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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
1vqk 08029 fac-3Oph U:01503(OP1), A:01504(OP2), C:01679(OP1) 08362, 08364
1vqk 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 08357, 08358, 08359 C:02542
1vql 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04257, A9500, A9524
1vql 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 03018, 08322, 08323 C:02542
1vql 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 04208, 08309, 09800 U:02484 A:02532, G:02482
1vqm 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 03022, 08324, 08325
1vqm 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04264, A9500, A9523
1vqn 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 04212, 08301, 09802 U:02484 A:02532, G:02482
1vqn 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04261, A9500, A9524
1vqn 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 03019, 08315, 08316
1vqo 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04283, A9500, A9523
1vqo 08029 fac-3Oph U:01503(OP1), A:01504(OP2), C:01679(OP1) 03837, 08376, 08378
1vqo 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 03025, 08370, 08371 C:02542
1vqp 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 04277, A9500, A9523
1vqp 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 04227, 08328, 09804 U:02484 A:02532, G:02482 G:02482
1vqp 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 03024, 08342, 08343
1vs5 A1554 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A1653, A1654, A1655 A:A1196
1vs5 A1590 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A1830, A1831, A1832 G:A1504, U:A1498 A:A1500
1vs6 B2995 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3431, B3432, B3433 C:B2507
1vs6 B2941 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3193, B3194, B3195 C:B1306
1vs6 B2989 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B3413, B3414, B3415 U:B762, G:B763
1vs6 B2986 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3404, B3405, B3406 A:B2497, G:B2447
1vs7 A1594 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A1850, A1851, A1852 U:A1498, G:A1504 A:A1500
1vs8 B2971 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3344, B3345, C454
1vs8 B2995 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3438, B3439, B3440 C:B2507

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>