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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 1k73




1K73 (3.01Å) -- RIBOSOME : Co-crystal structure of anisomycin bound to the 50s ribosomal subunit
List of all 55 Mg2+ binding sites in the PDB structure 1k73 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"
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Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1k73 A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3219, A3609, A7481, A7870 C:A910, U:A909 G:A911, G:A1292
1k73 A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3622, A3814, A7803, A7804 G:A2616 G:A2618
1k73 A8030 cis-2Oph U:A1748(OP1), U:A1749(OP2) A3635, A7778, A7779, A7789 G:A2585, G:A2584
1k73 A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5882, A6270, A7887, A7923 C:A2745, U:A2749
1k73 A8052 cis-2Oph U:A1125(OP1), G:B3092(OP1) A3618, A7902, B8390, B8418 C:A1126 C:A1129, G:B3090
1k73 A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7840, A7841, A7842, A9818 A:A2649 U:A1371
1k73 A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A4201, A4488, A7857, A7910 C:A1431 A:A1691, C:A1692 U:A1722, A:A1691
1k73 A8086 cis-2Oph A:A532(OP1), U:A533(OP1) A3728, A3972, A7860, A7861 C:A534 A:A2814, U:A10
1k73 A8107 cis-2Oph A:A1106(OP2), A:A1107(OP2) A7890, A7891, A7892, A7893 C:A1103, C:A1104 A:A1107
1k73 A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3617, A7855, A7856, A9239 A:A882, C:A884 U:A883, A:A1836
1k73 A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4319, A7769, A7770 U:A625 U:A626
1k73 A8079 cis-2Oph·Nb A:A167(OP1), C:A168(OP2) A:A165(N7) A3606, A3612, A3623 G:A164, A:A165 G:A164
1k73 A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7862, A7912, A7913
1k73 A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3741, A7794, A7795
1k73 A8001 fac-3Oph A:A2483(OP2), C:A2533(OP2), C:A2534(OP2) A3611, A7791, A9176 U:A2484 A:A2532, G:A2482 G:A2482
1k73 A8006 fac-3Oph U:A821(OP2), C:A822(OP2), G:A854(OP1) A3613, A3748, A9808 G:A856, U:A855
1k73 A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3661, C8511, C8534
1k73 A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A4095, A9610
1k73 A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3624, A7785, A7868 G:A2466, G:A2293
1k73 A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3355, A7781, A9006 G:A833

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>