MgRNA: Classification of Mg2+ binding sites in RNA crystal structures Back to Classification Home Download this subset in: CSV, XML, JSON List of Mg2+ binding sites in structure 4dhc 4DHC (3.2Å) -- RIBOSOME : Crystal structure of yaej bound to the 70s ribosome List of all 80 Mg2+ binding sites in the PDB structure 4dhc in the benchmark dataset (switch to full dataset) Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID" Page 1 of 4 | « Previous | Next » | 1 | 2 | 3 | 4

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4dhc A3685 3Pout·Bout A4705, A4706, A4707, A4708, A4709, A4710 A:A2657, C:A2658, G:A2659 G:A2659 4dhc A3674 2Pout·2Bout A4661, A4662, A4663, A4664, A4665, A4666 A:A1579, A:A1580 G:A1416, G:A1581 4dhc A3673 Bout A4655, A4656, A4657, A4658, A4659, A4660 G:A1388 4dhc A3671 Ob G:A1271(O6) A4647, A4648, A4649, A4650 G:A1324 G:A1325 4dhc A3670 Oph·Pout A:A981(OP1) A4643, A4644, A4645, A4646 C:A982 G:A978, G:A979 4dhc A3666 2Bout A4629, A4630, A4631, A4632, A4633, A4634 G:A599, G:A598 4dhc A3662 2Pout·Rout·Bout A4613, A4614, A4615, A4616, A4617, 1202 G:A248, U:A387 G:A386 G:A386 4dhc A3659 Oph·Pout A:A2322(OP2) A4601, A4602, A4603, A4604 G:A2321 G:A2323, G:A2331, U:A2332, A:A2322 4dhc A3658 cis-2Oph A:A2758(OP2), G:A2759(OP2) A4597, A4598, A4599, A4600 U:A2756 4dhc A3657 Pout·2Bout A4593, A4594, A4595, A4596 C:A1892 G:A1845, G:A1846 4dhc A3652 Ob U:A2028(O4) A4573, A4574, A4575, A4576, A4577 A:A2033 G:A2029, G:A2027 4dhc A3651 cis-2Oph A:A526(OP1), C:A527(OP1) A4569, A4570, A4571, A4572 A:A528 4dhc A3639 Pout·3Bout A4532, A4533, A4534, A4535, A4536 G:A2845 G:A2848, G:A2845, U:A2847 4dhc A3634 2Pout·2Bout A4517, A4518, A4519, A4520, A4521, A4652 C:A1398, U:A1397 G:A1400, G:A1385 4dhc A3632 4Pout·2Bout A4510, A4511, A4512, A4513, A4514, A4515 G:A2578, A:A2614, A:A2051, U:A2613 A:A2614, A:A2051 4dhc A3631 Pout·3Bout A4504, A4505, A4506, A4507, A4508, A4509 U:A1267 G:A2010, G:A2009, U:A2011 4dhc A3630 3Pout·Bout A4499, A4500, A4501, A4502, A4503 G:A1987, C:A2551, A:A1669 G:A1954 4dhc A3625 Nb G:A2375(N7) A4487, A4488, A4489, A4490 A:A2377 4dhc A3598 2Pout·Bout A4436, A4437, A4438, A4439, A4440 A:A1809, G:A1807 G:A1807 4dhc A3583 Pout·2Bout A4400, A4401, A4402, R303, R304 G:A2004 G:A1650, G:A1651

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].

---

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
For any help please contact <dust@iwonka.med.virginia.edu>