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 4tpf 4TPF (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to flopristin and linopristin. this file contains the 50s subunit of the second 70s ribosome with flopristin and linopristin bound. List of all 128 Mg2+ binding sites in the PDB structure 4tpf 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 7 | « Previous | Next » | 1 | 2 | 3 | 4 | 5 | 6 | 7

Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout 4tpf 2101 Pout·2Bout A3715, A3716, A3717, A3718, A3719, 2201 U:A686 G:A770, G:A771 4tpf B201 Oph A:B58(OP2) B301, B302, B303, B304 G:B56 A:B58, A:B59, U:B22, G:B23 4tpf B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, G:B96, A:B94 4tpf B203 Oph·2Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B101, A:B73 A:B101, G:B102 4tpf A3002 3Bout A3201, A3202, A3203, A3204, A3205, A3206 U:A521, U:A18, A:A522 4tpf A3003 3Pout·4Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 U:A29, G:A473, G:A30, C:A31 4tpf A3004 Oph U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A123, G:A122 4tpf A3005 Oph·Pout U:A120(OP1) A3218, A3219, A3220, A3221, A3222 A:A119 G:A124, G:A123 4tpf A3006 Oph·3Pout A:A218(OP2) A3223, A3224, A3225, A3226, A3227 A:A217, U:A427, A:A428 A:A218, A:A219, G:A220 4tpf A3007 Oph·Pout G:A297(OP2) A3228, A3229, A3230, A3231, A3232 G:A338 G:A298 4tpf A3008 Oph U:A419(OP1) A3233, A3234, A3235, A3236, A3237 G:A230 4tpf A3009 Oph·2Pout G:A450(OP2) A3238, A3239, A3240, E301, E302 U:A451, G:A452 4tpf A3010 Oph·Nb A:A453(OP1) G:A450(N7) A3241, A3242, A3243, A3244 A:A449 A:A449 4tpf A3011 cis-2Oph A:A526(OP1), C:A527(OP1) A3245, A3246, A3247, A3248 A:A528 4tpf A3012 4Pout A3249, A3250, A3251, A3252, A3253, J201 G:A559, A:A1008, G:A2038, C:A560 4tpf A3013 Oph·2Pout U:A567(OP1) A3254, A3255, A3256, A3257, A3258 G:A809, G:A808 U:A810, G:A809 4tpf A3014 3Pout·Bout A3259, A3260, A3261, A3262, A3263, L201 C:A944, U:A568, G:A831 A:A945 4tpf A3015 Oph·2Pout A:A574(OP2) A3264, A3265, A3266, A3267, A3268 U:A576, U:A573 U:A576, G:A577 4tpf A3016 2Pout·Rout·Bout A3269, A3270, A3271, A3272, A3273, E303 U:A2016, G:A1256 U:A1255 U:A1255 4tpf A3017 3Bout A3274, A3275, A3276, A3277, A3278, E304 U:A1258, C:A581, G:A1259

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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