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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 4tp3



4TP3 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to dalfopristin. this file contains the 50s subunit of the second 70s ribosome with dalfopristin bound.
List of all 128 Mg2+ binding sites in the PDB structure 4tp3 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
4tp3 A3132 Ob U:A2593(O4) A3784, A3785, A3786, C309, C310 G:A2592, C:A2591 G:A2592
4tp3 A3089 Ob G:A1125(O6) A3600, A3601, A3602, A3603, A3604 C:A1123, A:A1028 G:A1124
4tp3 B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, A:B94
4tp3 A3101 Ob U:A2419(O4) A3661, A3662, A3663, A3664, 3101 A:A2418 A:A2418
4tp3 A3094 Ob U:A1440(O4) A3626, A3627, A3628, A3629 A:A1439 A:A1551, G:A1441
4tp3 A3022 Ob U:A746(O4) A3304, A3305, A3306, D301, D302 U:A744, U:A2580, C:A2611, C:A2610
4tp3 A3045 Nb G:A1358(N7) A3399, A3400, A3401, A3402 G:A1358, C:A1357, C:A1370 G:A1371
4tp3 A3020 2Nb G:A733(N7), A:A761(N7) A3294, A3295, A3296, A3297 A:A761, G:A733, G:A760, C:A732
4tp3 A3078 Oph A:A299(OP2) A3549, A3550, A3551, A3552, U201 U:A339, A:A300, G:A338
4tp3 A3053 Oph A:A1678(OP2) A3435, A3436, A3437, A3438, A3439 A:A1679
4tp3 A3060 Oph·Pout C:A2025(OP2) A3469, A3470, A3471, A3472, A3473 U:A2034 A:A2033 C:A2025
4tp3 A3050 Oph·Pout A:A1664(OP2) A3420, A3421, A3422, A3423, A3424 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666
4tp3 A3036 Oph·Pout A:A1156(OP2) A3362, A3363, A3364, A3365, A3366 A:A1155 G:A997
4tp3 A3081 Oph·Pout A:A572(OP1) A3561, A3562, A3563, A3564, A3565 A:A983 U:A573
4tp3 A3004 Oph·Pout U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A122 G:A123, G:A121, G:A122
4tp3 B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B73 A:B101, G:B102
4tp3 A3091 Oph·Pout G:A1360(OP2) A3610, A3611, A3612, A3613 A:A1359 G:A1361
4tp3 A3100 Oph·Pout U:A2022(OP1) A3656, A3657, A3658, A3659, A3660 C:A2023 A:A529 A:A529
4tp3 A3033 Oph·Pout A:A945(OP1) A3350, A3351, A3352, A3353, A3354 G:A831 G:A831, U:A832
4tp3 A3005 Oph·Pout U:A120(OP1) A3218, A3219, A3220, A3221, A3222 A:A119 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].

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>