MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON Representative site 1vs5:A1545, See in JSmolClick on the image to toggle views Site type: Pout·Bout Schematic drawing for Pout·Bout List of all 223 Mg2+ binding sites with the site type Pout·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 8 of 9 | « 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 4gas A1633 Pout·Bout A1853, A1854, A1855, A1856, A1857, A1858 G:A1079 G:A1077 4gau A3112 Pout·Bout A3721, A3722, A3723, A3724, A3725, A3726 U:A686 G:A770 4gau A3067 Pout·Bout A3519, A3520, A3521, A3522, A3523 C:A2310 G:A2304 4gd1 A1619 Pout·Bout A1789, A1790, A1791, A1792, A1793, A1794 G:A1079 G:A1077 4ji1 A1748 Pout·Bout A2177, A2178, A2179, A2180, A2181, A2182 G:A803 G:A771 4ji1 A1809 Pout·Bout A2545, A2546, A2547, A2548, E307, E308 G:A1079 G:A1077 4ji7 A2002 Pout·Bout A3517, A3518, A3519, A3520, A3521, A3522 G:A1079 G:A1077 4ji8 A1893 Pout·Bout A2870, A2871, A2872, A2873, A2874, A2875 G:A129 C:A131 4ji8 A1638 Pout·Bout A2073, A2074, A2075, A2076 C:A754 G:A587 4nvy A3165 Pout·Bout A4048, A4049, A4050, A4051 G:A803 G:A771 4nvz A3346 Pout·Bout A4192, A4193, A4194, A4195, A4196 C:A597 G:A2057 4nxm A1702 Pout·Bout A2069, A2070, A2071, N201 A:A1360 C:A980 4peb A3069 Pout·Bout A3522, A3523, A3524, A3525, A3526 C:A2310 G:A2304 4pec A3091 Pout·Bout A3615, A3616, A3617, A3618, A3619, A3620 U:A1409 G:A1410 4pec A3115 Pout·Bout A3713, A3714, A3715, A3716, A3717, 2102 U:A686 G:A770 4qcn A3606 Pout·Bout A4999, A5000, A5001, A5002 A:A2000 A:A1737 4qcn A3484 Pout·Bout A4631, A4632, A4633, A4634, A4635, A4636 G:A2869 G:A2867 4qcn A3547 Pout·Bout A4836, A4837, A4838, A4839, A4840 A:A2389 G:A2387 4qcp A3549 Pout·Bout A4753, A4754, A4755, A4756, A4757 A:A1419 U:A1576 4qcp A3514 Pout·Bout A4684, A4685, A4686, A4687 G:A312 G:A301 4qcq A3110 Pout·Bout A4006, A4007, A4008, A4009 U:A871 G:A853 4qcr A3508 Pout·Bout A4650, A4651, A4652, A4653, A4654, A4655 G:A2869 G:A2867 4qcr A3629 Pout·Bout A5021, A5022, A5023, A5024 A:A2000 A:A1737 4qct A3530 Pout·Bout A4706, A4707, A4708, A4709 G:A312 A:A314 4qct A3568 Pout·Bout A4784, A4785, A4786, A4787, A4788 A:A1419 U:A1576

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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