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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
2qbc B3504 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B4029, B4030, B4031 U:B762, G:B763
2qbc B3409 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3954, B3955, B3956
2qbc B3528 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B4047, B4048, B4049 C:B2507
2qbd A2060 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A2061, A2062, A2063 A:A1196
2qbd A2284 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A2285, A2286, A2287 G:A1504, U:A1498 A:A1500
2qbe B3028 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3636, B3637, B3638
2qbe B3476 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3998, B3999, B4000 U:B2449 A:B2497
2qbe B3512 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B4025, B4026, B4027 C:B2507
2qbe B3217 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3788, B3789, B3790 C:B1306
2qbe B3488 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B4007, B4008, B4009 U:B762, G:B763
2qbf A1592 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A1850, A1851, A1852 U:A1498, G:A1504 A:A1500
2qbf A1555 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A1664, A1665, A1666 A:A1196
2qbg B2988 fac-3Oph A:B2448(OP2), C:B2498(OP2), C:B2499(OP2) B3419, B3420, B3421 U:B2449 G:B2447, A:B2497
2qbg B2973 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3354, B3355, C412
2qbg B2978 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3375, B3376, B3377 C:B1306
2qbg B2991 fac-3Oph A:B730(OP2), C:B731(OP2), A:B761(OP1) B3428, B3429, B3430 U:B762, G:B763
2qbh A1590 fac-3Oph A:A1499(OP2), A:A1500(OP2), G:A1505(OP2) A1829, A1830, A1831 G:A1504, U:A1498 A:A1500
2qbi B2909 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3039, B3040, B3041
2qbi B2941 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3189, B3190, B3191 C:B1306
2qbi B2995 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3427, B3428, B3429 C:B2507
2qbj A1555 fac-3Oph C:A1054(OP1), A:A1197(OP1), G:A1198(OP2) A1664, A1665, A1666 A:A1196
2qbk B2997 fac-3Oph C:B2573(OP1), G:B2574(OP1), C:B2575(OP2) B3442, B3443, B3444 C:B2507
2qbk B2978 fac-3Oph A:B1395(OP1), A:B1603(OP1), C:B1604(OP2) B3372, B3373, B3374 C:B1306
2qbk B2973 fac-3Oph A:B783(OP2), G:B784(OP2), A:B2589(OP1) B3350, B3351, B3352
2qex 08006 fac-3Oph U:0821(OP2), C:0822(OP2), G:0854(OP1) 03443, 03580, 09639 U:0855, G:0856

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>