`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3i20:A2925, See in JSmolMgRNA representative site for type OB Click on the image to toggle views


Site type: Ob

Schematic drawing for
Ob
MgRNA type OB
List of all 468 Mg2+ binding sites with the site type Ob 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 9 of 19 | | | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2i2t B2936 Ob U:B746(O4) B3175, B3176, B3177, B3178, B3179 C:B2610, C:B2611, U:B744 G:B745
1vs6 B2936 Ob U:B746(O4) B3169, B3170, B3171, B3172, B3173 U:B744, C:B2611, C:B2610 G:B745
2qbi B2936 Ob U:B746(O4) B3166, B3167, B3168, B3169, D210 C:B2610, C:B2611, U:B744 G:B745
2qov B2936 Ob U:B746(O4) B3167, B3168, B3169, B3170, B3171 U:B744, C:B2610, C:B2611
2qoz B2936 Ob U:B746(O4) B3660, B3661, B3662, B3663, D3170 U:B744, C:B2610, C:B2611, U:B2580
2z4l B2937 Ob U:B746(O4) B3166, B3167, B3168, B3169, D210 C:B2610, C:B2611, U:B744 G:B745
2aw4 B2939 Ob C:B2499(O2) B3180, B3181, B3182, B3183, B3184 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2i2t B2939 Ob C:B2499(O2) B3190, B3191, B3192, B3193, B3194 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454
1vs6 B2939 Ob C:B2499(O2) B3184, B3185, B3186, B3187, B3188 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qbi B2939 Ob C:B2499(O2) B3180, B3181, B3182, B3183, B3184 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qov B2939 Ob C:B2499(O2) B3182, B3183, B3184, B3185, B3186 G:B2032 C:B2055, U:B2500, G:B2454, G:B2032
2qoz B2939 Ob C:B2499(O2) B3674, B3675, B3676, B3677, B3678 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2z4l B2940 Ob C:B2499(O2) B3180, B3181, B3182, B3183, B3184 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2aw4 B2946 Ob G:B2304(O6) B3207, B3208, B3209, B3210, B3211 G:B2303
2i2t B2946 Ob G:B2304(O6) B3217, B3218, B3219, B3220, B3221 A:B2311, C:B2310 U:B2302, G:B2303
1vs6 B2946 Ob G:B2304(O6) B3211, B3212, B3213, B3214, B3215 G:B2303
1vs8 B2962 Ob G:B2304(O6) B3295, B3296, B3297, B3298, B3299 A:B2311, C:B2310
2awb B2963 Ob G:B2304(O6) B3298, B3299, B3300, B3301, B3302 C:B2310
2i2v B2963 Ob G:B2304(O6) B3305, B3306, B3307, B3308, B3309 C:B2310 U:B2302
2qbg B2964 Ob G:B2304(O6) B3306, B3307, B3308, B3309, B3310 G:B2308 U:B2302, G:B2303
1vs8 B2970 Ob U:B746(O4) B3339, B3340, B3341, B3342, B3343 U:B744, C:B2610, C:B2611
2awb B2971 Ob U:B746(O4) B3340, B3341, B3342, B3343, B3344 U:B744, C:B2610, C:B2611
2i2v B2971 Ob U:B746(O4) B3349, B3350, B3351, B3352, D854 C:B2610, C:B2611, U:B744 G:B745
2qbg B2972 Ob U:B746(O4) B3350, B3351, B3352, B3353, D408 C:B2611, U:B744 G:B745
2qp1 B2972 Ob U:B746(O4) B3853, B3854, B3855, B3856, D408 U:B744, C:B2610, C:B2611

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>