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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 4tpb



4TPB (2.8Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to dalfopristin and quinupristin. this file contains the 50s subunit of the second 70s ribosome with dalfopristin and quinupristin bound.
List of all 127 Mg2+ binding sites in the PDB structure 4tpb 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
4tpb A3089 Ob G:A1125(O6) A3600, A3601, A3602, A3603, A3604 A:A1028 G:A1124
4tpb A3022 Ob U:A746(O4) A3305, A3306, A3307, D301, D302 U:A744, U:A2580, C:A2611, C:A2610
4tpb B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, A:B94
4tpb A3132 Ob U:A2593(O4) A3785, A3786, A3787, A3788, C308 G:A2592, C:A2591 G:A2592
4tpb A3101 Ob U:A2419(O4) A3661, A3662, A3663, A3664, 3101 A:A2418
4tpb A3029 Nb A:A1253(N7) A3333, A3334, A3335, A3336 U:A810, U:A811 C:A565
4tpb A3045 Nb G:A1358(N7) A3399, A3400, A3401, A3402 C:A1357, G:A1358, C:A1370 G:A1371
4tpb A3020 2Nb G:A733(N7), A:A761(N7) A3295, A3296, A3297, A3298 A:A761, G:A733, G:A760, C:A732
4tpb A3078 Oph A:A299(OP2) A3549, A3550, A3551, A3552, U201 U:A339, A:A300, G:A338
4tpb A3053 Oph A:A1678(OP2) A3435, A3436, A3437, A3438, A3439 A:A1679
4tpb A3060 Oph·Pout C:A2025(OP2) A3469, A3470, A3471, A3472, A3473 U:A2034 A:A2033
4tpb A3050 Oph·Pout A:A1664(OP2) A3420, A3421, A3422, A3423, A3424 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666
4tpb A3036 Oph·Pout A:A1156(OP2) A3362, A3363, A3364, A3365, A3366 A:A1155 G:A1157, G:A997
4tpb A3081 Oph·Pout A:A572(OP1) A3561, A3562, A3563, A3564, A3565 A:A983 U:A573
4tpb A3033 Oph·Pout A:A945(OP1) A3350, A3351, A3352, A3353, A3354 G:A831 G:A831, U:A832
4tpb B203 Oph·Pout G:B100(OP2) B309, B310, B311, B312, B313 A:B73 A:B101, G:B102
4tpb A3127 Oph·Pout A:A1676(OP2) A3762, A3763, A3764, A3765, A3766 C:A1675 A:A1676, A:A1677
4tpb A3100 Oph·Pout U:A2022(OP1) A3656, A3657, A3658, A3659, A3660 C:A2023 A:A529 A:A529
4tpb A3091 Oph·Pout G:A1360(OP2) A3610, A3611, A3612, A3613 A:A1359 G:A1361
4tpb A3005 Oph·Pout U:A120(OP1) A3218, A3219, A3220, A3221, A3222 A:A119 G:A124

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>