`

MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
Back to Classification Home Download this subset in: CSV, XML, JSON

List of Mg2+ binding sites in structure 4dhc



4DHC (3.2Å) -- RIBOSOME : Crystal structure of yaej bound to the 70s ribosome
List of all 80 Mg2+ binding sites in the PDB structure 4dhc in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "Site type" or "Mg2+ ID"
Page 2 of 4 | | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4dhc A3581 Pout·4Bout A4392, A4393, A4394, A4395, A4396 G:A495 A:A482, G:A496, G:A494, G:A495
4dhc A3579 3Pout A4385, A4386, A4387, A4388, A4389 C:A1370, U:A773, G:A1356
4dhc A3574 Oph·3Pout U:A2016(OP1) A4369, A4370, A4371, A4372, A4373 A:A2059, U:A2017, A:A2058 U:A1255 U:A1255
4dhc A3571 Oph A:A800(OP1) A4359, A4360, A4361, A4362, A4363 G:A799 C:A192, A:A191, A:A800
4dhc A3569 Ob G:A271(O6) A4352, A4353, A4354, A4355 A:A270, G:A271 G:A271, G:A271
4dhc A3543 Oph A:A2598(OP1) A4295, A4296, A4297, D406
4dhc A3532 Oph·2Pout A:A1495(OP2) A4262, A4263, A4264, A4265 A:A1496, A:A1494 A:A1496, A:A1495
4dhc A3518 Pout·2Bout A4230, A4231, A4232, A4233, A4234 A:A340 G:A341, G:A342
4dhc A3516 Ob G:A240(O6) A4225, A4226, A4227, A4228 A:A256
4dhc A3513 Oph U:A847(OP2) A4215, A4216, A4217, A4218 G:A928, G:A927
4dhc A3510 3Bout A4208, A4209, A4210, A4211, A4212 G:A1309, G:A1310, G:A1311
4dhc A3506 cis-2Oph A:A1664(OP1), A:A1665(OP2) A4196, A4197, A4198, A4199
4dhc A3503 trans-2Oph U:A2682(OP2), A:A2721(OP1) A4187, A4188, A4189, A4190 C:A2683, G:A2722
4dhc A3491 Oph A:A2227(OP2) A4155, A4156, A4157, A4158 G:A2090, C:A2229, U:A2092
4dhc A3488 Oph·2Pout G:A739(OP1) A4144, A4145, A4146, A4147, A4148 U:A1779, U:A1778 A:A1784
4dhc A3486 3Pout·2Rout·Bout A4137, A4138, A4139, A4140 C:A1617, G:A1619, A:A1609 C:A1617, A:A1608 G:A1619
4dhc A3474 cis-2Oph U:A787(OP1), C:A790(OP2) A4103, A4104, A4105, A4106 A:A789, C:A791
4dhc A3470 cis-2Oph G:A370(OP2), A:A422(OP2) A4092, A4093, A4094 A:A423 C:A366 G:A370, A:A423
4dhc A3467 Oph·2Pout U:A2406(OP1) A4082, A4083, A4084, A4085 U:A2408, G:A2409 G:A2405 G:A2410, U:A2408, G:A2409
4dhc A3459 Bout A4061, A4062, A4063, A4064 G:A83

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>