MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 3r8s:A2999, See in JSmolClick on the image to toggle views Site type: 2Pout·2Rout·2Bout Schematic drawing for 2Pout·2Rout·2Bout List of all 12 Mg2+ binding sites with the site type 2Pout·2Rout·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 1

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 3oas A2977 2Pout·2Rout·2Bout A3387, A3388, A3389, A3390, A3391, A3392 U:A2387, A:A2386 C:A2385, U:A2384 C:A2326, U:A2387 1vt2 A2978 2Pout·2Rout·2Bout A3390, A3391, A3392, A3393, A3394, A3395 U:A2387, A:A2386 C:A2385, U:A2384 C:A2326, U:A2387 3orb A2997 2Pout·2Rout·2Bout A3481, A3482, A3483, A3484, A3485, A3486 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613 3r8s A2999 2Pout·2Rout·2Bout A3544, A3545, A3546, A3547, A3548, A3549 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613 4pec A3026 2Pout·2Rout·2Bout A3320, A3321, A3322, A3323, A3324 A:A204, A:A800 G:A799, A:A203 A:A191, C:A192 4tp3 A3027 2Pout·2Rout·2Bout A3323, A3324, A3325, A3326, A3327 A:A204, A:A800 G:A799, A:A203 A:A190, A:A191 4gar A3094 2Pout·2Rout·2Bout A3642, A3643, A3644, A3645, A3646, A3647 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613 4peb A3095 2Pout·2Rout·2Bout A3646, A3647, A3648, A3649, A3650, A3651 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613 4tov A3097 2Pout·2Rout·2Bout A3644, A3645, A3646, A3647, A3648, A3649 C:A1617, G:A1619 C:A1617, A:A1608 G:A1619, G:A1613 3v2f A3328 2Pout·2Rout·2Bout A4350, A4351, A4352, A4353 C:A1617, A:A1609 C:A1617, A:A1608 G:A1613, G:A1619 4nvx A3350 2Pout·2Rout·2Bout A4285, A4286, A4287, A4288 A:A1609, C:A1617 A:A1608, C:A1617 G:A1613, G:A1619 4dha A3658 2Pout·2Rout·2Bout A4580, A4581, A4582, A4583, A4584, A4585 G:A570, A:A973 G:A972, U:A569 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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