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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 2qba



2QBA (3.54Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with gentamicin. this file contains the 50s subunit of the first 70s ribosome, with gentamicin bound. the entire crystal structure contains two 70s ribosomes and is described in
List of all 105 Mg2+ binding sites in the PDB structure 2qba 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 6 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qba B3206 Ob C:B2499(O2) B3780, B3781, B3782, B3783, B3784 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qba B3188 Ob U:B746(O4) B3765, B3766, B3767, B3768, B3769 U:B744, C:B2610, C:B2611 G:B745
2qba B3321 2Nb G:B733(N7), A:B761(N7) B3873, B3874, B3875, B3876 A:B761, G:B760, C:B732, G:B733
2qba B3164 2Nb G:B1358(N7), G:B1371(N7) B3745, B3746, B3747, B3748 G:B1358, G:B1371, C:B1357
2qba B3270 Oph G:B536(OP2) B3832, B3833, B3834, B3835, B3836 G:B536, G:B537
2qba B3253 Oph U:B120(OP2) B3818, B3819, B3820, B3821, B3822 G:B122, G:B123, G:B121
2qba B3338 Oph A:B800(OP1) B3884, B3885, B3886, B3887, B3888 G:B799 C:B192, A:B800, A:B191
2qba B3175 Oph U:B419(OP1) B3754, B3755, B3756, B3757, B3758 G:B230
2qba B3394 Oph A:B1678(OP2) B3930, B3931, B3932, B3933, B3934 A:B1678, A:B1679
2qba B3418 Oph A:B2033(OP1) B3950, B3951, B3952, B3953 G:B2027, U:B2028
2qba B3376 Oph·Pout A:B1664(OP2) B3915, B3916, B3917, B3918, B3919 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
2qba B3353 Oph·Pout A:B1156(OP2) B3896, B3897, B3898, B3899, B3900 A:B1155 G:B1157, G:B997, C:B998
2qba B3276 Oph·Pout U:B567(OP1) B3837, B3838, B3839, B3840, B3841 G:B809 U:B810
2qba B3444 Oph·Pout A:B2270(OP2) B3971, B3972, B3973, B3974, B3975 A:B2267 A:B2268, A:B2266 G:B2271
2qba B3151 Oph·Pout A:B945(OP1) B3734, B3735, B3736, B3737, B3738 G:B831 A:B829 G:B831
2qba B3590 Oph·Pout A:B1676(OP2) B4086, B4087, B4088, B4089, B4090 C:B1675 A:B1677, A:B1676
2qba B3056 Oph·2Pout C:B1153(OP2) B3657, B3658, B3659, B3660 U:B999, C:B998 C:B1152
2qba B3044 Oph·2Pout A:B2518(OP2) B3647, B3648, B3649, B3650, B3651 U:B2519, A:B2541 A:B2541
2qba B3038 Oph·2Pout U:B1647(OP2) B3642, B3643, B3644, B3645, B3646 U:B1325, A:B1272 A:B1616 A:B1616
2qba B3032 Oph·2Pout G:B2588(OP2) B3639, B3640, B3641, C274, C275 A:B2589, A:B2587 G:B2588, A:B2589

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>