MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qam:B3600, See in JSmolClick on the image to toggle views Site type: 3Pout·Rout·2Bout Schematic drawing for 3Pout·Rout·2Bout List of all 58 Mg2+ binding sites with the site type 3Pout·Rout·2Bout 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 1 of 3 | « Previous | Next » | 1 | 2 | 3

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1vs6 B3012 3Pout·Rout·2Bout B3502, B3503, B3504, B3505, B3506, B3507 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 1vs8 B3010 3Pout·Rout·2Bout B3495, B3496, B3497, B3498, B3499, B3500 A:B973, G:B570, U:B569 A:B972 A:B820, A:B821 1vt2 A3028 3Pout·Rout·2Bout A3597, A3598, A3599, A3600, A3601, A3602 G:A570, A:A973, U:A569 A:A972 A:A820, U:A568 2aw4 B3012 3Pout·Rout·2Bout B3498, B3499, B3500, B3501, B3502, B3503 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2awb B3011 3Pout·Rout·2Bout B3496, B3497, B3498, B3499, B3500, B3501 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2i2p A1583 3Pout·Rout·2Bout A1800, A1801, A1802, A1803, A1804 A:A607, A:A608, G:A293 G:A292 C:A631, A:A630 2i2t B3012 3Pout·Rout·2Bout B3506, B3507, B3508, B3509, B3510, B3511 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2i2v B3011 3Pout·Rout·2Bout B3503, B3504, B3505, B3506, B3507, B3508 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qam B3600 3Pout·Rout·2Bout B4098, B4099, B4100, B4101, B4102, B4103 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qao B3602 3Pout·Rout·2Bout B4105, B4106, B4107, B4108, B4109, B4110 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qba B3600 3Pout·Rout·2Bout B4094, B4095, B4096, B4097, B4098, B4099 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qbc B3602 3Pout·Rout·2Bout B4105, B4106, B4107, B4108, B4109, B4110 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qbe B3600 3Pout·Rout·2Bout B4094, B4095, B4096, B4097, B4098, B4099 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qbg B3012 3Pout·Rout·2Bout B3505, B3506, B3507, B3508, B3509, B3510 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qbk B3012 3Pout·Rout·2Bout B3498, B3499, B3500, B3501, B3502, B3503 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qov B3012 3Pout·Rout·2Bout B3500, B3501, B3502, B3503, B3504, B3505 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qox B3011 3Pout·Rout·2Bout B3500, B3501, B3502, B3503, B3504, B3505 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qoz B3012 3Pout·Rout·2Bout B3990, B3991, B3992, B3993, B3994, B3995 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2qp1 B3012 3Pout·Rout·2Bout B4008, B4009, B4010, B4011, B4012, B4013 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2z4l B3013 3Pout·Rout·2Bout B3498, B3499, B3500, B3501, B3502, B3503 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 2z4n B3013 3Pout·Rout·2Bout B3503, B3504, B3505, B3506, B3507, B3508 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 3df2 B3600 3Pout·Rout·2Bout B4601, B4602, B4603, B4604, B4605, B4606 G:B570, A:B973, U:B569 A:B972 A:B820, A:B821 3egz B501 3Pout·Rout·2Bout B301, B302, B303, B304, B305, B306 G:B10, G:B9, A:B22 A:B8 G:B10, U:B11 3i1p A3028 3Pout·Rout·2Bout A3591, A3592, A3593, A3594, A3595, A3596 G:A570, A:A973, U:A569 A:A972 A:A820, U:A568 3i1r A3032 3Pout·Rout·2Bout A3620, A3621, A3622, A3623, A3624, A3625 G:A570, A:A973, U:A569 A:A972 A:A820, A:A821

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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