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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"
Page 1 of 4 | « Previous | | 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 B216 2Pout B335, B336, B337, B338, B339, B340 U:B55, A:B25
4dhc A3375 Ob·Nb G:A2592(N7), U:A2593(O4) A3787, A3788, A3789, A3790 C:A2591, G:A2592
4dhc A3377 Oph·3Pout G:A1828(OP2) A3793, A3794, A3795, A3796 C:A1827, A:A1972, C:A1788 G:A1828
4dhc A3379 2Pout·Bout A3800, A3801, A3802, A3803, A3804 U:A1313, C:A1333 G:A1334
4dhc A3384 2Nb G:A733(N7), A:A761(N7) A3815, A3816, A3817, A3818 G:A760, A:A761, G:A733 C:A732
4dhc A3385 cis-2Oph A:A1269(OP2), A:A2005(OP1) A3819, A3820, A3821, A3822 A:A1268, C:A2006 A:A1269
4dhc A3386 Oph·Pout G:A1776(OP2) A3823, A3824, A3825, A3826 A:A1981 G:A1776
4dhc A3387 Oph·2Pout C:A1774(OP1) A3827, A3828, A3829, A3830, A3831 A:A1786, U:A1775 G:A1772 G:A1772, G:A1776
4dhc A3392 Oph·4Pout G:A741(OP1) A3837, A3838, A3839, A3840, A3841 C:A1983, A:A1784, G:A2608, A:A1785
4dhc A3396 cis-2Oph C:A192(OP1), U:A2243(OP1) A3847, A3848, A3849, A3850 A:A199, U:A193
4dhc A3397 6Bout A3851, A3852, A3853, A3854, A3855, A3856 G:A2238, G:A2242, A:A2241, U:A2074, U:A2243, U:A2075
4dhc A3402 Oph·3Pout U:A963(OP1) A3867, A3868, A3869, A3870, A3871 C:A2498, A:A2497, G:A947
4dhc A3406 Oph·2Pout G:A1647(OP2) A3875, A3876, A3877, A3878, A3879 A:A1272, G:A1325 A:A1616, C:A1646 A:A1616
4dhc A3409 cis-2Oph G:A2056(OP2), A:A2057(OP2) A3885, A3886, A3887 U:A2504 A:A2058, A:A2057
4dhc A3410 Nb G:A2032(N7) A3888, A3889, A3890, A3891, A3892 G:A2032 G:A2454 C:A2055, C:A2499, A:A2572, U:A2500
4dhc A3411 Mg2+ bound by non-RNA C:A1658(OP1) A3893, A3894, E403, E404 HIS:E135(NE2) U:A1659, G:A744 G:A743
4dhc A3412 Nb G:A2002(N7) A3895, A3896, A3897, A3898, A3899 G:A2002 G:A2004
4dhc A3416 Oph·Pout C:A574(OP1) A3908, A3909, A3910, A3911, A3912 C:A2055 G:A2035
4dhc A3417 Pout·Bout A3913, A3914, A3915, A3916 C:A574 G:A577
4dhc A3418 2Pout·4Bout A3917, A3918, A3919, A3920, A3921 C:A2452, A:A2453 A:A2453, G:A2454, G:A2455, A:A2497

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>