`

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 3ccj



3CCJ (2.7Å) -- RIBOSOME : Structure of anisomycin resistant 50s ribosomal subunit: 23s rrna mutation c2534u
List of all 9 Mg2+ binding sites in the PDB structure 3ccj 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 1
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3ccj 08012 Oph·3Pout G:0456(OP2) 03618, 07317, 07677, 09431, C8559 A:0455, U:0457, G:0458
3ccj 08004 Oph·Ob A:0459(OP1) G:0456(O6) 03778, 07676, 09056, 09791 A:0455, A:0460, C:0478, A:0477 A:0455
3ccj 08021 Oph·Ob A:01448(OP2) U:01677(O4) 03695, 03706, 07710, S8998 C:01675, G:01676
3ccj 08023 cis-2Oph U:01748(OP1), U:01749(OP2) 03635, 07678, 07679, 07689 G:02585
3ccj 08007 cis-2Oph G:02611(OP1), A:02612(OP1) 03735, 07354, 07686, 07687 G:02094, G:02093 U:02610
3ccj 08011 trans-2Oph A:0844(OP1), A:01689(OP1) 03617, 07701, 09012, 09032 G:01688 A:0844, A:01689, C:01690, A:0882, C:01692
3ccj 08002 cis-2Oph·Ob A:02483(OP1), U:02534(OP1) G:0627(O6) 04311, 07669, 07670 U:02535 U:0625 U:0626
3ccj 08001 fac-3Oph A:02483(OP2), C:02533(OP2), U:02534(OP2) 03612, 07691, 09188 U:02484 A:02532, G:02482 G:02482
3ccj 08084 mer-3Oph C:01103(OP1), A:01106(OP2), A:01107(OP2) 07788, 07789, 07790 C:01104 A:01107

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>