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 2awb 2AWB (3.46Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli at 3.5 a resolution. this file contains the 50s subunit of the second 70s ribosome. the entire crystal structure contains two 70s ribosomes and is described in remark 400. List of all 104 Mg2+ binding sites in the PDB structure 2awb 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 2awb B2963 Ob G:B2304(O6) B3298, B3299, B3300, B3301, B3302 C:B2310 2awb B2971 Ob U:B746(O4) B3340, B3341, B3342, B3343, B3344 U:B744, C:B2610, C:B2611 2awb B2941 2Nb G:B1358(N7), G:B1371(N7) B3195, B3196, B3197, B3198 G:B1371, G:B1358, C:B1357, C:B1370 2awb B2965 Oph U:B419(OP1) B3309, B3310, B3311, B3312, B3313 G:B230 2awb B2947 Oph A:B1678(OP2) B3220, B3221, B3222, B3223, B3224 A:B1679 2awb B2946 Oph U:B120(OP2) B3215, B3216, B3217, B3218, B3219 G:B122, G:B123 2awb B2922 Oph A:B800(OP1) B3101, B3102, B3103, B3104, B3105 G:B799 A:B191, C:B192, A:B800 2awb B2943 Oph·Pout G:B536(OP2) B3202, B3203, B3204, B3205, B3206 G:B535 G:B536, G:B537 2awb B2950 Oph·Pout U:B120(OP1) B3234, B3235, B3236, B3237, B3238 G:B122 G:B124, G:B123 2awb B2913 Oph·Pout A:B1664(OP2) B3058, B3059, B3060, B3061, B3062 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666, G:B1663 2awb B2940 Oph·Pout A:B2270(OP2) B3190, B3191, B3192, B3193, B3194 A:B2267 G:B2271 2awb B2931 Oph·Pout A:B945(OP1) B3146, B3147, B3148, B3149, B3150 G:B831 G:B831 2awb B3009 Oph·Pout A:B1676(OP2) B3488, B3489, B3490, B3491, B3492 C:B1675 A:B1676, A:B1677 2awb B2978 Oph·Pout U:B1647(OP2) B3369, B3370, B3371, B3372, B3373 A:B1272 C:B1646, A:B1616 A:B1616 2awb B2926 Oph·Pout A:B1156(OP2) B3120, B3121, B3122, B3123, B3124 A:B1155 G:B1157, C:B998 2awb B2928 Oph·2Pout C:B2025(OP2) B3131, B3132, B3133, B3134, D231 G:B2024, U:B2034 2awb B2918 Oph·2Pout G:B1187(OP2) B3082, B3083, B3084, B3085, B3086 C:B817, C:B816 G:B1185 G:B818, G:B1187 2awb B2914 Oph·2Pout U:B567(OP1) B3063, B3064, B3065, B3066, B3067 G:B808, G:B809 G:B809, U:B810 2awb B2912 Oph·2Pout G:B1776(OP2) B3053, B3054, B3055, B3056, B3057 U:B1775, A:B1981 G:B1776 2awb B2911 Oph·2Pout A:B1970(OP2) B3048, B3049, B3050, B3051, B3052 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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