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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 3oat



3OAT (3.25Å) -- RIBOSOME/ANTIBIOTIC : Crystal structure of the e. coli ribosome bound to telithromycin. this file contains the 50s subunit of the first 70s ribosome with telithromycin bound.
List of all 78 Mg2+ binding sites in the PDB structure 3oat 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 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
3oat A2973 Ob C:A2499(O2) A3361, A3362, A3363, A3364, A3365 G:A2032 G:A2454 C:A2055, U:A2500, G:A2032, G:A2454
3oat A2989 Ob G:A1125(O6) A3433, A3434, A3435, A3436, A3437 A:A1028 A:A1126
3oat B602 Ob U:B95(O4) B603, B604, B605, B606, B607 U:B80, G:B96
3oat A2924 Ob U:A746(O4) A3138, A3139, A3140, A3141, D210 C:A2611, C:A2610 G:A745
3oat A2922 2Nb G:A733(N7), A:A761(N7) A3128, A3129, A3130, A3131 G:A733, A:A761 C:A732
3oat A2947 2Nb G:A1358(N7), G:A1371(N7) A3238, A3239, A3240, A3241 G:A1371, C:A1357
3oat A2929 Oph A:A800(OP1) A3158, A3159, A3160, A3161, A3162 G:A799 A:A191, C:A192, A:A800
3oat A2910 Oph U:A419(OP1) A3069, A3070, A3071, A3072, A3073 G:A230
3oat A2978 Oph A:A299(OP2) A3383, A3384, A3385, A3386, A3387 U:A339, A:A299, G:A338
3oat A2986 Oph·Pout A:A981(OP1) A3421, A3422, A3423, A3424, A3425 G:A978
3oat A2955 Oph·Pout A:A1678(OP2) A3274, A3275, A3276, A3277, A3278 A:A1679 A:A1678, A:A1679
3oat A2935 Oph·Pout A:A945(OP1) A3184, A3185, A3186, A3187, A3188 G:A831 G:A831, U:A832, C:A944
3oat A2907 Oph·Pout U:A120(OP1) A3055, A3056, A3057, A3058, 247 G:A123 G:A123, G:A124
3oat A3028 Oph·Pout A:A1676(OP2) A3594, A3595, A3596, A3597, A3598 C:A1675 A:A1677, A:A1676
3oat A2931 Oph·Pout U:A810(OP1) A3167, A3168, A3169, A3170 U:A811 C:A565 A:A1253
3oat A3000 Oph·Pout U:A2022(OP1) A3490, A3491, A3492, A3493, A3494 C:A2023 C:A2021 A:A529
3oat A2906 Oph·Pout U:A120(OP2) A3050, A3051, A3052, A3053, A3054 G:A121 G:A122, G:A123, G:A121
3oat A2957 Oph·2Pout G:A1776(OP2) A3284, A3285, A3286, A3287, A3288 A:A1981, U:A1775 G:A1776
3oat A2956 Oph·2Pout C:A1774(OP1) A3279, A3280, A3281, A3282, A3283 U:A1775, A:A1786 A:A1772 A:A1772, G:A1776
3oat A2951 Oph·2Pout U:A1647(OP2) A3254, A3255, A3256, A3257, A3258 U:A1325, C:A1617 C:A1646, A:A1616 A:A1616

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>