`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON
Representative site 3r8s:A2932, See in JSmolMgRNA representative site for type OP-NB Click on the image to toggle views


Site type: Oph·Nb

Schematic drawing for
Oph·Nb
MgRNA type OP-NB
List of all 134 Mg2+ binding sites with the site type Oph·Nb 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 3 of 6 | | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qbi B2963 Oph·Nb U:B810(OP1) A:B1253(N7) B3291, B3292, B3293, B3294 U:B811 C:B565
2qbi B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3501, B3502, B3503, L610 G:B1190
2qbk B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3504, B3505, B3506, B3507 U:B1188, G:B1190
2qbk B2948 Oph·Nb U:B810(OP1) A:B1253(N7) B3225, B3226, B3227, B3228 U:B811 C:B565
2qov B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3506, B3507, L3502, L3503 G:B1190
2qov B2963 Oph·Nb U:B810(OP1) A:B1253(N7) B3295, B3296, B3297, B3298 U:B811 C:B565
2qox B2948 Oph·Nb U:B810(OP1) A:B1253(N7) B3226, B3227, B3228, B3229 U:B811 C:B565
2qoz B2963 Oph·Nb U:B810(OP1) A:B1253(N7) B3785, B3786, B3787, B3788 U:B811 C:B565
2qoz B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3996, B3997, B3998, L3504 U:B1188, G:B1190
2qp1 B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B4014, B4015, B4016, B4017 U:B1188
2qp1 B2948 Oph·Nb U:B810(OP1) A:B1253(N7) B3732, B3733, B3734, B3735 U:B811 C:B565
2z4l B3014 Oph·Nb A:B1189(OP2) G:B1190(N7) B3504, B3505, B3506, B3507 U:B1188, G:B1190
2z4l B2964 Oph·Nb U:B810(OP1) A:B1253(N7) B3293, B3294, B3295, B3296 U:B811 C:B565
2z4n B3014 Oph·Nb A:B1189(OP2) G:B1190(N7) B3509, B3510, B3511, L146 U:B1188, G:B1190
2z4n B2949 Oph·Nb U:B810(OP1) A:B1253(N7) B3228, B3229, B3230, B3231 U:B811 C:B565
3df2 B3344 Oph·Nb U:B810(OP1) A:B1253(N7) B4345, B4346, B4347, B4348 U:B811 C:B565
3df4 B3609 Oph·Nb A:B1189(OP2) G:B1190(N7) B4610, B4613, L4611, L4612 U:B1188
3df4 B3257 Oph·Nb U:B810(OP1) A:B1253(N7) B4258, B4259, B4260, B4261 U:B811 C:B565
3i1p A2911 Oph·Nb A:A453(OP1) G:A450(N7) A3077, A3078, A3079, A3080 A:A449 A:A449
3i1p A2975 Oph·Nb G:A2269(OP1) A:A2267(N7) A3372, A3373, A3374, A3375 G:A2271
3i1r A2932 Oph·Nb U:A810(OP1) A:A1253(N7) A3175, A3176, A3177, A3178 U:A811 C:A565
3i20 A2932 Oph·Nb U:A810(OP1) A:A1253(N7) A3176, A3177, A3178, A3179 U:A811 C:A565
3i22 A2974 Oph·Nb G:A2269(OP1) A:A2267(N7) A3374, A3375, A3376, A3377 G:A2269, G:A2271
3i22 A2911 Oph·Nb A:A453(OP1) G:A450(N7) A3075, A3076, A3077, A3078 A:A449 A:A449
3oas A2911 Oph·Nb A:A453(OP1) G:A450(N7) A3074, A3075, A3076, A3077 A:A449 A:A449

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>