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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 A3409 cis-2Oph G:A2056(OP2), A:A2057(OP2) A3885, A3886, A3887 U:A2504 A:A2058, A:A2057
4dhc A3470 cis-2Oph G:A370(OP2), A:A422(OP2) A4092, A4093, A4094 A:A423 C:A366 G:A370, A:A423
4dhc A3474 cis-2Oph U:A787(OP1), C:A790(OP2) A4103, A4104, A4105, A4106 A:A789, C:A791
4dhc A3506 cis-2Oph A:A1664(OP1), A:A1665(OP2) A4196, A4197, A4198, A4199
4dhc A3651 cis-2Oph A:A526(OP1), C:A527(OP1) A4569, A4570, A4571, A4572 A:A528
4dhc A3658 cis-2Oph A:A2758(OP2), G:A2759(OP2) A4597, A4598, A4599, A4600 U:A2756
4dhc A3503 trans-2Oph U:A2682(OP2), A:A2721(OP1) A4187, A4188, A4189, A4190 C:A2683, G:A2722
4dhc A3434 trans-2Oph C:A1298(OP2), U:A1639(OP2) A3974, A3975, A3976, A3977 C:A1297, C:A1638 C:A2710 G:A1299
4dhc A3436 fac-3Oph A:A2711(OP1), A:A2712(OP2), G:A2714(OP2) A3982, A3983, A3984 A:A2713, C:A2710
4dhc A3459 Bout A4061, A4062, A4063, A4064 G:A83
4dhc A3673 Bout A4655, A4656, A4657, A4658, A4659, A4660 G:A1388
4dhc A3666 2Bout A4629, A4630, A4631, A4632, A4633, A4634 G:A599, G:A598
4dhc A3510 3Bout A4208, A4209, A4210, A4211, A4212 G:A1309, G:A1310, G:A1311
4dhc A3419 5Bout A3922, A3923, A3924, A3925, A3926 G:A2455, C:A2456, G:A2495, U:A2457, G:A2494
4dhc A3397 6Bout A3851, A3852, A3853, A3854, A3855, A3856 G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075
4dhc A3417 Pout·Bout A3913, A3914, A3915, A3916 C:A574 G:A577
4dhc A3518 Pout·2Bout A4230, A4231, A4232, A4233, A4234 A:A340 G:A341, G:A342
4dhc A3657 Pout·2Bout A4593, A4594, A4595, A4596 C:A1892 G:A1845, G:A1846
4dhc A3583 Pout·2Bout A4400, A4401, A4402, R303, R304 G:A2004 G:A1650, G:A1651
4dhc A3639 Pout·3Bout A4532, A4533, A4534, A4535, A4536 G:A2845 G:A2848, G:A2845, U:A2847

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>