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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 4tpf



4TPF (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to flopristin and linopristin. this file contains the 50s subunit of the second 70s ribosome with flopristin and linopristin bound.
List of all 128 Mg2+ binding sites in the PDB structure 4tpf 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
4tpf A3133 Ob U:A2593(O4) A3785, A3786, C309, C310, C311 C:A2591 G:A2592, G:A2599, A:A2600
4tpf A3102 Ob U:A2419(O4) A3663, A3664, A3665, 3101, 3102 A:A2418
4tpf B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, G:B96, A:B94
4tpf A3023 Ob U:A746(O4) A3303, A3304, A3305, A3306, D301 U:A744, C:A2611, C:A2610 G:A745
4tpf A3073 Ob C:A2499(O2) A3528, A3529, A3530, A3531, A3532 G:A2032 C:A2055, U:A2500, G:A2454, A:A2453, G:A2032
4tpf A3090 Ob G:A1125(O6) A3603, A3604, A3605, A3606, A3607 A:A1028 G:A1124
4tpf A3095 Ob U:A1440(O4) A3629, A3630, A3631, A3632 A:A1439 G:A1441, A:A1551
4tpf A3046 Nb G:A1358(N7) A3399, A3400, A3401, A3402 C:A1357, G:A1358, C:A1370 G:A1371
4tpf A3021 2Nb G:A733(N7), A:A761(N7) A3293, A3294, A3295, A3296 A:A761, G:A733, G:A760, C:A732
4tpf A3004 Oph U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A123, G:A122
4tpf B201 Oph A:B58(OP2) B301, B302, B303, B304 G:B56 A:B58, A:B59, U:B22, G:B23
4tpf A3054 Oph A:A1678(OP2) A3435, A3436, A3437, A3438, A3439 A:A1678, A:A1679
4tpf A3028 Oph A:A800(OP1) A3321, A3322, A3323, A3324, A3325 G:A799, A:A203 A:A191
4tpf A3079 Oph A:A299(OP2) A3553, A3554, A3555, A3556, U201 U:A339, G:A338
4tpf A3008 Oph U:A419(OP1) A3233, A3234, A3235, A3236, A3237 G:A230
4tpf A3034 Oph·Pout A:A945(OP1) A3348, A3349, A3350, A3351, A3352 G:A831 G:A831, U:A832
4tpf A3007 Oph·Pout G:A297(OP2) A3228, A3229, A3230, A3231, A3232 G:A338 G:A298
4tpf A3078 Oph·Pout A:A14(OP2) A3549, A3550, A3551, A3552 G:A15
4tpf A3069 Oph·Pout G:A2269(OP1) A3508, A3509, A3510, A3511 A:A2268 G:A2271, A:A2267
4tpf A3061 Oph·Pout C:A2025(OP2) A3470, A3471, A3472, A3473, A3474 U:A2034 A:A2033 U:A1130

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>