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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 A3670 Oph·Pout A:A981(OP1) A4643, A4644, A4645, A4646 C:A982 G:A978, G:A979
4dhc A3387 Oph·2Pout C:A1774(OP1) A3827, A3828, A3829, A3830, A3831 A:A1786, U:A1775 G:A1772 G:A1772, G:A1776
4dhc A3406 Oph·2Pout G:A1647(OP2) A3875, A3876, A3877, A3878, A3879 A:A1272, G:A1325 A:A1616, C:A1646 A:A1616
4dhc A3423 Oph·2Pout A:A567(OP1) A3937, A3938, A3939, A3940, A3941 G:A808, G:A809 G:A809, U:A810
4dhc A3430 Oph·2Pout G:A770(OP2) A3959, A3960, A3961, 7201 G:A686, G:A771 G:A770
4dhc A3433 Oph·2Pout U:A1639(OP1) A3970, A3971, A3972, A3973 G:A1296, C:A1297
4dhc A3448 Oph·2Pout G:A446(OP2) A4020, A4021, A4022, A4023, A4024 C:A1200, C:A445 U:A1199 G:A446
4dhc A3453 Oph·2Pout A:A802(OP1) A4036, A4037, A4038, A4039, A4040 G:A674, A:A675 U:A803, G:A674
4dhc A3467 Oph·2Pout U:A2406(OP1) A4082, A4083, A4084, A4085 U:A2408, G:A2409 G:A2405 G:A2410, U:A2408, G:A2409
4dhc A3488 Oph·2Pout G:A739(OP1) A4144, A4145, A4146, A4147, A4148 U:A1779, U:A1778 A:A1784
4dhc A3532 Oph·2Pout A:A1495(OP2) A4262, A4263, A4264, A4265 A:A1496, A:A1494 A:A1496, A:A1495
4dhc A3377 Oph·3Pout G:A1828(OP2) A3793, A3794, A3795, A3796 C:A1827, A:A1972, C:A1788 G:A1828
4dhc A3402 Oph·3Pout U:A963(OP1) A3867, A3868, A3869, A3870, A3871 C:A2498, A:A2497, G:A947
4dhc A3452 Oph·3Pout A:A2062(OP1) A4032, A4033, A4034, A4035 C:A2443, G:A2061, G:A2444 G:A2444
4dhc A3574 Oph·3Pout U:A2016(OP1) A4369, A4370, A4371, A4372, A4373 A:A2059, U:A2017, A:A2058 U:A1255 U:A1255
4dhc A3392 Oph·4Pout G:A741(OP1) A3837, A3838, A3839, A3840, A3841 C:A1983, A:A1784, G:A2608, A:A1785
4dhc A3429 Oph·4Pout C:A1636(OP2) A3955, A3956, A3957, A3958 G:A1299, U:A1300, A:A1637, A:A1301
4dhc A3435 cis-2Oph A:A2711(OP1), A:A2712(OP1) A3978, A3979, A3980, A3981 C:A1297
4dhc A3385 cis-2Oph A:A1269(OP2), A:A2005(OP1) A3819, A3820, A3821, A3822 A:A1268, C:A2006 A:A1269
4dhc A3396 cis-2Oph C:A192(OP1), U:A2243(OP1) A3847, A3848, A3849, A3850 A:A199, U:A193

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>