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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 1yjn



1YJN (3Å) -- RIBOSOME : Crystal structure of clindamycin bound to the g2099a mutant 50s ribosomal subunit of haloarcula marismortui
List of all 63 Mg2+ binding sites in the PDB structure 1yjn 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 3 of 4 | | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1yjn 08079 cis-2Oph·Nb A:0167(OP1), C:0168(OP2) A:0165(N7) 03621, 03627, 03640 G:0164, A:0165 G:0164
1yjn 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 07764, 07765
1yjn 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07778, 07779, 09396 C:02542
1yjn 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03626, 07761, 09177 U:02484 G:02482, A:02532
1yjn 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03679, 09020, 09832
1yjn 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03622, 07762, 07763 G:01837 A:01839
1yjn 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03366, 07751, 09006 G:0833
1yjn 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 03641, 07755, 07840 G:02466
1yjn 08081 mer-3Oph C:01420(OP1), C:01421(OP2), G:01438(OP1) 04114, 09614
1yjn 08033 fac-3Oph·Ob A:01747(OP2), U:01748(OP2), G:02585(OP1) U:01749(O4) 03833, 09682 U:02586
1yjn 08063 3Bout 04199, 07005, 07430, 07745, 07823, C8673 G:01364, U:01362, G:01363
1yjn 08038 6Bout 03637, 03662, 03684, 03686, 07798, 09283 G:02271, G:02275, U:02115, U:02116, A:02274, U:02276
1yjn B8055 2Pout 03772, 03810, 06426, 07702, B8963, B8964 U:02721, C:02720
1yjn 08100 2Pout·2Bout 03782, 04270, 05525, 06169, 07837, 07838 U:02078, C:02077 G:02079, G:02080
1yjn 08107 2Pout·Rout·2Bout 06114, 07485, 07867, 07868, 07869 U:01977, A:01978 U:01977 G:01986, G:02000
1yjn 08071 2Pout·3Bout 04128, 06069, 07418, 07549, 07821, 07822 A:01815, C:01816 U:01813, C:01818, U:01817
1yjn 08056 Mg2+ bound by non-RNA A:02757(OP1) 03681, 07824, 09987, B8856 ASN:B335(O) A:02719, C:02720, G:02758
1yjn 08010 Mg2+ bound by non-RNA G:0836(OP1), U:02615(OP1) 03857, 09367, B8825 GLN:B230(OE1) G:02616
1yjn K8069 Mg2+ bound by non-RNA 03428, 04261, 06061, K2121, K7871 ASN:K42(OD1) U:01749, A:02583, G:02584
1yjn 08115 poly-nuclear Mg2+ site 03676, 03702, 03883, 06735, A8848 G:01849, U:01850

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/)
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