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 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" Page 1 of 6 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 1vs8 B2970 Ob U:B746(O4) B3339, B3340, B3341, B3342, B3343 U:B744, C:B2610, C:B2611 1vs8 B2962 Ob G:B2304(O6) B3295, B3296, B3297, B3298, B3299 A:B2311, C:B2310 1vs8 B2921 2Nb G:B733(N7), A:B761(N7) B3096, B3097, B3098, B3099 A:B761, G:B733, G:B760, C:B732 1vs8 B2940 2Nb G:B1358(N7), G:B1371(N7) B3191, B3192, B3193, B3194 G:B1371, G:B1358, C:B1357, C:B1370 1vs8 B2922 Oph A:B800(OP1) B3100, B3101, B3102, B3103, B3104 G:B799 A:B191, C:B192, A:B800 1vs8 B2946 Oph A:B1678(OP2) B3216, B3217, B3218, B3219, B3220 A:B1679 1vs8 B2964 Oph U:B419(OP1) B3306, B3307, B3308, B3309, B3310 G:B230 1vs8 B2945 Oph U:B120(OP2) B3211, B3212, B3213, B3214, B3215 G:B122, G:B123 1vs8 B3002 Oph·Pout G:B1828(OP2) B3465, B3466, B3467, B3468, B3469 G:B1972 U:B1827 G:B1828 1vs8 B2977 Oph·Pout U:B1647(OP2) B3368, B3369, B3370, B3371, B3372 A:B1272 C:B1646, A:B1616 A:B1616 1vs8 B2949 Oph·Pout U:B120(OP1) B3230, B3231, B3232, B3233, B3234 G:B123 G:B124, G:B123 1vs8 B2942 Oph·Pout G:B536(OP2) B3198, B3199, B3200, B3201, B3202 G:B535 G:B536, G:B537 1vs8 B2926 Oph·Pout A:B1156(OP2) B3119, B3120, B3121, B3122, B3123 A:B1155 G:B1157, C:B998 1vs8 B3008 Oph·Pout A:B1676(OP2) B3487, B3488, B3489, B3490, B3491 C:B1675 A:B1676, A:B1677 1vs8 B2913 Oph·Pout A:B1664(OP2) B3057, B3058, B3059, B3060, B3061 G:B1992 A:B1664, A:B1665, G:B1992, G:B1666, G:B1667, G:B1663 1vs8 B2931 Oph·Pout A:B945(OP1) B3145, B3146, B3147, B3148, B3149 G:B831 U:B832, G:B831 1vs8 B2918 Oph·2Pout G:B1187(OP2) B3081, B3082, B3083, B3084, B3085 C:B817, C:B816 G:B1185 G:B818, G:B1187 1vs8 B2914 Oph·2Pout U:B567(OP1) B3062, B3063, B3064, B3065, B3066 G:B808, G:B809 U:B810, G:B809 1vs8 B2912 Oph·2Pout G:B1776(OP2) B3052, B3053, B3054, B3055, B3056 U:B1775, A:B1981 G:B1776 1vs8 B2911 Oph·2Pout A:B1970(OP2) B3047, B3048, B3049, B3050, B3051 G:B1835, A:B1900 U:B1834 G:B1835

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].

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