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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 4kix



4KIX (2.9Å) -- RIBOSOME : Control of ribosomal subunit rotation by elongation factor g
List of all 11 Mg2+ binding sites in the PDB structure 4kix 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4kix A3126 Oph·Or C:A510(OP1), U:A511(OP2) C:A509(O3') A3758, A3759, A3760 G:A512
4kix A3009 Oph·Ob A:A453(OP1) G:A450(O6) A3243, A3244
4kix A3073 cis-2Oph A:A2711(OP2), G:A2714(OP2) A3541, A3542, A3543 C:A2710
4kix A3023 trans-2Oph A:A751(OP1), A:A1614(OP1) A3307, A3308, A3309, A3310 G:A1613 A:A789, A:A751, A:A1614, C:A1617
4kix A3123 cis-2Oph·Nb A:A197(OP1), C:A198(OP2) A:A195(N7) A3748 G:A194
4kix A3105 fac-3Oph A:A730(OP2), C:A731(OP2), A:A761(OP1) A3296, A3685, A3686 G:A763 U:A1775
4kix A3104 fac-3Oph A:A1780(OP1), U:A1782(OP1), A:A1783(OP2) A3682, A3683, A3688 U:A1781 A:A1783
4kix A3046 fac-3Oph A:A1395(OP2), A:A1603(OP1), C:A1604(OP2) A3406, A3408 C:A1306
4kix A3107 trans,cis-4Oph U:A826(OP1), C:A2427(OP1), G:A2428(OP1), G:A2429(OP1) A3691 U:A827
4kix A3040 trans,trans-4Oph G:A1271(OP2), A:A1272(OP1), U:A1647(OP1), U:A1648(OP1) A3380, A3381
4kix A3002 Pout·4Bout A3207, A3209, A3210, A3211, A3212 A:A28 U:A29, G:A473, G:A474, G:A30

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>