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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 3i1n



3I1N (3.19Å) -- RIBOSOME : Crystal structure of the e. coli 70s ribosome in an intermediate state of ratcheting
List of all 85 Mg2+ binding sites in the PDB structure 3i1n 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 5 | « Previous | | 1 | 2 | 3 | 4 | 5
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3i1n A3004 Ob U:A2419(O4) A3515, A3516, A3517, 3626, 3629 A:A2418
3i1n A2975 Ob C:A2499(O2) A3377, A3378, A3379, A3380, A3381 G:A2032 C:A2055, U:A2500, G:A2454, G:A2032
3i1n A3036 Ob U:A2593(O4) A3635, A3636, A3637, C776, C778 G:A2592 G:A2592, C:A2594, G:A2599
3i1n B122 Ob U:B95(O4) B656, B657, B658, B659, B660 U:B80, G:B96
3i1n A2925 Ob U:A746(O4) A3147, A3148, A3149, A3150, A3151 U:A744, C:A2611, C:A2610 G:A745
3i1n A2992 Ob G:A1125(O6) A3453, A3454, A3455, A3456, A3457 A:A1028 A:A1126
3i1n A2923 2Nb G:A733(N7), A:A761(N7) A3137, A3138, A3139, A3140 G:A733, A:A761 C:A732
3i1n A2906 Oph U:A120(OP2) A3053, A3054, A3055, A3056, A3057 G:A122, G:A123, G:A121
3i1n A2981 Oph A:A299(OP2) A3402, A3403, A3404, A3405, A3406 U:A339, A:A299, G:A338
3i1n A2930 Oph A:A800(OP1) A3168, A3169, A3170, A3171, A3172 G:A799 A:A191, C:A192, A:A800
3i1n A2910 Oph U:A419(OP1) A3072, A3073, A3074, A3075, A3076 G:A230
3i1n A2953 Oph·Pout A:A1664(OP2) A3270, A3271, A3272, A3273, A3274 G:A1992 G:A1667, A:A1664, A:A1665, G:A1992, G:A1666
3i1n A2932 Oph·Pout U:A810(OP1) A3178, A3179, A3180, A3181 U:A811 C:A565 A:A1253
3i1n A2956 Oph·Pout A:A1678(OP2) A3285, A3286, A3287, A3288, A3289 A:A1679 A:A1678, A:A1679
3i1n A2989 Oph·Pout A:A981(OP1) A3441, A3442, A3443, A3444, A3445 G:A978
3i1n A2907 Oph·Pout U:A120(OP1) A3058, A3059, A3060, A3061, 2159 G:A123 G:A123, G:A124
3i1n A3003 Oph·Pout U:A2022(OP1) A3510, A3511, A3512, A3513, A3514 C:A2023 C:A2021 A:A529
3i1n A2931 Oph·2Pout A:A802(OP1) A3173, A3174, A3175, A3176, A3177 A:A675, G:A674 U:A803, A:A804
3i1n A2917 Oph·2Pout A:A574(OP2) A3107, A3108, A3109, A3110, A3111 U:A576, U:A573 U:A576, G:A577, G:A578
3i1n A2909 Oph·2Pout G:A297(OP2) A3067, A3068, A3069, A3070, A3071 U:A296, G:A338 G:A298, G:A297

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/)
For any help please contact <dust@iwonka.med.virginia.edu>