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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 1vqo:08005, See in JSmolMgRNA representative site for type mer-3OP Click on the image to toggle views


Site type: mer-3Oph

Schematic drawing for
mer-3Oph
MgRNA type mer-3OP
List of all 430 Mg2+ binding sites with the site type mer-3Oph in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
Page 4 of 18 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
1vq7 08007 mer-3Oph U:0832(OP2), A:01839(OP1), A:01840(OP2) 03679, 07976, 09328 G:0833
1vq7 48119 mer-3Oph A:02637(OP1), A:4176(OP1), C:4175(OP1) 08231, 47911, 47912 U:02620, C:02636 A:02474
1vq7 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 03935, 07987, 07988 G:01837 A:01839
1vq8 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04205, 08305, 08306 G:01837 A:01839
1vq9 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04174, 08202, 08203 G:01837 A:01839
1vqk 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04216, 08345, 08346 G:01837 A:01839
1vql 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04205, 08310, 08311 G:01837 A:01839
1vqm 08118 mer-3Oph A:02637(OP1), DA:4179(OP1), C:4180(OP1) 08448, 08449, 47911 C:02636, U:02620 A:02474
1vqm 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04212, 08311, 08312 G:01837 A:01839
1vqn 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04208, 08302, 08303 G:01837 A:01839
1vqo 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04227, 08357, 08358 G:01837 A:01839
1vqp 08008 mer-3Oph U:0919(OP1), C:02464(OP1), A:02465(OP1) 04241, 08322, 08404 G:02466, C:0920
1vqp 08118 mer-3Oph A:02637(OP1), A:4176(OP1), C:4175(OP1) 08474, 08475, 47923 C:02636, U:02620 A:02474
1vqp 08005 mer-3Oph A:01836(OP1), U:01838(OP1), A:01839(OP2) 04223, 08329, 08330 G:01837 A:01839
1vs5 A1595 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1853, A1854, A1855 A:A288 G:A117, U:A118
1vs5 A1552 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1646, A1647, A1648 C:A1501, G:A1504
1vs5 A1547 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1621, A1622, A1623 U:A571 A:A574
1vs6 B2990 mer-3Oph C:B740(OP2), A:B1783(OP1), A:B1784(OP2) B3416, B3417, B3418 U:B741
1vs6 B3009 mer-3Oph C:B1314(OP1), C:B1315(OP2), G:B1332(OP1) B3491, B3492, B3493
1vs6 B2988 mer-3Oph A:B1780(OP1), U:B1782(OP1), A:B1783(OP2) B3410, B3411, B3412 A:B1783
1vs6 B2964 mer-3Oph U:B827(OP1), G:B2429(OP2), A:B2430(OP2) B3299, B3300, B3301
1vs6 B2928 mer-3Oph C:B948(OP1), G:B962(OP1), U:B963(OP2) B3130, B3131, B3132 A:B947
1vs7 A1560 mer-3Oph A:A1500(OP1), G:A1505(OP1), A:A1508(OP1) A1681, A1682, A1683 C:A1501, G:A1504 U:A1506
1vs7 A1599 mer-3Oph A:A116(OP2), G:A117(OP2), G:A289(OP2) A1873, A1874, A1875 A:A288 G:A117, U:A118
1vs7 A1545 mer-3Oph A:A572(OP2), A:A573(OP2), A:A574(OP2) A1611, A1612, A1613 U:A571 A:A574

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/)
For any help please contact <dust@iwonka.med.virginia.edu>