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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 4tox



4TOX (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to flopristin. this file contains the 50s subunit of the second 70s ribosome with flopristin bound.
List of all 129 Mg2+ binding sites in the PDB structure 4tox 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 7 | « Previous | | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tox A3065 Or G:A2061(O5') A3489, A3490, A3491, A3492 G:A2502 C:A2501, A:A2060 G:A2446, G:A2445
4tox A3023 Ob U:A746(O4) A3305, A3306, A3307, A3308, D301 U:A744, C:A2611, C:A2610
4tox A3090 Ob G:A1125(O6) A3604, A3605, A3606, A3607, A3608 A:A1028 G:A1124
4tox A3102 Ob U:A2419(O4) A3664, A3665, A3666, 3101, 3102 A:A2418
4tox B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, G:B96, A:B94
4tox A3133 Ob U:A2593(O4) A3787, A3788, A3789, C308, C309 G:A2592, C:A2591 G:A2592
4tox A3046 Nb G:A1358(N7) A3399, A3400, A3401, A3402 C:A1357, G:A1358, C:A1370 G:A1371
4tox A3021 2Nb G:A733(N7), A:A761(N7) A3295, A3296, A3297, A3298 A:A761, G:A733, G:A760, C:A732
4tox A3004 Oph U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A122, G:A123, G:A121
4tox A3015 Oph·Pout A:A574(OP2) A3263, A3264, A3265, A3266, A3267 U:A576
4tox A3013 Oph·Pout U:A567(OP1) A3253, A3254, A3255, A3256, A3257 G:A809 U:A810, G:A809
4tox A3008 Oph·Pout U:A419(OP1) A3232, A3233, A3234, A3235, A3236 G:A230 G:A230
4tox A3079 Oph·Pout A:A299(OP2) A3553, A3554, A3555, A3556, A3557 C:A336 U:A339, G:A338
4tox A3028 Oph·Pout A:A800(OP1) A3322, A3323, A3324, A3325, A3326 A:A204 G:A799, A:A203 A:A191, C:A192
4tox A3051 Oph·Pout A:A1664(OP2) A3420, A3421, A3422, A3423, A3424 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666
4tox A3037 Oph·Pout A:A1156(OP2) A3361, A3362, A3363, A3364, A3365 A:A1155 G:A997
4tox A3034 Oph·Pout A:A945(OP1) A3349, A3350, A3351, A3352, A3353 G:A831 C:A944 G:A831, U:A832
4tox A3054 Oph·Pout A:A1678(OP2) A3435, A3436, A3437, A3438, A3439 A:A1677 A:A1678, A:A1679
4tox A3007 Oph·Pout G:A297(OP2) A3227, A3228, A3229, A3230, A3231 G:A338 G:A298, G:A297
4tox A3005 Oph·Pout U:A120(OP1) A3218, A3219, A3220, A3221, 2201 G:A123 G:A124, G:A123

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].

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