MgRNA: Classification of Mg2+ binding sites in RNA crystal structures

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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

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"
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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
1jj2 08110 Oph·Nb U:0903(OP1) A:01357(N7) 03453, 04939, 05576, 09028 U:0904 G:0622, A:01356
1k73 A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3922, A5404, A6038, A9508 U:A904 G:A622, A:A1356
1k8a A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3514, A4975, A5603, A9098 U:A904 G:A622
1k9m A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3915, A5401, A6036, A9504 U:A904 G:A622, A:A1356
1kc8 A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3930, A5406, A6029, A9507 U:A904 G:A622, A:A1356
1kd1 A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3920, A5400, A6026, A9501 U:A904 G:A622, A:A1356
1kqs 08110 Oph·Nb U:0903(OP1) A:01357(N7) 03434, 04904, 05533, 09020 U:0904 G:0622, A:01356
1m1k A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3520, A5002, A5635, A9100 U:A904 G:A622, A:A1356
1nji A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3917, A5399, A6031, A9501 U:A904 G:A622, A:A1356
1o3z A307 Oph·Nb A:A8(OP2) G:A9(N7) A501, A577, A600, A614 G:A9 G:A7, G:A10
1o3z B306 Oph·Nb A:B8(OP2) G:B9(N7) B503, B505, B507, B560 G:B9 G:B10
1q7y A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3435, A4901, A5528, A9025 U:A904 G:A622, A:A1356
1q82 A8110 Oph·Nb U:A903(OP1) A:A1357(N7) A3436, A4897, A5517, A9024 U:A904 G:A622, A:A1356
1qvf 08110 Oph·Nb U:0903(OP1) A:01357(N7) 03438, 04886, 05519, 09029 U:0904 G:0622, A:01356
1s72 08109 Oph·Nb U:0903(OP1) A:01357(N7) 03447, 04927, 05558, 09027 U:0904 G:0622, A:01356
1vq8 08110 Oph·Nb U:0903(OP1) A:01357(N7) 04515, 05964, 06570 U:0904 G:0622
1vq8 08084 Oph·Nb A:01742(OP2) G:02033(N7) 03369, 04227, 08370 G:02033 G:01743, G:01744, G:01745, A:01742
1vs6 B2963 Oph·Nb U:B810(OP1) A:B1253(N7) B3295, B3296, B3297, B3298 U:B811 C:B565, G:B1252
1vs6 B3013 Oph·Nb A:B1189(OP2) G:B1190(N7) B3508, B3509, B3510, B3511 U:B1188, G:B1190
1vs8 B3011 Oph·Nb A:B1189(OP2) G:B1190(N7) B3501, B3502, B3503, B3504 U:B1188, G:B1190
1vt2 A2975 Oph·Nb G:A2269(OP1) A:A2267(N7) A3376, A3377, A3378, A3379 A:A2268 G:A2271
1vt2 A2912 Oph·Nb A:A453(OP1) G:A450(N7) A3075, A3076, A3077, A3078 A:A449 A:A449
1y99 A760 Oph·Nb A:A8(OP2) G:A9(N7) A122, A761, A762, A763 G:A9 G:A10
1yhq 08087 Oph·Nb U:0903(OP1) A:01357(N7) 03010, 04418, 05880, 06508 U:0904 A:01356, G:0622
1yi2 08109 Oph·Nb U:0903(OP1) A:01357(N7) 03923, 05385, 06014, 09510 U:0904 G:0622, A:01356

Site type used in the classification is a string abbreviation of ligand composition in Mg2+ coordination sphere
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>