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

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Representative site 2qao:B3320, See in JSmolMgRNA representative site for type 3PO-4BO        Click on the image to toggle views

Site type: 3Pout·4Bout

Schematic drawing for

MgRNA type 3PO-4BO
List of all 24 Mg2+ binding sites with the site type 3Pout·4Bout 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
1vs8 B2938 3Pout·4Bout B3180, B3181, B3182, B3183, B3184, B3185 A:B447, A:B28, U:B29 G:B473, U:B29, C:B31, G:B474
2qam B3110 3Pout·4Bout B3700, B3701, B3702, B3703, B3704, B3705 A:B28, A:B447, U:B29 U:B29, G:B473, G:B30, G:B474
2qao B3320 3Pout·4Bout B3881, B3882, B3883, B3884, B3885, B3886 A:B582, G:B583, A:B1253 A:B582, G:B583, C:B584, G:B585
2qbe B3110 3Pout·4Bout B3701, B3702, B3703, B3704, B3705, B3706 A:B28, A:B447, U:B29 U:B29, G:B473, G:B474, G:B30
2qbi B2983 3Pout·4Bout B3384, B3385, B3386, B3387, B3388, B3389 A:B2451, C:B2452, A:B2453 A:B2453, G:B2454, A:B2497, G:B2455
2qbi B2923 3Pout·4Bout B3102, B3103, B3104, B3105, B3106, B3107 U:B29, A:B28, A:B447 U:B29, G:B473, G:B30, G:B474
2qov B2983 3Pout·4Bout B3388, B3389, B3390, B3391, B3392, B3393 C:B2452, A:B2453, A:B2451 A:B2453, G:B2454, A:B2497, G:B2455
2qov B2956 3Pout·4Bout B3261, B3262, B3263, B3264, B3265, B3266 A:B582, A:B1253, G:B583 A:B582, C:B584, G:B585, G:B583
2qoz B2923 3Pout·4Bout B3597, B3598, B3599, B3600, B3601, B3602 U:B29, A:B28, A:B447 G:B473, G:B474, U:B29, G:B30
2qoz B2983 3Pout·4Bout B3878, B3879, B3880, B3881, B3882, B3883 A:B2451, C:B2452, A:B2453 A:B2497, G:B2454, G:B2455, A:B2453
2z4l B2984 3Pout·4Bout B3386, B3387, B3388, B3389, B3390, B3391 A:B2451, C:B2452, A:B2453 A:B2497, G:B2454, G:B2455, A:B2453
2z4n B2931 3Pout·4Bout B3141, B3142, B3143, B3144, B3145, B3146 A:B2451, A:B2453, C:B2452 A:B2453, G:B2454, A:B2497, G:B2455
3ofz A2905 3Pout·4Bout A3044, A3045, A3046, A3047, A3048, A3049 U:A29, A:A447, A:A28 G:A473, G:A474, U:A29, G:A30
3r8t A2905 3Pout·4Bout A3076, A3077, A3078, A3079, A3080, A3081 U:A29, A:A28, A:A447 G:A474, U:A29, G:A473, G:A30
3v23 A3608 3Pout·4Bout A5042, A5043, A5044, A5045, A5046, A5047 U:A29, A:A447, A:A28 G:A474, G:A473, U:A29, G:A30
3v2d A3402 3Pout·4Bout A4838, A4839, A4840, A4841, A4842, A4843 U:A29, A:A447, A:A28 G:A474, G:A473, U:A29, G:A30
4a17 0325 3Pout·4Bout 08371, 08372, 08373, 08374, 08375, 08376 G:365, G:366, A:364 U:3109, G:3108, G:365, G:366
4gar A3002 3Pout·4Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A447, A:A28 U:A29, G:A30, C:A31, G:A474
4tp1 A3072 3Pout·4Bout A3527, A3528, A3529, A3530, A3531, A3532 C:A2452, A:A2453, A:A2451 A:A2453, G:A2454, G:A2455, A:A2497
4tp3 A3080 3Pout·4Bout A3557, A3558, A3559, A3560 A:A2407, A:A2406, U:A2408 G:A2410, A:A2411, U:A2408, G:A2409
4tp7 A3081 3Pout·4Bout A3557, A3558, A3559, A3560 A:A2406, G:A411, A:A2407 A:A2411, A:A2407, U:A2408, G:A2409
4tpb A3080 3Pout·4Bout A3557, A3558, A3559, A3560 G:A411, A:A2407, A:A2406 G:A2410, A:A2411, U:A2408, G:A2409
4tpf A3072 3Pout·4Bout A3522, A3523, A3524, A3525, A3526, A3527 A:A2453, A:A2451, C:A2452 A:A2497, A:A2453, G:A2454, G:A2455
4tpf A3003 3Pout·4Bout A3207, A3208, A3209, A3210, A3211, A3212 U:A29, A:A28, A:A447 U:A29, G:A473, G:A30, C:A31

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>