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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dhc A3458 Pout·3Bout A4055, A4056, A4057, A4058, A4059, A4060 A:A103 G:A79, G:A80, G:A81
4dhc A3631 Pout·3Bout A4504, A4505, A4506, A4507, A4508, A4509 U:A1267 G:A2010, G:A2009, U:A2011
4dhc A3581 Pout·4Bout A4392, A4393, A4394, A4395, A4396 G:A495 A:A482, G:A496, G:A494, G:A495
4dhc B216 2Pout B335, B336, B337, B338, B339, B340 U:B55, A:B25
4dhc A3379 2Pout·Bout A3800, A3801, A3802, A3803, A3804 U:A1313, C:A1333 G:A1334
4dhc A3424 2Pout·Bout A3942, A3943, A3944, P301 G:A831, G:A944 A:A2448
4dhc A3598 2Pout·Bout A4436, A4437, A4438, A4439, A4440 A:A1809, G:A1807 G:A1807
4dhc A3662 2Pout·Rout·Bout A4613, A4614, A4615, A4616, A4617, 1202 G:A248, U:A387 G:A386 G:A386
4dhc A3634 2Pout·2Bout A4517, A4518, A4519, A4520, A4521, A4652 C:A1398, U:A1397 G:A1400, G:A1385
4dhc A3674 2Pout·2Bout A4661, A4662, A4663, A4664, A4665, A4666 A:A1579, A:A1580 G:A1416, G:A1581
4dhc A3431 2Pout·3Bout A3962, A3963, A3964, A3965, A3966 G:A686, C:A687 U:A688, A:A689, G:A771
4dhc A3418 2Pout·4Bout A3917, A3918, A3919, A3920, A3921 C:A2452, A:A2453 A:A2453, G:A2454, G:A2455, A:A2497
4dhc A3579 3Pout A4385, A4386, A4387, A4388, A4389 C:A1370, U:A773, G:A1356
4dhc A3630 3Pout·Bout A4499, A4500, A4501, A4502, A4503 G:A1987, C:A2551, A:A1669 G:A1954
4dhc A3447 3Pout·Bout A4015, A4016, A4017, A4018, A4019 U:A475, A:A478, G:A476 G:A476
4dhc A3685 3Pout·Bout A4705, A4706, A4707, A4708, A4709, A4710 A:A2657, C:A2658, G:A2659 G:A2659
4dhc A3486 3Pout·2Rout·Bout A4137, A4138, A4139, A4140 C:A1617, G:A1619, A:A1609 C:A1617, A:A1608 G:A1619
4dhc A3445 3Pout·5Bout A4007, A4008, A4009, A4010, A4011 U:A29, A:A28, A:A447 U:A29, G:A30, C:A31, G:A474, G:A473
4dhc A3632 4Pout·2Bout A4510, A4511, A4512, A4513, A4514, A4515 G:A2578, A:A2614, A:A2051, U:A2613 A:A2614, A:A2051
4dhc A3411 Mg2+ bound by non-RNA C:A1658(OP1) A3893, A3894, E403, E404 HIS:E135(NE2) U:A1659, G:A744 G:A743

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>