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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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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 | | 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 B2936 Ob U:B746(O4) B3169, B3170, B3171, B3172, B3173 U:B744, C:B2611, C:B2610 G:B745
1vs6 B2946 Ob G:B2304(O6) B3211, B3212, B3213, B3214, B3215 G:B2303
1vs6 B2939 Ob C:B2499(O2) B3184, B3185, B3186, B3187, B3188 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
1vs6 B2932 Nb G:B1371(N7) B3149, B3150, B3151, B3152 G:B1358, G:B1371, C:B1357, C:B1370 G:B1358
1vs6 B2959 2Nb G:B733(N7), A:B761(N7) B3276, B3277, B3278, B3279 G:B733, G:B760, A:B761, C:B732
1vs6 B2948 Oph U:B120(OP2) B3222, B3223, B3224, B3225, B3226 G:B122, G:B123, G:B121
1vs6 B2962 Oph A:B800(OP1) B3290, B3291, B3292, B3293, B3294 A:B191, C:B192
1vs6 B2972 Oph A:B1678(OP2) B3336, B3337, B3338, B3339, B3340 A:B1678, A:B1679
1vs6 B2934 Oph U:B419(OP1) B3158, B3159, B3160, B3161, B3162 G:B230
1vs6 B3010 Oph A:B1676(OP2) B3494, B3495, B3496, B3497, B3498 C:B1675 A:B1677, A:B1676
1vs6 B2930 Oph·Pout A:B945(OP1) B3138, B3139, B3140, B3141, B3142 G:B831 G:B831, U:B832
1vs6 B2913 Oph·Pout G:B297(OP2) B3054, B3055, B3056, B3057, B3058 G:B338 G:B298
1vs6 B2911 Oph·Pout U:B1647(OP2) B3044, B3045, B3046, B3047, B3048 U:B1325 C:B1646, A:B1616 A:B1616
1vs6 B2950 Oph·Pout A:B526(OP1) B3232, B3233, B3234, B3235 C:B527
1vs6 B2951 Oph·Pout G:B536(OP2) B3236, B3237, B3238, B3239, B3240 G:B535 G:B537
1vs6 B2969 Oph·Pout A:B1664(OP2) B3321, B3322, B3323, B3324, B3325 G:B1992 G:B1667, A:B1664, A:B1665, G:B1992, G:B1666
1vs6 B2965 Oph·Pout A:B1156(OP2) B3302, B3303, B3304, B3305, B3306 A:B1155 G:B1157
1vs6 B2954 Oph·Pout A:B574(OP2) B3251, B3252, B3253, B3254, B3255 U:B576 U:B576, G:B577
1vs6 B2910 Oph·Pout G:B2588(OP2) B3039, B3040, B3041, B3042, B3043 A:B2589 A:B2589
1vs6 B2905 Oph·2Pout A:B802(OP1) B3015, B3016, B3017, B3018, B3019 G:B674, A:B675 U:B803, A:B804

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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