MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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List of Mg2+ binding sites in structure 1kd1

1KD1 (3Å) -- RIBOSOME : Co-crystal structure of spiramycin bound to the 50s ribosomal subunit of haloarcula marismortui
List of all 44 Mg2+ binding sites in the PDB structure 1kd1 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
1kd1 A8112 Nb A:A187(N1) A3723, A3764, A9127, A9328, A9561 U:A207, C:A155 G:A206 C:A438, C:A188
1kd1 A8111 Nb G:A2609(N7) A3296, A3693, A3716, A5599, A5747 G:A2609 U:A2610, G:A2606
1kd1 A8039 Oph·Pout U:A115(OP2) A3959, A5105, A7812, A7813, A9900 G:A112 A:A114 A:A119, G:A118, A:A117
1kd1 A8092 Oph·2Pout C:A1844(OP2) A3640, A3656, A7900 A:A1843, A:A1845 A:A1845
1kd1 A8083 Oph·2Pout A:A1754(OP2) A3702, A4145, A6354, A7844, A7897 C:A1753, A:A1755 A:A1755, A:A1754
1kd1 A8068 Oph·2Pout A:A2568(OP2) A3748, A4820, A6219, A7890, A9726 A:A2569, G:A2567 A:A2569, A:A2568
1kd1 A8019 Oph·2Pout A:A2011(OP2) A4144, A7235, A7779, A7780, A7781 A:A1941, G:A1891 U:A1890 G:A1891, C:A1892
1kd1 A8021 Oph·3Pout G:A2304(OP2) A3633, A3634, A7766, A7767, A9954 A:A2301, A:A2303, A:A2305 A:A2305, G:A2304, U:A2306
1kd1 A8072 Oph·3Pout U:A954(OP1) A3231, A3989, A7416, A7834, A7891 C:A2298, G:A2299, A:A2301
1kd1 A8040 Oph·3Pout U:A392(OP2) A3785, A4638, A7864, A7865, A9682 U:A391, C:A171, U:A172
1kd1 A8037 Oph·3Pout A:A2553(OP2) A3131, A3209, A3644, A7862, A9077 C:A2575, A:A2576, U:A2554 C:A2552 A:A2576
1kd1 A8032 Oph·3Pout U:A2115(OP1) A3721, A3784, A4185, A9982, C8633 U:A2116, G:A2272, C:A2273
1kd1 A8012 Oph·4Pout G:A28(OP1) A3226, A3643, A7855, A9037, A9630 C:A1305, U:A1304, C:A1343, G:A1344
1kd1 A8093 Oph·Or G:A1071(OP1) A:A1070(O2') A3646, A3678, A3718, A9674 G:A627 A:A914, A:A913, G:A1071
1kd1 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3866, A4007, A4149, N8648 G:A267, U:A268
1kd1 A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3628, A3952, A6168, A9388 A:A1487, U:A1488 G:A1489, G:A1490
1kd1 A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3920, A5400, A6026, A9501 U:A904 G:A622, A:A1356
1kd1 A8029 cis-2Oph U:A1503(OP1), C:A1679(OP1) A7796, A7797, A7798, A7799 A:A1504
1kd1 A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3219, A3609, A7468, A7856 C:A910, U:A909 G:A911, G:A1292
1kd1 A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3655, A4157, A7750, A9032 C:A2536, A:A2101 G:A2480, G:A2481, A:A2101

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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