MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 2qbb:A2049, See in JSmolClick on the image to toggle views Site type: 2Pout·Bout Schematic drawing for 2Pout·Bout List of all 169 Mg2+ binding sites with the site type 2Pout·Bout 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 5 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 3ofq A3029 2Pout·Bout A3600, A3601, A3602, A3603 U:A1188, A:A1189 G:A1190 3df4 B3074 2Pout·Bout B4075, B4076, B4077, B4078, B4079, B4080 A:B2033, U:B2026 U:B2028 4gau A3087 2Pout·Bout A3616, A3617, A3618, A3619 A:A1359, G:A1360 G:A1361 4nw0 A3090 2Pout·Bout A4038, A4039, A4040, A4041 U:A804, G:A803 G:A771 4gar A3090 2Pout·Bout A3620, A3621, A3622, A3623, A3624, A3625 U:A1409, G:A1408 G:A1410 4gar A3114 2Pout·Bout A3719, A3720, A3721, A3722, A3723, A3724 U:A686, C:A687 G:A770 4tp9 A3120 2Pout·Bout A3733, A3734, A3735, A3736, A3737, A3738 A:A1000, A:A1001 G:A1002 4tpf A3125 2Pout·Bout A3753, A3754, A3755, A3756 C:A787, U:A790 A:A1780 4gau A3132 2Pout·Bout A3808, A3809, A3810, A3811, A3812, A3813 G:A2004, A:A1650 G:A1651 4pec A3133 2Pout·Bout A3789, A3790, A3791, A3792, A3793, 4201 A:A2741, A:A2740 G:A2742 4tp3 A3133 2Pout·Bout A3787, A3788, A3789, A3790, A3791, 4201 A:A2741, A:A2740 G:A2742 4tpb A3133 2Pout·Bout A3789, A3790, A3791, A3792, A3793, 4201 A:A2741, A:A2740 G:A2742 4gar A3133 2Pout·Bout A3803, A3804, A3805, A3806, N201, N202 G:A2004, A:A1650 A:A1650 4peb A3133 2Pout·Bout A3796, A3797, A3798, A3799, 4201, 4202 A:A2741, A:A2740 G:A2742 4tox A3134 2Pout·Bout A3790, A3791, A3792, A3793, A3794, 4201 A:A2741, A:A2740 G:A2742 4tp7 A3134 2Pout·Bout A3786, A3787, A3788, A3789, A3790, 4201 A:A2740, A:A2741 G:A2742 4tov A3135 2Pout·Bout A3796, A3797, A3798, A3799, A3800, 4201 A:A2740, A:A2741 G:A2742 3df4 B3262 2Pout·Bout B4263, B4264, B4265, B4266, B4267 G:B297, G:B338 G:B298 3v25 A3321 2Pout·Bout A3826, A3827, A3828, A3829 G:A1904, G:A2597 G:A2595 2qao B3337 2Pout·Bout B3895, B3896, B3897, B3898, B3899, B3900 G:B1653, G:B2819 A:B2821 3v23 A3346 2Pout·Bout A4058, A4059, A4060, A4061, A4062, A4063 G:A1283, U:A1282 G:A1283 3v27 A3347 2Pout·Bout A4013, A4014, A4015, A4016, A4017 C:A1611, C:A1615 G:A1613 3v27 A3361 2Pout·Bout A4075, A4076, A4077, A4078, A4079 G:A2482, C:A2483 G:A2484 3v23 A3361 2Pout·Bout A4114, A4115, A4116, A4117, A4118 A:A340, G:A341 G:A341 4dhc A3379 2Pout·Bout A3800, A3801, A3802, A3803, A3804 U:A1313, C:A1333 G:A1334

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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