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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 1q7y



1Q7Y (3.2Å) -- RIBOSOME : Crystal structure of ccdap-puromycin bound at the peptidyl transferase center of the 50s ribosomal subunit
List of all 38 Mg2+ binding sites in the PDB structure 1q7y 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
1q7y A8113 Nb A:A2112(N7) A3262, A3433, A5625, A5890 A:A2112, G:A2111
1q7y A8051 Oph·Pout G:A641(OP2) A3610, A7292, A7293 A:A1355 G:A642, G:A641
1q7y A8083 Oph·Pout A:A1754(OP2) A3216, A3659, A5845, A7319, A7369 C:A1753 A:A1755, A:A1754
1q7y A8084 Oph·Pout A:A1742(OP2) A3145, A7320, A8768, A8888, A9267 G:A2033 G:A1744, G:A1745, A:A1742, G:A1743, G:A2033
1q7y A8019 Oph·Pout A:A2011(OP2) A3658, A6726, A7257, A7258, A7259 A:A1941 C:A1940, U:A1890 G:A1891, C:A1892
1q7y A8020 Oph·2Pout C:A1830(OP1) A7241, A7260, A8643, A8646, A8714 U:A1831, A:A1842 G:A1828 G:A1828, G:A1832
1q7y A8068 Oph·2Pout A:A2568(OP2) A3261, A4324, A5714, A7364, G920 A:A2569, G:A2567 A:A2569, A:A2568
1q7y A8092 Oph·2Pout C:A1844(OP2) A3155, A3169, A7372 A:A1843, A:A1845
1q7y A8021 Oph·3Pout G:A2304(OP2) A3149, A7244, A7245, A9479 A:A2305, A:A2303, A:A2301 A:A2305, G:A2304, U:A2306
1q7y A8032 Oph·3Pout U:A2115(OP1) A3235, A3296, A3696, A9506, C8629 U:A2116, G:A2272, C:A2273
1q7y A8035 Oph·3Pout G:A1484(OP2) A3225, A7280, A7281, A7336, A7337 C:A1455, C:A1456, A:A1485 C:A1483 G:A1484, U:A1457
1q7y A8040 Oph·3Pout U:A392(OP2) A3297, A7340, A7341, A9208 C:A171, U:A172, U:A391
1q7y A8058 Oph·3Pout G:A2013(OP2) A3272, A7296, A7297, C8630, C8632 G:A1884, U:A1883, C:A2626
1q7y A8027 Oph·Ob C:A240(OP1) G:A269(O6) A3382, A3520, A3663, A7334 G:A267, U:A268
1q7y A8028 Oph·Ob A:A1448(OP2) U:A1677(O4) A3186, A3208, A3220, T8317 G:A1676
1q7y A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3435, A4901, A5528, A9025 U:A904 G:A622, A:A1356
1q7y A8023 cis-2Oph G:A2617(OP2), G:A2618(OP2) A3137, A3328, A7264, A7265 G:A2616 G:A2618, U:A2619
1q7y A8013 cis-2Oph G:A877(OP1), G:A2623(OP1) A3152, A3163, A8541, C8628 C:A2475, A:A2624 G:A885
1q7y A8014 cis-2Oph G:A2102(OP2), G:A2537(OP2) A3168, A3671, A7228, A8555 G:A2481 G:A2102, C:A2536, A:A2101 G:A2480, G:A2481, A:A2101
1q7y A8018 cis-2Oph A:A1291(OP1), G:A1292(OP2) A3124, A6951, A7331, A9732 C:A910, U:A909 G:A1292, G:A911

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].

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