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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 1yhq:08001, See in JSmolMgRNA representative site for type fac-3OP Click on the image to toggle views


Site type: fac-3Oph

Schematic drawing for
fac-3Oph
MgRNA type fac-3OP
List of all 392 Mg2+ binding sites with the site type fac-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"
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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
1vs8 B2995 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3438, B3439, B3440 C:B2507
1vs8 B2971 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3344, B3345, C454
1vs8 B2986 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3411, B3412, B3413 U:B2449 G:B2447, A:B2497
1vt2 A2952 fac-3Oph A:A1395(OP1), A:A1603(OP1), C:A1604(OP2) A3263, A3264, A3265 C:A1306
1yhq 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04163, A8980, A8999
1yhq 08019 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08308, 08309, 09894 C:02542
1yhq 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 04111, 08293, 09675 U:02484 A:02532, G:02482
1yi2 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07754, 07755, 09395 C:02542
1yi2 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03613, 07737, 09174 U:02484 G:02482, A:02532
1yi2 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03743, 07740, 07741
1yi2 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03663, A8811, A8832
1yij 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03755, 07752, 07753
1yij 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03675, 09020, A8830
1yij 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07766, 07767, 09397 C:02542
1yij 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03625, 07749, 09178 U:02484 G:02482, A:02532
1yj9 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03430, 07562, 08998 U:02484 G:02482, A:02532
1yj9 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07579, 07580, 09212 C:02542
1yj9 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03482, 08843, 09647
1yj9 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03560, 07565, 07566
1yjn 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07778, 07779, 09396 C:02542
1yjn 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03679, 09020, 09832
1yjn 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03626, 07761, 09177 U:02484 G:02482, A:02532
1yjn 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 07764, 07765
1yjw 78006 fac-3Oph U:0821(OP2), C:0822(OP2), G:0854(OP1) 05832, 05945, 05951 G:0856, U:0855
1yjw 78001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 09077, 09083, 09181 U:02484 G:02482, A:02532

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>