`

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 4too



4TOO (3Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to linopristin. this file contains the 50s subunit of the second 70s ribosome with linopristin bound.
List of all 127 Mg2+ binding sites in the PDB structure 4too 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
4too A3089 Ob G:A1125(O6) A3599, A3600, A3601, A3602, A3603
4too A3022 Ob U:A746(O4) A3302, A3303, A3304, A3305, D301 U:A744, C:A2611, C:A2610
4too A3133 Ob U:A2593(O4) A3783, A3784, A3785, C308, C309 G:A2592, C:A2591 G:A2592
4too B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, A:B94
4too A3101 Ob U:A2419(O4) A3659, A3660, A3661, 3101, 3102 A:A2418
4too A3072 Nb C:A2055(N3) A3525, A3526, A3527, A3528, A3529 U:A2504, C:A2499, U:A2500, G:A2032, A:A2453, G:A2454
4too A3045 Ob·Nb G:A1358(O6) A3396, A3397, A3398, A3399 G:A1358, G:A1371 G:A1371
4too A3020 2Nb G:A733(N7), A:A761(N7) A3292, A3293, A3294, A3295 A:A761, G:A733, G:A760, C:A732
4too A3003 Oph U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A122, G:A123, G:A121
4too B201 Oph A:B58(OP2) B301, B302, B303, B304 G:B56 A:B58, A:B59, U:B22, G:B23
4too A3033 Oph·Pout A:A945(OP1) A3345, A3346, A3347, A3348, A3349 G:A831 C:A944 G:A831, U:A832
4too A3027 Oph·Pout A:A800(OP1) A3318, A3319, A3320, A3321, A3322 A:A204 G:A799, A:A203 A:A191
4too A3014 Oph·Pout A:A574(OP2) A3264, A3265, A3266, A3267, A3268 U:A576
4too A3036 Oph·Pout A:A1156(OP2) A3357, A3358, A3359, A3360, A3361 A:A1155 C:A998, G:A1157
4too A3078 Oph·Pout A:A299(OP2) A3549, A3550, A3551, A3552, U201 C:A336 A:A300, G:A338
4too A3060 Oph·Pout C:A2025(OP2) A3467, A3468, A3469, A3470, A3471 U:A2034 A:A2033 U:A2026
4too A3059 Oph·Pout A:A1970(OP2) A3462, A3463, A3464, A3465, A3466 G:A1835 U:A1834 G:A1835, C:A1836
4too A3053 Oph·Pout A:A1678(OP2) A3432, A3433, A3434, A3435, A3436 A:A1677 A:A1678, A:A1679
4too A3050 Oph·Pout A:A1664(OP2) A3417, A3418, A3419, A3420, A3421 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666
4too A3006 Oph·Pout G:A297(OP2) A3227, A3228, A3229, A3230, A3231 G:A338 G:A298, G:A297

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>