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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 3i1r



3I1R (3.81Å) -- RIBOSOME : Crystal structure of the e. coli 70s ribosome in an intermediate state of ratcheting
List of all 137 Mg2+ binding sites in the PDB structure 3i1r 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
3i1r A2975 Ob C:A2499(O2) A3375, A3376, A3377, A3378, A3379 G:A2032 C:A2055, U:A2500, G:A2032, G:A2454
3i1r A2925 Ob U:A746(O4) A3145, A3146, A3147, A3148, A3149 U:A744, C:A2611, C:A2610 G:A745
3i1r A2992 Ob G:A1125(O6) A3452, A3453, A3454, A3455, A3456 A:A1028 A:A1126
3i1r A3003 Ob U:A2419(O4) A3513, A3514, 3626, 3629, 3630 A:A2418
3i1r A3035 Ob U:A2593(O4) A3636, A3637, A3638, C776, C778 G:A2592 G:A2592, C:A2594
3i1r B122 Ob U:B95(O4) B656, B657, B658, B659, V660 G:B96
3i1r A2948 2Nb G:A1358(N7), G:A1371(N7) A3246, A3247, A3248, A3249 G:A1371, C:A1357, C:A1370
3i1r A2923 2Nb G:A733(N7), A:A761(N7) A3135, A3136, A3137, A3138 A:A761, C:A732, G:A733
3i1r A2981 Oph A:A299(OP2) A3400, A3401, A3402, A3403, A3404 U:A339, G:A338
3i1r A2930 Oph A:A800(OP1) A3165, A3166, A3167, A3168, A3169 G:A799 A:A191, C:A192, A:A800
3i1r A2964 Oph A:A2033(OP1) A3322, A3323, A3324, A3325 G:A2027, G:A2029
3i1r A2910 Oph U:A419(OP1) A3071, A3072, A3073, A3074, A3075 G:A230
3i1r A2939 Oph·Pout A:A1156(OP2) A3204, A3205, A3206, A3207, A3208 A:A1155 C:A998, G:A1157
3i1r A2915 Oph·Pout U:A567(OP1) A3095, A3096, A3097, A3098, A3099 G:A809 G:A809, U:A810
3i1r A2909 Oph·Pout G:A297(OP2) A3066, A3067, A3068, A3069, A3070 G:A338 G:A298, G:A297
3i1r A2907 Oph·Pout U:A120(OP1) A3057, A3058, A3059, A3060, 2159 G:A123 G:A123, G:A124
3i1r A3030 Oph·Pout A:A1676(OP2) A3612, A3613, A3614, A3615, A3616 C:A1675 A:A1677, A:A1676
3i1r A3002 Oph·Pout U:A2022(OP1) A3508, A3509, A3510, A3511, A3512 C:A2023 C:A2021, A:A529 A:A529
3i1r A2984 Oph·Pout A:A572(OP1) A3413, A3414, A3415, A3416, A3417 A:A983 A:A572
3i1r A2956 Oph·Pout A:A1678(OP2) A3282, A3283, A3284, A3285, A3286 A:A1679 A:A1678, A:A1679

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].

Developed by Heping Zheng and Ivan Shabalin at Minor lab (http://olenka.med.virginia.edu/CrystUVa/)
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