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 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 1vs6 B2905 Oph·2Pout A:B802(OP1) B3015, B3016, B3017, B3018, B3019 G:B674, A:B675 U:B803, A:B804 1vs6 B2906 5Bout B3020, B3021, B3022, B3023, B3024, B3025 U:B2074, U:B2243, U:B2075, G:B2238, G:B2242 1vs6 B2907 2Bout B3026, B3027, B3028, B3029, B3030, E202 U:B580, G:B1259 1vs6 B2908 3Pout·Rout B3031, B3032, B3033, B3034, B3035, B3036 C:B560, A:B1008, G:B559 C:B1007 1vs6 B2910 Oph·Pout G:B2588(OP2) B3039, B3040, B3041, B3042, B3043 A:B2589 A:B2589 1vs6 B2911 Oph·Pout U:B1647(OP2) B3044, B3045, B3046, B3047, B3048 U:B1325 C:B1646, A:B1616 A:B1616 1vs6 B2912 Oph·3Pout A:B2518(OP2) B3049, B3050, B3051, B3052, B3053 U:B2519, A:B2541, C:B2540 A:B2541 1vs6 B2913 Oph·Pout G:B297(OP2) B3054, B3055, B3056, B3057, B3058 G:B338 G:B298 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 B2916 Oph·3Pout U:B2074(OP1) B3067, B3068, B3069, B3070, B3071 U:B2240, U:B2075, G:B2239 G:B2238 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 B2918 3Bout B3077, B3078, B3079, B3080, B3081, B3082 U:B521, G:B17, U:B18 1vs6 B2919 Oph·Ob C:B2248(OP2) U:B2249(O4) B3083, B3084, B3085, B3086 C:B2066, A:B2247, G:B2253 1vs6 B2920 Oph·3Pout G:B1828(OP1) B3087, B3088, B3089, B3090, B3091 G:B1972, G:B1973, A:B1772 1vs6 B2921 2Pout B3092, B3093, B3094, B3095, B3096, B3097 A:B947, G:B822 1vs6 B2922 2Pout·4Bout B3098, B3099, B3100, B3101, B3102, B3103 A:B2009, U:B1267 G:B2010, U:B2011, G:B2012, A:B2009 1vs6 B2923 2Pout·3Bout B3104, B3105, B3106, B3107, B3108, B3109 U:B29, A:B447 G:B474, U:B29, G:B30 1vs6 B2924 3Bout B3110, B3111, B3112, B3113, B3114, B3115 A:B756, A:B739, G:B757 1vs6 B2925 Oph·2Pout G:B1187(OP2) B3116, B3117, B3118, B3119, B3120 C:B816, C:B817 G:B1185 G:B1187, G:B818

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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