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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 1q81



1Q81 (2.95Å) -- RIBOSOME : Crystal structure of minihelix with 3' puromycin bound to a- site of the 50s ribosomal subunit.
List of all 58 Mg2+ binding sites in the PDB structure 1q81 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
1q81 A8112 Nb A:A187(N1) A3240, A3280, A8652, A8847, A9083 U:A207, C:A155 G:A206 C:A438, C:A188
1q81 A8011 2Nb G:A824(N7), G:A854(N7) A3472, A3795, A3926, A4033 G:A854, G:A824, U:A823, C:A853
1q81 A8083 Oph·Pout A:A1754(OP2) A3219, A3661, A5866, A7328, A7380 C:A1753 A:A1755, A:A1754
1q81 A8019 Oph·Pout A:A2011(OP2) A3660, A6726, A7265, A7266, A7267 A:A1941 U:A1890 G:A1891, C:A1892
1q81 A8051 Oph·Pout G:A641(OP2) A3614, A7301, A7302 A:A1355 A:A1355, G:A642
1q81 A8039 Oph·2Pout U:A115(OP2) A4611, A7296, A7297, A9425 G:A112, G:A116 A:A119, G:A118, A:A117
1q81 A8068 Oph·2Pout A:A2568(OP2) A3265, A4330, A5735, A7374, A9248 A:A2569, G:A2567 A:A2569, A:A2568
1q81 A8036 Oph·2Pout G:A956(OP2) A3183, A7291, A7292, A7293, A8881 A:A1006, A:A955 A:A957, G:A956
1q81 A8092 Oph·2Pout C:A1844(OP2) A3158, A3173, A7383 A:A1843, A:A1845 A:A1845
1q81 A8037 Oph·3Pout A:A2553(OP2) A3161, A7347, A8603, A9646, A9725 A:A2576, U:A2554, C:A2575 C:A2552 A:A2576
1q81 A8035 Oph·3Pout G:A1484(OP2) A3228, A7289, A7290, A7345, A7346 C:A1456, A:A1485, C:A1455 G:A1484, U:A1457
1q81 A8032 Oph·3Pout U:A2115(OP1) A3238, A3301, A9504, C8565, C8641 U:A2116, G:A2272, C:A2273 G:A2271
1q81 A8021 Oph·3Pout G:A2304(OP2) A3151, A3152, A7252, A7253, A9479 A:A2301, A:A2305, A:A2303 A:A2305, G:A2304, U:A2306
1q81 A8040 Oph·3Pout U:A392(OP2) A4148, A7349, A7350, A9204 C:A171, U:A172, U:A391
1q81 A8017 Oph·3Pout G:A456(OP2) A3134, A7246, A8926, E8361, E8464 A:A455, U:A457, G:A458
1q81 A8091 Oph·3Pout G:A918(OP1) A5984, A7333, A8617, A9060, A9837 C:A2294, C:A2391, A:A2465 A:A2465
1q81 A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3388, A3524, A3665, A7343 G:A267, U:A268
1q81 A8062 Oph·Ob G:A1489(OP2) G:A1491(O6) A3145, A3471, A5687, A8907 G:A1490, A:A1487 G:A1489, G:A1490
1q81 A8004 Oph·Ob A:A459(OP1) G:A456(O6) A3295, A7245, A8569, A9293 A:A455, A:A460, A:A477 A:A455
1q81 A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3155, A3167, A8541, C8640 C:A2475, A:A2624 G:A885

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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