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 3 of 4 | « Previous | Next » | 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 A3458 Pout·3Bout A4055, A4056, A4057, A4058, A4059, A4060 A:A103 G:A79, G:A80, G:A81 4dhc A3454 Oph A:A53(OP2) A4041, A4042, A4043, A4044, A4045 G:A54, G:A55 4dhc A3453 Oph·2Pout A:A802(OP1) A4036, A4037, A4038, A4039, A4040 G:A674, A:A675 U:A803, G:A674 4dhc A3452 Oph·3Pout A:A2062(OP1) A4032, A4033, A4034, A4035 C:A2443, G:A2061, G:A2444 G:A2444 4dhc A3448 Oph·2Pout G:A446(OP2) A4020, A4021, A4022, A4023, A4024 C:A1200, C:A445 U:A1199 G:A446 4dhc A3447 3Pout·Bout A4015, A4016, A4017, A4018, A4019 U:A475, A:A478, G:A476 G:A476 4dhc A3445 3Pout·5Bout A4007, A4008, A4009, A4010, A4011 U:A29, A:A28, A:A447 U:A29, G:A30, C:A31, G:A474, G:A473 4dhc A3443 Oph·Pout C:A975(OP1) A4001, A4002, A4003, A4004 A:A984 C:A975 4dhc A3440 Oph·Pout C:A249(OP1) A3993, A3994, A3995, A3996 U:A2431 C:A2394 G:A248 4dhc A3436 fac-3Oph A:A2711(OP1), A:A2712(OP2), G:A2714(OP2) A3982, A3983, A3984 A:A2713, C:A2710 4dhc A3435 cis-2Oph A:A2711(OP1), A:A2712(OP1) A3978, A3979, A3980, A3981 C:A1297 4dhc A3434 trans-2Oph C:A1298(OP2), U:A1639(OP2) A3974, A3975, A3976, A3977 C:A1297, C:A1638 C:A2710 G:A1299 4dhc A3433 Oph·2Pout U:A1639(OP1) A3970, A3971, A3972, A3973 G:A1296, C:A1297 4dhc A3431 2Pout·3Bout A3962, A3963, A3964, A3965, A3966 G:A686, C:A687 U:A688, A:A689, G:A771 4dhc A3430 Oph·2Pout G:A770(OP2) A3959, A3960, A3961, 7201 G:A686, G:A771 G:A770 4dhc A3429 Oph·4Pout C:A1636(OP2) A3955, A3956, A3957, A3958 G:A1299, U:A1300, A:A1637, A:A1301 4dhc A3424 2Pout·Bout A3942, A3943, A3944, P301 G:A831, G:A944 A:A2448 4dhc A3423 Oph·2Pout A:A567(OP1) A3937, A3938, A3939, A3940, A3941 G:A808, G:A809 G:A809, U:A810 4dhc A3422 Oph·Pout G:A2447(OP2) A3932, A3933, A3934, A3935, A3936 G:A2502 U:A576 G:A2502 4dhc A3419 5Bout A3922, A3923, A3924, A3925, A3926 G:A2455, C:A2456, G:A2495, U:A2457, G:A2494

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].

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