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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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List of Mg2+ binding sites in structure 4gau



4GAU (3.3Å) -- RIBOSOME/ANTIBIOTIC : Allosteric control of the ribosome by small-molecule antibiotics
List of all 120 Mg2+ binding sites in the PDB structure 4gau 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 6 | | | 1 | 2 | 3 | 4 | 5 | 6
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4gau A3052 Oph·2Pout G:A1776(OP2) A3447, A3448, A3449, A3450, A3451 U:A1775, A:A1981 G:A1980 G:A1776
4gau A3055 Oph·2Pout G:A2592(OP1) A3463, A3464, A3465, A3466 G:A1973, G:A1968
4gau A3079 Oph·2Pout C:A817(OP2) A3578, A3579, A3580, A3581 G:A818, G:A1186 G:A818, G:A1187, G:A1186
4gau A3086 Oph·2Pout A:A1327(OP2) A3611, A3612, A3613, A3614, A3615 U:A1326, A:A1328 A:A1328, G:A1324
4gau A3114 Oph·2Pout G:A862(OP2) A3729, A3730, A3731, A3732, A3733 A:A861, A:A910 G:A862, A:A863
4gau A3115 Oph·2Pout A:A1938(OP2) A3734, A3735, A3736, A3737, A3738 C:A1957, C:A1958
4gau A3118 Oph·2Pout G:A1828(OP2) A3749, A3750, A3751, A3752, A3753 G:A1972, C:A1788 G:A1828
4gau A3070 Oph·3Pout A:A2518(OP2) A3535, A3536, A3537, A3538, A3539 U:A2519, A:A2541, C:A2540 A:A2541
4gau A3082 Oph·3Pout A:A981(OP1) A3594, A3595, A3596, A3597, A3598 C:A982, G:A561, G:A978
4gau A3107 Oph·3Pout C:A31(OP1) A3704, A3705, A3706, A3707, A3708 U:A1199, G:A1239, U:A1240 A:A1214
4gau A3040 Oph·3Pout G:A1333(OP2) A3390, A3391, A3392, A3393, A3394 C:A1314, G:A1332, U:A1313
4gau A3037 Oph·3Pout A:A2005(OP1) A3380, A3381, A3382, A3383 A:A1268, A:A1269, C:A2006 C:A1270, A:A1269
4gau A3022 Oph·3Pout G:A2588(OP1) A3313, A3314, A3315, A3316 A:A2589, G:A784, G:A2599
4gau A3018 Oph·3Pout G:A760(OP2) A3292, A3293, A3294, A3295 A:A761, C:A732, G:A733 G:A733
4gau A3131 Oph·3Pout C:A944(OP2) A3805, A3806, A3807, L306, L307 G:A831, U:A832, A:A943
4gau A3053 Oph·4Pout G:A1828(OP1) A3452, A3453, A3454, A3455, A3456 A:A1772, A:A1773, G:A1972, G:A1973
4gau A3071 Oph·Or C:A2611(OP2) G:A2576(O2') A3540, A3541, A3542, A3543 C:A2579, U:A2580 C:A2610 G:A2505, G:A2581
4gau A3064 Oph·Ob C:A2248(OP2) U:A2249(O4) A3506, A3507, A3508, A3509 A:A2247, C:A2066
4gau A3032 Oph·Nb C:A1153(OP2) G:A1154(N7) A3357, A3358, A3359, Q301 U:A999, C:A998, G:A1154
4gau A3075 Oph·Nb A:A422(OP2) G:A370(N7) A3559, A3560, A3561, A3562 G:A370, A:A423 G:A424

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>