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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 2qbe



2QBE (3.3Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with ribosome recycling factor (rrf). this file contains the 50s subunit of the first 70s ribosome, with rrf bound. the entire crystal structure contains two 70s ribosomes and is
List of all 109 Mg2+ binding sites in the PDB structure 2qbe 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
2qbe B3418 Ob U:B2028(O4) B3950, B3951, B3952, B3953 A:B2033 G:B2029, G:B2027
2qbe B3240 Ob G:B2304(O6) B3806, B3807, B3808, B3809, B3810 G:B2303, U:B2302
2qbe B3206 Ob C:B2499(O2) B3779, B3780, B3781, B3782, B3783 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454
2qbe B3188 Ob U:B746(O4) B3765, B3766, B3767, B3768, D210 C:B2610, C:B2611, U:B744 G:B745
2qbe B3164 Nb G:B1371(N7) B3746, B3747, B3748, B3749 G:B1358, C:B1357, C:B1370 G:B1358
2qbe B3321 2Nb G:B733(N7), A:B761(N7) B3873, B3874, B3875, B3876 A:B761, G:B760, C:B732, G:B733
2qbe B3253 Oph U:B120(OP2) B3817, B3818, B3819, B3820, B3821 G:B122, G:B123
2qbe B3175 Oph U:B419(OP1) B3754, B3755, B3756, B3757, B3758 G:B230
2qbe B3338 Oph A:B800(OP1) B3884, B3885, B3886, B3887, B3888 G:B799 A:B191, C:B192, A:B800
2qbe B3353 Oph A:B1156(OP2) B3896, B3897, B3898, B3899, B3900 A:B1155 G:B1157, C:B998
2qbe B3376 Oph·Pout A:B1664(OP2) B3915, B3916, B3917, B3918, B3919 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
2qbe B3270 Oph·Pout G:B536(OP2) B3831, B3832, B3833, B3834, B3835 G:B535 G:B536, G:B537
2qbe B3151 Oph·Pout A:B945(OP1) B3735, B3736, B3737, B3738, B3739 G:B831 G:B831, U:B832
2qbe B3394 Oph·Pout A:B1678(OP2) B3930, B3931, B3932, B3933, B3934 A:B1679 A:B1678, A:B1679
2qbe B3412 Oph·Pout C:B2025(OP2) B3945, B3946, B3947, B3948, B3949 G:B2024
2qbe B3038 Oph·Pout U:B1647(OP2) B3643, B3644, B3645, B3646, B3647 U:B1325 C:B1646, A:B1616
2qbe B3124 Oph·2Pout G:B1187(OP2) B3713, B3714, B3715, B3716, B3717 C:B816, C:B817 G:B1185 G:B1187, G:B818
2qbe B3050 Oph·2Pout G:B297(OP2) B3653, B3654, B3655, B3656, B3657 U:B296, G:B298 G:B298, G:B297
2qbe B3032 Oph·2Pout G:B2588(OP2) B3639, B3640, B3641, B3642, C273 A:B2587, A:B2589 G:B2588, A:B2589
2qbe B3001 Oph·2Pout A:B802(OP1) B3613, B3614, B3615, B3616, B3617 G:B674, A:B675 U:B803, A:B804

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>