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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 4gau



4GAU (3.3Å) -- RIBOSOME/ANTIBIOTIC : Allosteric control of the ribosome by small-molecule antibiotics
List of all 120 Mg2+ binding sites in the PDB structure 4gau 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
4gau A3097 Ob U:A2419(O4) A3669, A3670, A3671, 3101, 3102 A:A2418
4gau A3192 Ob U:A746(O4) A3302, A3303, A3304, A3305, D401 U:A744, U:A2580, C:A2611, C:A2610
4gau A3069 Ob C:A2499(O2) A3530, A3531, A3532, A3533, A3534 G:A2032 C:A2055, U:A2500, G:A2032, G:A2454, A:A2453
4gau A3085 Ob G:A1125(O6) A3606, A3607, A3608, A3609, A3610 A:A1027, A:A1028
4gau A3074 Oph A:A299(OP2) A3555, A3556, A3557, A3558, U201 G:A338
4gau A3007 Oph U:A419(OP1) A3233, A3234, A3235, A3236, A3237 G:A230
4gau A3058 Oph A:A2033(OP1) A3477, A3478, A3479, A3480 G:A2029
4gau A3024 Oph A:A800(OP1) A3323, A3324, A3325, A3326, A3327 A:A203 C:A192, A:A191
4gau A3047 Oph·Pout A:A1664(OP2) A3422, A3423, A3424, A3425, A3426 G:A1992 A:A1665, G:A1666, G:A1667, G:A1992
4gau A3033 Oph·Pout A:A1156(OP2) A3360, A3361, A3362, A3363, A3364 A:A1155 U:A999, G:A1157, G:A997, C:A998
4gau A3030 Oph·Pout A:A945(OP1) A3349, A3350, A3351, A3352, A3353 G:A831 G:A831, U:A832
4gau A3025 Oph·Pout A:A802(OP1) A3328, A3329, A3330, A3331, A3332 G:A674 U:A803, A:A804, G:A674
4gau A3096 Oph·Pout U:A2022(OP1) A3664, A3665, A3666, A3667, A3668 C:A2023 A:A529 A:A529
4gau A3050 Oph·Pout A:A1678(OP2) A3437, A3438, A3439, A3440, A3441 A:A1679 A:A1678, A:A1679, U:A1680
4gau A3020 Oph·Pout A:A751(OP1) A3306, A3307, A3308, A3309 A:A1614 G:A1613 A:A789, C:A1617
4gau A3094 Oph·Pout C:A1658(OP1) A3653, A3654, A3655, A3656, A3657 U:A744 A:A743
4gau A3084 Oph·Pout C:A1013(OP2) A3602, A3603, A3604, A3605 A:A1014 A:A1014
4gau A3077 Oph·Pout A:A572(OP1) A3567, A3568, A3569, A3570, A3571 A:A983 A:A572
4gau A3056 Oph·Pout A:A1970(OP2) A3467, A3468, A3469, A3470, A3471 A:A1900 G:A1835
4gau A3009 Oph·Pout A:A453(OP1) A3243, A3244, E401, E402 A:A449 G:A450

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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