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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 3r8t




3R8T (3Å) -- RIBOSOME : Structures of the bacterial ribosome in classical and hybrid states of trna binding
List of all 95 Mg2+ binding sites in the PDB structure 3r8t 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
3r8t B615 Ob U:B95(O4) B616, B617, B618, B619, B620 U:B80, A:B94
3r8t A2974 Ob C:A2499(O2) A3403, A3404, A3405, A3406, A3407 G:A2032 C:A2055, U:A2500, G:A2454, G:A2032
3r8t A2924 Ob U:A746(O4) A3173, A3174, A3175, A3176, D210 U:A2580, C:A2611, C:A2610, U:A744 G:A745
3r8t A2991 Ob G:A1125(O6) A3479, A3480, A3481, A3482, A3483 A:A1028
3r8t A3003 Ob U:A2419(O4) A3539, A3540, A3541, 3587, 3591 A:A2418
3r8t A3035 Ob U:A2593(O4) A3665, A3666, A3667, C765, C768 G:A2592, C:A2591 G:A2592, G:A2599
3r8t A2947 2Nb G:A1358(N7), G:A1371(N7) A3275, A3276, A3277, A3278 G:A1371, G:A1358, C:A1357
3r8t A2980 Oph A:A299(OP2) A3428, A3429, A3430, A3431, A3432 G:A338
3r8t A2910 Oph U:A419(OP1) A3101, A3102, A3103, A3104, A3105 C:A418 G:A230
3r8t A2963 Oph A:A2033(OP1) A3350, A3351, A3352, A3353 G:A2027, U:A2028, G:A2029
3r8t A3037 Oph·Pout A:A943(OP2) A3674, A3675, A3676, A3677, L777 U:A832 A:A943
3r8t A3030 Oph·Pout A:A1676(OP2) A3641, A3642, A3643, A3644, A3645 C:A1675 A:A1677, A:A1676
3r8t A2983 Oph·Pout A:A572(OP1) A3441, A3442, A3443, A3444, R466 A:A983 A:A572
3r8t B610 Oph·Pout A:B58(OP2) B611, B612, B613, B614 A:B57 G:B23
3r8t A2938 Oph·Pout A:A1156(OP2) A3233, A3234, A3235, A3236, A3237 A:A1155
3r8t A2917 Oph·Pout A:A574(OP2) A3133, A3134, A3135, A3136, A3137 U:A573 U:A576
3r8t A2907 Oph·Pout U:A120(OP1) A3087, A3088, A3089, A3090, 247 G:A123 G:A124, G:A123
3r8t A2915 Oph·Pout U:A567(OP1) A3123, A3124, A3125, A3126, A3127 G:A809 U:A810, G:A809
3r8t A2961 Oph·2Pout A:A1970(OP2) A3341, A3342, A3343, A3344, A3345 G:A1835, A:A1900 G:A1835, C:A1836
3r8t A2956 Oph·2Pout C:A1774(OP1) A3316, A3317, A3318, A3319, A3320 U:A1775, A:A1786 A:A1772, G:A1776, A:A1789

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>