`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
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"
Page 8 of 16 | | | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2i2v B2987 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3420, B3421, B3422 U:B2449 G:B2447, A:B2497
2i2v B2972 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3353, B3354, B3355
2otj 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03633, 07774, 09179 U:02484 G:02482, A:02532
2otj 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03765, 07777, 07778
2otj 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07789, 07790, 09402
2otj 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03684, 09838, A8811
2otl 08003 fac-3Oph A:0876(OP2), G:0877(OP2), A:02624(OP1) 03677, 09021, A8732
2otl 08001 fac-3Oph A:02483(OP2), C:02533(OP2), C:02534(OP2) 03627, 07760, 09173 U:02484 G:02482, A:02532
2otl 08016 fac-3Oph A:01504(OP1), A:01678(OP1), C:01679(OP2) 03757, 07763, 07764
2otl 08026 fac-3Oph C:02608(OP1), G:02609(OP1), U:02610(OP2) 07776, 07777, 07778 C:02542
2qal A2060 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A2061, A2062, A2063 A:A1196
2qal A2284 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A2285, A2286, A2287 G:A1504 A:A1499, A:A1500
2qam B3488 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B4010, B4011, B4012 U:B762, G:B763
2qam B3512 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B4028, B4029, B4030 C:B2507
2qam B3217 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3787, B3788, B3789 C:B1306
2qan A2073 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A2074, A2075, A2076 A:A1196
2qan A2302 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A2303, A2304, A2305 G:A1504
2qao B3409 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3956, B3957, C412
2qao B3492 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B4020, B4021, B4022 U:B2449 G:B2447, A:B2497
2qao B3504 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B4029, B4030, B4031 U:B762, G:B763
2qao B3528 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B4047, B4048, B4049 C:B2507
2qba B3217 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3789, B3790, B3791 C:B1306
2qba B3488 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B4007, B4008, B4009 U:B762, G:B763
2qba B3512 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B4025, B4026, B4027 C:B2507
2qbb A2073 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A2430, A2431, A2432 A:A1196

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>