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 A8112 Nb A:A187(N1) A3718, A3759, A9126, A9325, A9561 U:A207, C:A155 G:A206 C:A438, C:A188
1nji A8111 Nb G:A2609(N7) A3297, A3688, A3712, A5600, A5748 G:A2609 U:A2610, G:A2606
1nji A8075 2Or A:A907(O2'), A:A908(O4') A3630, A3907, A4930, A7828 U:A1270 A:A1328, A:A907
1nji A8097 2Ob G:A863(O6), U:A864(O4) A3336, A3664, A3668, A5551 G:A782, U:A862
1nji A8051 Oph·Pout G:A641(OP2) A4094, A7812, A7813 A:A1355 A:A1355, G:A642, G:A641
1nji A8083 Oph·Pout A:A1754(OP2) A3698, A4142, A6356, A7839, A7895 C:A1753 A:A1755, A:A1754
1nji A8039 Oph·Pout U:A115(OP2) A3956, A5094, A7807, A7808, A9904 G:A112 A:A119, G:A118, A:A117
1nji A8019 Oph·2Pout A:A2011(OP2) A4141, A7233, A7774, A7775, A7776 A:A1941, G:A1891 U:A1890 G:A1891, C:A1892
1nji A8068 Oph·2Pout A:A2568(OP2) A3743, A4815, A6222, A7887, A9728 A:A2569, G:A2567 A:A2569, A:A2568
1nji A8052 Oph·2Pout U:A1125(OP1) A3617, A7883, B8389, B8418 C:A1126, G:B3092 C:A1129, G:B3090
1nji A8040 Oph·2Pout U:A392(OP2) A3780, A4637, A7860, A7861, A9682 U:A391, C:A171
1nji A8037 Oph·3Pout A:A2553(OP2) A3132, A3206, A3641, A7858, A9079 C:A2575, A:A2576, U:A2554 C:A2552 A:A2576
1nji A8032 Oph·3Pout U:A2115(OP1) A3716, A3779, A4181, A9984, C8629 U:A2116, G:A2272, C:A2273
1nji A8072 Oph·3Pout U:A954(OP1) A3228, A3987, A7412, A7829, A7888 C:A2298, G:A2299, A:A2301
1nji A8021 Oph·3Pout G:A2304(OP2) A3631, A3632, A7761, A7762, A9958 A:A2301, A:A2305, A:A2303 A:A2305, G:A2304, U:A2306
1nji A8035 Oph·4Pout G:A1484(OP2) A3707, A7800, A7801, A7856, A7857 C:A1456, C:A1483, A:A1485, C:A1455 G:A1484, U:A1457
1nji A8060 Oph·5Pout G:A175(OP2) A7818, A7819, A7820, A9167 C:A173, G:A225, U:A172, G:A393, U:A392
1nji A8091 Oph·5Pout G:A918(OP1) A3321, A6484, A7844, A9093, A9539 G:A2293, C:A2294, C:A2391, A:A2465, U:A919 A:A2465
1nji A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3865, A4005, A4146, N8641 G:A267, U:A268
1nji A8004 Oph·Ob A:A459(OP1) G:A456(O6) A3773, A7754, A9048, A9772 A:A455, A:A460, A:A477 A:A455

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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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