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

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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"
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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
4dhc A3671 Ob G:A1271(O6) A4647, A4648, A4649, A4650 G:A1324 G:A1325
4dhc A3652 Ob U:A2028(O4) A4573, A4574, A4575, A4576, A4577 A:A2033 G:A2029, G:A2027
4dhc A3569 Ob G:A271(O6) A4352, A4353, A4354, A4355 A:A270, G:A271 G:A271, G:A271
4dhc A3516 Ob G:A240(O6) A4225, A4226, A4227, A4228 A:A256
4dhc A3412 Nb G:A2002(N7) A3895, A3896, A3897, A3898, A3899 G:A2002 G:A2004
4dhc A3625 Nb G:A2375(N7) A4487, A4488, A4489, A4490 A:A2377
4dhc A3410 Nb G:A2032(N7) A3888, A3889, A3890, A3891, A3892 G:A2032 G:A2454 C:A2055, C:A2499, A:A2572, U:A2500
4dhc A3375 Ob·Nb G:A2592(N7), U:A2593(O4) A3787, A3788, A3789, A3790 C:A2591, G:A2592
4dhc A3384 2Nb G:A733(N7), A:A761(N7) A3815, A3816, A3817, A3818 G:A760, A:A761, G:A733 C:A732
4dhc A3513 Oph U:A847(OP2) A4215, A4216, A4217, A4218 G:A928, G:A927
4dhc A3543 Oph A:A2598(OP1) A4295, A4296, A4297, D406
4dhc A3454 Oph A:A53(OP2) A4041, A4042, A4043, A4044, A4045 G:A54, G:A55
4dhc A3491 Oph A:A2227(OP2) A4155, A4156, A4157, A4158 G:A2090, C:A2229, U:A2092
4dhc A3571 Oph A:A800(OP1) A4359, A4360, A4361, A4362, A4363 G:A799 C:A192, A:A191, A:A800
4dhc A3659 Oph·Pout A:A2322(OP2) A4601, A4602, A4603, A4604 G:A2321 G:A2323, G:A2331, U:A2332, A:A2322
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 A3422 Oph·Pout G:A2447(OP2) A3932, A3933, A3934, A3935, A3936 G:A2502 U:A576 G:A2502
4dhc A3416 Oph·Pout C:A574(OP1) A3908, A3909, A3910, A3911, A3912 C:A2055 G:A2035
4dhc A3386 Oph·Pout G:A1776(OP2) A3823, A3824, A3825, A3826 A:A1981 G:A1776

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].

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