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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 1vs8



1VS8 (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with the antibiotic kasugamyin at 3.5a resolution. this file contains the 50s subunit of one 70s ribosome. the entire crystal structure contains two 70s ribosomes and is
List of all 104 Mg2+ binding sites in the PDB structure 1vs8 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
1vs8 B2959 trans-2Oph A:B751(OP1), A:B1614(OP1) B3279, B3280, B3281, B3282 G:B1613 A:B1614, C:B1615, C:B1617, A:B789
1vs8 B2919 trans-2Oph U:B999(OP2), C:B1153(OP2) B3086, B3087, B3088, B3089 C:B998 C:B1152 G:B1154
1vs8 B3005 trans-2Oph C:B787(OP1), U:B790(OP2) B3477, B3478, B3479, B3480 C:B791
1vs8 B3004 cis-2Oph·Or U:B1379(OP2), G:B1380(OP2) A:B1378(O2') B3474, B3475, B3476 G:B1380
1vs8 B2987 cis-2Oph·Ob A:B2448(OP1), C:B2499(OP1) G:B570(O6) B3414, B3415, B3416 A:B2030
1vs8 B3009 cis-2Oph·Nb C:B510(OP1), U:B511(OP2) G:B512(N7) B3492, B3493, B3494
1vs8 B3006 cis-2Oph·Nb A:B197(OP1), C:B198(OP2) A:B195(N7) B3481, B3482, B3483
1vs8 B3007 fac-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3484, B3485, B3486
1vs8 B2971 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3344, B3345, C454
1vs8 B2986 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3411, B3412, B3413 U:B2449 G:B2447, A:B2497
1vs8 B2989 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B3420, B3421, B3422 U:B762, G:B763
1vs8 B2995 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3438, B3439, B3440 C:B2507
1vs8 B2990 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3423, B3424, B3425 U:B741
1vs8 B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3417, B3418, B3419 A:B1783
1vs8 B2994 mer-3Oph·Or U:B1023(OP2), G:B1024(OP2), G:B1026(OP1) G:B1025(O2') B3436, B3437 C:B1135
1vs8 B2998 fac-3Oph·Ob A:B1669(OP2), C:B1670(OP2), G:B2550(OP1) U:B1671(O4) B3449, B3450 C:B2551
1vs8 B2991 trans,cis-4Oph U:B826(OP1), C:B2427(OP1), G:B2428(OP1), G:B2429(OP1) B3426, B3427 U:B827
1vs8 B2954 trans,trans-4Oph G:B1271(OP2), A:B1272(OP1), U:B1647(OP1), U:B1648(OP1) B3255, B3256
1vs8 B2963 2Bout B3300, B3301, B3302, B3303, B3304, B3305 G:B17, U:B18
1vs8 B2955 2Bout B3257, B3258, B3259, B3260, B3261, B3262 U:B434, A:B42

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>