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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 3i1t




3I1T (3.81Å) -- RIBOSOME : Crystal structure of the e. coli 70s ribosome in an intermediate state of ratcheting
List of all 128 Mg2+ binding sites in the PDB structure 3i1t 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 | | 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
3i1t A2926 Ob U:A746(O4) A3154, A3155, A3156, A3157, D259 C:A2611, C:A2610 G:A745
3i1t A2995 Ob G:A1125(O6) A3471, A3472, A3473, A3474, A3475 A:A1028 G:A1124
3i1t A3000 Ob U:A2419(O4) A3493, A3494, A3495, A3496, 3611
3i1t A3032 Ob U:A2593(O4) A3614, A3615, A3616, C741, C745 G:A2592, C:A2591 C:A2594, G:A2592
3i1t A3014 Ob U:A1602(O4) A3542, A3543, A3544, T665 G:A1601, C:A1600
3i1t A2933 Nb A:A1253(N7) A3181, A3182, A3183, A3184 U:A810, U:A811
3i1t A2977 Nb G:A2304(N7) A3384, A3385, A3386, A3387, A3388 G:A2308 G:A2303
3i1t A2950 2Nb G:A1358(N7), G:A1371(N7) A3256, A3257, A3258, A3259 G:A1358, C:A1357
3i1t A2924 2Nb G:A733(N7), A:A761(N7) A3144, A3145, A3146, A3147 A:A761, G:A733, G:A760, C:A732
3i1t A2910 Oph U:A419(OP1) A3071, A3072, A3073, A3074, A3075 G:A230
3i1t A2987 Oph A:A299(OP2) A3434, A3435, A3436, A3437, U544 A:A299, G:A338, U:A339, A:A300
3i1t A2922 Oph A:A621(OP2) A3135, A3136, A3137, L238
3i1t A2958 Oph A:A1678(OP2) A3292, A3293, A3294, A3295, A3296 A:A1678, A:A1679
3i1t A2913 Oph G:A536(OP2) A3084, A3085, A3086, A3087, A3088
3i1t A2911 Oph·Pout A:A453(OP1) A3076, A3077, A3078, A3079 A:A449 G:A450, A:A449
3i1t A2909 Oph·Pout G:A297(OP2) A3066, A3067, A3068, A3069, A3070 G:A338 G:A297, G:A298
3i1t A2908 Oph·Pout U:A120(OP1) A3061, A3062, A3063, A3064, A3065 G:A123 G:A123, G:A124
3i1t A2942 Oph·Pout G:A1187(OP2) A3220, A3221, A3222, A3223, A3224 C:A816
3i1t A2941 Oph·Pout A:A1156(OP2) A3215, A3216, A3217, A3218, A3219 A:A1155 G:A1157, G:A997
3i1t A2936 Oph·Pout A:A945(OP1) A3194, A3195, A3196, A3197, A3198 G:A831 U:A832, G:A831

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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