`

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 8 of 19 | | | 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
3ofc A2973 Ob C:A2499(O2) A3369, A3370, A3371, A3372, A3373 G:A2032 G:A2454 C:A2055, U:A2500, G:A2032, G:A2454
3ofc A3034 Ob U:A2593(O4) A3628, A3629, A3630, A3631, C767 G:A2592, C:A2594, G:A2599
3ofd A3013 Ob U:A1602(O4) A3540, A3541, A3542, T640 G:A1601, C:A1600, A:A1342 C:A1600
3ofd A2926 Ob U:A746(O4) A3151, A3152, A3153, A3154, A3155 U:A744, C:A2611, C:A2610 G:A745
3ofd A2994 Ob G:A1125(O6) A3466, A3467, A3468, A3469, A3470 A:A1028
3ofd A2999 Ob U:A2419(O4) A3491, A3492, A3493, A3494, 3571
3ofd A3032 Ob U:A2593(O4) A3617, A3618, A3619, C735, C739 C:A2594, G:A2592
3ofd B590 Ob U:B95(O4) B591, B592, B593, B595, V594 U:B80
3ofo A1567 Ob G:A1108(O6) A1739, A1740, A1741, A1742 C:A1096
3ofp A1553 Ob G:A1417(O6) A1664, A1665, A1666, A1667, A1668 G:A1416 G:A1415, G:A1482
3ofq A3032 Ob U:A2593(O4) A3615, A3616, A3617, C735, C739 G:A2592, C:A2591 G:A2592
3ofq B590 Ob U:B95(O4) B591, B592, B593, V594, V595 U:B80
3ofq A3000 Ob U:A2419(O4) A3492, A3493, 3568, 3570, 3571
3ofq A2927 Ob U:A746(O4) A3150, A3151, A3152, A3153, A3154 U:A2580, C:A2611, C:A2610, U:A744 G:A745
3ofr A3003 Ob U:A2419(O4) A3504, A3505, A3506, 3574, 3577 A:A2418
3ofr A2925 Ob U:A746(O4) A3140, A3141, A3142, A3143, A3144 C:A2611, U:A744, C:A2610 G:A745
3ofr A2991 Ob G:A1125(O6) A3443, A3444, A3445, A3446, A3447 A:A1028
3ofr B609 Ob U:B95(O4) B610, B611, B612, B613, V614 U:B80, G:B96
3ofr A2975 Ob C:A2499(O2) A3372, A3373, A3374, A3375, A3376 G:A2032 G:A2454 U:A2500, G:A2032, G:A2454, C:A2055
3ofy A1536 Ob G:A362(O6) A1584, A1585, A1586, A1587, A1588 G:A361
3ofy A1553 Ob G:A1417(O6) A1667, A1668, A1669, A1670, A1671 G:A1416 G:A1415
3ofz B609 Ob U:B95(O4) B610, B611, B612, B613, B614 U:B80, G:B96
3ofz A3033 Ob U:A2593(O4) A3618, A3619, A3620, C760, C762 G:A2592, C:A2594, G:A2599
3ofz A2973 Ob C:A2499(O2) A3364, A3365, A3366, A3367, A3368 G:A2032 G:A2454 C:A2055, U:A2500, G:A2032, G:A2454
3ofz A3001 Ob U:A2419(O4) A3496, A3497, A3498, 3574, 3578 A:A2418

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>