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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 1nji



1NJI (3Å) -- RIBOSOME : Structure of chloramphenicol bound to the 50s ribosomal subunit
List of all 54 Mg2+ binding sites in the PDB structure 1nji 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
1nji A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3626, A3949, A6173, A9389 G:A1490, A:A1487, U:A1488 G:A1489, G:A1490
1nji A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3917, A5399, A6031, A9501 U:A904 G:A622, A:A1356
1nji A8074 cis-2Oph A:A1286(OP1), A:A1287(OP1) A7826, A7827, A7889, A7890 A:A1287
1nji A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3216, A3606, A7462, A7851 C:A910, U:A909 G:A911, G:A1292
1nji A8022 cis-2Oph G:A2097(OP2), G:A2540(OP1) A3862, A7766, A9110, A9450 A:A2095 A:A2096 G:A2097
1nji A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3621, A3811, A7782, A7783 G:A2616 G:A2618
1nji A8048 cis-2Oph A:A2746(OP2), G:A2750(OP2) A5876, A6262, A7868, A7906 C:A2745, U:A2749
1nji A8061 cis-2Oph A:A1369(OP2), U:A2650(OP1) A7821, A7822, A7823, A9814 A:A2649 U:A1371
1nji A8080 cis-2Oph A:A1684(OP2), U:A1724(OP2) A4197, A4483, A7838, A7894 C:A1431 A:A1684, A:A1691 U:A1722, A:A1691
1nji A8086 cis-2Oph A:A532(OP1), U:A533(OP1) A3724, A3966, A7841, A7842 C:A534 A:A2814, U:A10
1nji A8107 cis-2Oph A:A1106(OP2), A:A1107(OP2) A7871, A7872, A7873, A7874 C:A1103, C:A1104 A:A1107
1nji A8077 trans-2Oph C:A880(OP1), U:A883(OP2) A3616, A7836, A7837, A9238 A:A882, C:A884 U:A883, A:A1836
1nji A8002 cis-2Oph·Ob A:A2483(OP1), C:A2534(OP1) G:A627(O6) A4314, A7747, A7748 U:A2535 U:A625 U:A626
1nji A8089 cis-2Oph·Nb A:A516(OP1), U:A517(OP2) G:A518(N7) A7843, A7896, A7897 C:A515
1nji A8003 fac-3Oph A:A876(OP2), G:A877(OP2), A:A2624(OP1) A3659, A9820, C8511
1nji A8016 fac-3Oph A:A1504(OP1), A:A1678(OP1), C:A1679(OP2) A3738, A7772, A7773
1nji A8026 fac-3Oph C:A2608(OP1), G:A2609(OP1), U:A2610(OP2) A7786, A7787, A9387 C:A2542
1nji A8007 mer-3Oph U:A832(OP2), A:A1839(OP1), A:A1840(OP2) A3353, A7759, A9007
1nji A8008 mer-3Oph U:A919(OP1), C:A2464(OP1), A:A2465(OP1) A3623, A7763, A7849 G:A2466
1nji A8081 mer-3Oph C:A1420(OP1), C:A1421(OP2), G:A1438(OP1) A4089, A9603

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/)
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