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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 3r8s



3R8S (3Å) -- RIBOSOME : Structures of the bacterial ribosome in classical and hybrid states of trna binding
List of all 101 Mg2+ binding sites in the PDB structure 3r8s 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
3r8s A3036 Ob U:A2593(O4) A3696, A3697, A3698, C766, C768 G:A2592, C:A2591 G:A2592, G:A2599, A:A2600, C:A2594
3r8s A2975 Ob C:A2499(O2) A3431, A3432, A3433, A3434, A3435 G:A2032 C:A2055, G:A2454, G:A2032
3r8s A2992 Ob G:A1125(O6) A3508, A3509, A3510, A3511, A3512 C:A1123, A:A1028 G:A1124
3r8s A2981 Oph A:A299(OP2) A3456, A3457, A3458, A3459, A3460 A:A299, G:A338
3r8s A2910 Oph U:A419(OP1) A3130, A3131, A3132, A3133, A3134
3r8s A2930 Oph A:A800(OP1) A3222, A3223, A3224, A3225, A3226 G:A799 A:A191, C:A192, A:A800
3r8s A2964 Oph A:A2033(OP1) A3378, A3379, A3380, A3381 G:A2027, U:A2028
3r8s A2984 Oph·Pout A:A572(OP1) A3469, A3470, A3471, A3472, A3473 A:A983 A:A572
3r8s A3003 Oph·Pout U:A2022(OP1) A3565, A3566, A3567, A3568, A3569 C:A2023 C:A2021, A:A529 A:A529
3r8s A2907 Oph·Pout U:A120(OP1) A3115, A3116, A3117, A3118, A3119 G:A123 G:A124, G:A123
3r8s A2963 Oph·Pout C:A2025(OP2) A3373, A3374, A3375, A3376, A3377 G:A2024
3r8s A2953 Oph·Pout A:A1664(OP2) A3323, A3324, A3325, A3326, A3327 G:A1992 G:A1667, A:A1664, A:A1665, G:A1992, G:A1666
3r8s A2972 Oph·Pout A:A2270(OP2) A3415, A3416, A3417, A3418, A3419 A:A2267 G:A2271, U:A2272
3r8s A3031 Oph·Pout A:A1676(OP2) A3672, A3673, A3674, A3675, A3676 C:A1675 A:A1677, A:A1676
3r8s A2939 Oph·Pout A:A1156(OP2) A3260, A3261, A3262, A3263, A3264 A:A1155 G:A1157, G:A997
3r8s A2936 Oph·Pout A:A945(OP1) A3248, A3249, A3250, A3251, A3252 G:A831 C:A944 G:A831, U:A832
3r8s A3038 Oph·Pout A:A943(OP2) A3703, A3704, A3705, L777, L779 U:A832
3r8s A2940 Oph·2Pout G:A1187(OP2) A3265, A3266, A3267, A3268, A3269 C:A816, C:A817 G:A1185 G:A818, G:A1187
3r8s A2938 Oph·2Pout C:A1153(OP2) A3256, A3257, A3258, A3259 U:A999, C:A998 G:A1154
3r8s A2931 Oph·2Pout A:A802(OP1) A3227, A3228, A3229, A3230, A3231 A:A675, G:A674 U:A803, A:A804

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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