`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 3cc7



3CC7 (2.7Å) -- RIBOSOME : Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation c2487u
List of all 29 Mg2+ binding sites in the PDB structure 3cc7 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 2 | « Previous | | 1 | 2
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3cc7 08065 Oph·Pout A:01742(OP2) 03670, 07896, 09266, 09397, 09782 G:02033 G:01744, G:01745, A:01742, G:01743, G:02033
3cc7 08013 Oph·2Pout A:02011(OP2) 04198, 07296, 07834, 07835, 07836 A:01941, G:01891 U:01890 G:01891, C:01892
3cc7 08014 Oph·2Pout C:01830(OP1) 07818, 07837, 09134, 09137, 09211 U:01831, A:01842 G:01828 G:01828, A:01845, G:01832
3cc7 08026 Oph·3Pout G:0956(OP2) 03704, 07859, 07860, 07861, 09390 A:01006, A:0955, A:0957 A:0957, G:0956
3cc7 08025 Oph·3Pout U:02115(OP1) 03028, 03826, 04237, A9012, A9085 G:02272, C:02273, U:02116
3cc7 08012 Oph·3Pout G:0456(OP2) 03656, 03985, 07454, 07815, 09438 A:0455, G:0458, U:0457
3cc7 08015 Oph·3Pout G:02304(OP2) 03002, 03673, 03674, 07821, 07822 A:02301, A:02305, A:02303 U:02306, A:02305, G:02304
3cc7 08010 Oph·Or G:02537(OP2) G:02102(O5') 03693, 04211, 07805, 09040 G:02481 C:02536, A:02101 G:02480, G:02481, A:02101
3cc7 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03820, 07814, 09055, 09808 A:0455, A:0460, A:0477 A:0455
3cc7 08021 Oph·Ob A:01448(OP2) U:01677(O4) 03712, 03734, 03746, S8994 G:01676
3cc7 08084 cis-2Oph A:01106(OP2), A:01107(OP2) 07925, 07926, 07927, 07928 C:01103, C:01104 A:01107
3cc7 08007 cis-2Oph G:02611(OP1), A:02612(OP1) 03774, 07489, 07824, 07825 G:02094, G:02093
3cc7 08041 cis-2Oph C:0162(OP1), U:02276(OP1) 07820, 07870, 07871, 09456 U:0163, A:0169
3cc7 08048 cis-2Oph A:01369(OP2), U:02650(OP1) 07877, 07878, 07879, 09853 A:02649 U:01371
3cc7 08058 cis-2Oph A:01286(OP1), A:01287(OP1) 07882, 07883, W7873, W7874 A:01287, U:01288
3cc7 08022 cis-2Oph U:01503(OP1), C:01679(OP1) 07848, 07849, 07850, 07851 A:01504
3cc7 08023 cis-2Oph U:01748(OP1), U:01749(OP2) 03675, 07816, 07817, 07827 G:02585, G:02584
3cc7 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03655, 07838, 09012, 09030 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3cc7 08002 cis-2Oph·Ob A:02483(OP1), C:02534(OP1) G:0627(O6) 04373, 07807, 07808 C:02533 U:0625 U:0626
3cc7 08019 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07844, 07845, 07846 C:02542

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>