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 1vs6 1VS6 (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 108 Mg2+ binding sites in the PDB structure 1vs6 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 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 1vs6 B2917 Oph·4Pout G:B1333(OP2) B3072, B3073, B3074, B3075, B3076 C:B1314, G:B1332, G:B1334, U:B1313 G:B1334, G:B1333 1vs6 B2978 Oph·Or G:B2502(OP2) G:B2061(O5') B3364, B3365, B3366, B3367 G:B2061 A:B2060 A:B2060, G:B2446 1vs6 B2943 Oph·Ob A:B453(OP1) G:B450(O6) B3201, B3202, B3203, B3204 A:B454, A:B449 A:B449 1vs6 B2976 Oph·Ob A:B2033(OP1) U:B2028(O4) B3356, B3357, B3358, B3359 1vs6 B2919 Oph·Ob C:B2248(OP2) U:B2249(O4) B3083, B3084, B3085, B3086 C:B2066, A:B2247, G:B2253 1vs6 B2996 Oph·Ob A:B1342(OP2) U:B1602(O4) B3434, B3435, B3436, B3437 G:B1601 1vs6 B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3508, B3509, B3510, B3511 U:B1188, G:B1190 1vs6 B2963 Oph·Nb U:B810(OP1) A:B1253(N7) B3295, B3296, B3297, B3298 U:B811 C:B565, G:B1252 1vs6 B2966 cis-2Oph A:B1268(OP1), C:B2006(OP1) B3307, B3308, B3309, B3310 G:B2049, G:B2048 1vs6 B2914 cis-2Oph U:B999(OP2), C:B1153(OP2) B3059, B3060, B3061, B3062 C:B1152, C:B998 1vs6 B2915 cis-2Oph G:B784(OP1), G:B2588(OP1) B3063, B3064, B3065, B3066 A:B2589, C:B2440 1vs6 B2926 cis-2Oph G:B1968(OP1), G:B2592(OP1) B3121, B3122, B3123, B3124 1vs6 B2938 cis-2Oph A:B2711(OP2), G:B2714(OP2) B3180, B3181, B3182, B3183 C:B2710 1vs6 B2940 cis-2Oph U:B1394(OP1), C:B1604(OP1) B3189, B3190, B3191, B3192 1vs6 B2945 cis-2Oph A:B945(OP2), C:B946(OP2) B3207, B3208, B3209, B3210 G:B822 C:B944 1vs6 B2958 cis-2Oph A:B621(OP2), G:B622(OP2) B3272, B3273, B3274, B3275 G:B622 1vs6 B2971 cis-2Oph C:B1670(OP1), U:B1671(OP2) B3332, B3333, B3334, B3335 1vs6 B2977 cis-2Oph G:B2056(OP2), G:B2057(OP2) B3360, B3361, B3362, B3363 U:B2504, G:B2505 A:B2503 G:B2056, G:B2057, A:B2058 1vs6 B2980 cis-2Oph A:B2268(OP1), G:B2269(OP1) B3373, B3374, B3375, B3376 A:B2267 G:B2271 1vs6 B2985 cis-2Oph C:B2579(OP1), C:B2611(OP2) B3400, B3401, B3402, B3403 C:B2612 G:B2576

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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