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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 4dha



4DHA (3.2Å) -- RIBOSOME : Crystal structure of yaej bound to the 70s ribosome
List of all 127 Mg2+ binding sites in the PDB structure 4dha 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
4dha A3800 Or A:A670(O2') A5086, A5087, A5088, A5089 C:A671, G:A666 U:A667, G:A668
4dha A3843 Ob G:A1814(O6) A5242, A5243, A5244, A5245 G:A1813, A:A1812 A:A1812, G:A1813
4dha A3691 Ob U:A2593(O4) A4707, A4708, A4709, A4710, A4711 C:A2591, G:A2592 G:A2599, G:A2592, A:A1971
4dha A3715 Ob G:A2371(O6) A4781, A4782, A4783, A4784 G:A2372, G:A2345
4dha A3683 Nb G:A307(N7) A4684, A4685, A4686, A4687 G:A309, U:A306, G:A307
4dha A3721 Nb G:A2353(N7) A4794, A4795, A4796, A4797 A:A2352 G:A2354
4dha A3674 Nb G:A2032(N7) A4646, A4647, A4648, A4649, A4650 G:A2032 C:A2055, A:A2572, G:A2454, C:A2499, U:A2500, A:A2453
4dha A3554 Nb G:A2002(N7) A4221, A4222, A4223, A4224 A:A2001, G:A2003
4dha A3677 Ob·Nb G:A2685(N7) A4663, A4664, A4665, A4666 G:A2686, U:A2684
4dha A3507 Ob·Nb G:A2303(O6) A4088, A4089, A4090, A4091 G:A2302
4dha A3815 2Nb G:A733(N7), A:A761(N7) A5142, A5143, A5144 C:A732, A:A761
4dha A3561 Oph C:A574(OP1) A4242, A4243, A4244, A4245, A4246 G:A2035
4dha A3695 Oph A:A800(OP1) A4720, A4721, A4722, A4723 A:A191, C:A192, A:A800
4dha A3667 Oph G:A2035(OP1) A4619, A4620, A4621, A4622 G:A2024, C:A2025, G:A2037, G:A2038
4dha A3584 Oph·Pout A:A1495(OP2) A4319, A4320, A4321, A4322 A:A1494 A:A1495, A:A1496
4dha A3651 Oph·Pout G:A2251(OP1) A4550, A4551, A4552, A4553, A4554 G:A2252 U:A2249 G:A2252, G:A2253
4dha A3648 Oph·Pout C:A1327(OP2) A4538, A4539, A4540, A4541, A4542 U:A1326 G:A1324
4dha A3645 Oph·Pout U:A72(OP1) A4524, A4525, A4526, X201 A:A71 A:A71, U:A112
4dha A3617 Oph·Pout G:A2719(OP2) A4432, A4433, A4434, A4435 U:A2687 U:A2688
4dha A3614 Oph·Pout C:A2254(OP2) A4421, A4422, A4423, A4424 G:A2255 G:A2256, G:A2255

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].

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