, A1652, A1653, A1654, A1655, N105 A:A1204, G:A1048, U:A1049, C:A1203 3ofd A2997 4Pout A3480, A3481, A3482, A3483, A3484, A3485 U:A1636, G:A1300, G:A1299, A:A1637 3ofd A3022 4Pout A3576, A3577, A3578, A3579 U:A790, C:A787, C:A791, C:A786 3ofo N102 4Pout A1653, A1654, A1655, N103, N106, N109 U:A1049, C:A1203, G:A1048, A:A1204 3ofq A2944 4Pout A3231, A3232, A3233, A3234 A:A1268, C:A2006, G:A2048, G:A2049 3ofq A2998 4Pout A3482, A3483, A3484, A3485, A3486, A3487 U:A1636, G:A1300, A:A1637, G:A1299 3ofx N101 4Pout A1654, A1655, A1656, A1657, A1658, N106 U:A1049, C:A1203, A:A1204, G:A1048

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].

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