`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 4tom



4TOM (3Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to linopristin. this file contains the 50s subunit of the first 70s ribosome with linopristin bound.
List of all 74 Mg2+ binding sites in the PDB structure 4tom 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
4tom A3114 Ob U:A1602(O4) A3713, A3714, A3715, A3716 A:A1342
4tom A3132 Ob U:A2593(O4) A3787, A3788, C307, C308, C309 G:A2592 C:A2594, G:A2599, G:A2592, A:A2600
4tom A3088 Ob G:A1125(O6) A3606, A3607, A3608, A3609, A3610 G:A1124
4tom A3021 Ob U:A746(O4) A3303, A3304, A3305, A3306, D301 C:A2610, C:A2611, U:A744 G:A745
4tom B202 Ob U:B95(O4) B305, B306, B307, B308, B309 U:B80, G:B96
4tom A3100 Ob U:A2419(O4) A3666, A3667, 3101, 3102, 3103 A:A2418
4tom A3071 Ob C:A2499(O2) A3530, A3531, A3532, A3533, A3534 G:A2032 C:A2055, U:A2500, G:A2032, G:A2454
4tom A3123 2Or A:A1378(O2') A3752, A3753, A3754 G:A1380, A:A1347 G:A1380
4tom A3044 2Nb G:A1358(N7), G:A1371(N7) A3401, A3402, A3403, A3404 G:A1358, G:A1371, C:A1357, C:A1370
4tom A3019 2Nb G:A733(N7), A:A761(N7) A3293, A3294, A3295, A3296 A:A761, G:A733, G:A760, C:A732
4tom A3007 Oph U:A419(OP1) A3233, A3234, A3235, A3236, A3237 G:A230
4tom A3060 Oph A:A2033(OP1) A3477, A3478, A3479, A3480 G:A2027, U:A2028
4tom A3077 Oph A:A299(OP2) A3555, A3556, A3557, A3558, U201 A:A299, G:A338
4tom A3099 Oph·Pout U:A2022(OP1) A3661, A3662, A3663, A3664, A3665 C:A2023 C:A2021 A:A529
4tom A3049 Oph·Pout A:A1664(OP2) A3422, A3423, A3424, A3425, A3426 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666
4tom A3004 Oph·Pout U:A120(OP1) A3218, A3219, A3220, A3221, A3222 G:A123 G:A124, G:A123
4tom B203 Oph·Pout G:B100(OP2) B310, B311, B312, B313, B314 A:B73 A:B101
4tom A3134 Oph·Pout A:A943(OP2) A3793, A3794, A3795, A3796, L306 U:A832
4tom A3003 Oph·Pout U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A121 G:A122, G:A123, G:A121
4tom A3041 Oph·2Pout U:A1313(OP1) A3385, A3386, A3387, A3388, A3389 G:A1333, G:A1334

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>