MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qou:A1560, See in JSmolClick on the image to toggle views Site type: Nb Schematic drawing for Nb List of all 284 Mg2+ binding sites with the site type Nb 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 4 of 12 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 2qoy A1560 Nb G:A362(N7) A1983, A1984, A1985, A1986, L1690 G:A362 2qp0 A1549 Nb G:A362(N7) A1914, A1915, A1916, A1917, A1918 G:A361, G:A362 G:A361 2qp0 A1567 Nb G:A324(N7) A2008, A2009, A2010, A2011, A2012 U:A323, G:A326 2z4k A1561 Nb G:A362(N7) A1684, A1685, A1686, A1687, A1688 A:A364, G:A362 2z4m A1550 Nb G:A362(N7) A1634, A1635, A1636, A1637, L124 G:A361, G:A362 G:A361 2z4m A1584 Nb G:A324(N7) A1805, A1806, A1807, A1808, A1809 U:A323, G:A324, G:A326 3cc2 08110 Nb G:02609(N7) 03250, 03274, 05175, 05321, 09844 G:02609 G:02606, U:02610 3cpw 08088 Nb A:0187(N1) 03037, 04161, 04200, 09621, 09807 C:0155, U:0207 G:0206 C:0188, C:0438 3cxc 08112 Nb A:0187(N1) 03120, 03319, 03549, 04675, 04718 C:0155, U:0207 G:0206 C:0188, C:0438 3d2g A81 Nb A:A29(N7) A99, A100, A101, A132, A158 A:A44 G:A28 G:A30 3df1 A2103 Nb G:A362(N7) A4104, A4105, A4106, A4107, A4108 G:A362, A:A364 3df3 A2036 Nb G:A362(N7) A4037, A4038, A4039, A4041, L4040 G:A361 G:A361 3df3 A2250 Nb G:A324(N7) A4251, A4252, A4253, A4254, A4255 G:A324, U:A323 3i1m A1565 Nb G:A324(N7) A1724, A1725, A1726, A1727, A1728 U:A323, G:A326, G:A324 3i1m A1536 Nb G:A362(N7) A1589, A1590, A1591, A1592, L124 A:A364, G:A362 3i1o A1562 Nb G:A324(N7) A1725, A1726, A1727, A1728, A1729 U:A323, G:A324 3i1q A1536 Nb G:A362(N7) A1587, A1588, A1589, L124, L125 G:A361 3i1q A1565 Nb G:A324(N7) A1720, A1721, A1722, A1723, A1724 U:A323, G:A326, G:A324 3i1s A1562 Nb G:A324(N7) A1726, A1727, A1728, A1729, T204 U:A323, G:A324 3i1t A2933 Nb A:A1253(N7) A3181, A3182, A3183, A3184 U:A810, U:A811 3i1t A2977 Nb G:A2304(N7) A3384, A3385, A3386, A3387, A3388 G:A2308 G:A2303 3i1z A1536 Nb G:A362(N7) A1589, A1590, A1591, A1592, L124 G:A362 3i1z A1565 Nb G:A324(N7) A1722, A1723, A1724, A1725, A1726 U:A323, G:A324 3i21 A3 Nb G:A362(N7) A1583, A1584, A1585, A1586, A1587 G:A361 3i22 A2932 Nb A:A1253(N7) A3180, A3181, A3182, A3183 U:A810, U:A811

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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