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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 2qao




2QAO (3.21Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with neomycin. this file contains the 50s subunit of the second 70s ribosome, with neomycin bound. the entire crystal structure contains two 70s ribosomes and is described in
List of all 109 Mg2+ binding sites in the PDB structure 2qao 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 1 of 6 | « Previous | | 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
2qao B3351 Ob G:B2304(O6) B3907, B3908, B3909, B3910, B3911 C:B2310 U:B2302, G:B2303
2qao B3403 Ob U:B746(O4) B3951, B3952, B3953, B3954, B3955 C:B2610, C:B2611, U:B744 G:B745
2qao B3468 Ob C:B2499(O2) B4002, B4003, B4004, B4005, B4006 C:B2055, U:B2500, G:B2454, G:B2032
2qao B3099 2Nb G:B733(N7), A:B761(N7) B3699, B3700, B3701, B3702 A:B761, G:B760, G:B733
2qao B3220 2Nb G:B1358(N7), G:B1371(N7) B3800, B3801, B3802, B3803 G:B1371, G:B1358, C:B1357, C:B1370
2qao B3364 Oph U:B419(OP1) B3918, B3919, B3920, B3921, B3922 G:B230
2qao B3104 Oph A:B800(OP1) B3703, B3704, B3705, B3706, B3707 G:B799, A:B203 C:B192, A:B800, A:B191
2qao B3251 Oph·Pout A:B1678(OP2) B3825, B3826, B3827, B3828, B3829 A:B1679 A:B1678, A:B1679
2qao B3245 Oph·Pout U:B120(OP2) B3820, B3821, B3822, B3823, B3824 G:B121 G:B121, G:B122, G:B123
2qao B3229 Oph·Pout G:B536(OP2) B3807, B3808, B3809, B3810, B3811 G:B535 G:B536, G:B537
2qao B3159 Oph·Pout A:B945(OP1) B3749, B3750, B3751, B3752, B3753 G:B831 G:B831, U:B832
2qao B3127 Oph·Pout A:B1156(OP2) B3722, B3723, B3724, B3725, B3726 A:B1155 G:B1157, C:B998
2qao B3052 Oph·Pout A:B1664(OP2) B3661, B3662, B3663, B3664, B3665 G:B1992 G:B1667, A:B1665, G:B1992, G:B1666
2qao B3474 Oph·Pout G:B2588(OP2) B4007, B4008, B4009, C477, C479 A:B2589 A:B2589
2qao B3058 Oph·Pout U:B567(OP1) B3666, B3667, B3668, B3669, B3670 G:B809 U:B810
2qao B3140 Oph·2Pout C:B2025(OP2) B3733, B3734, B3735, B3736, B3737 G:B2024, U:B2034 U:B1130
2qao B3081 Oph·2Pout G:B1187(OP2) B3685, B3686, B3687, B3688, R104 C:B816, C:B817 G:B1185 G:B818, G:B1187
2qao B3046 Oph·2Pout G:B1776(OP2) B3656, B3657, B3658, B3659, B3660 U:B1775, A:B1981 G:B1776
2qao B3040 Oph·2Pout A:B1970(OP2) B3651, B3652, B3653, B3654, B3655 G:B1835, A:B1900 U:B1834 G:B1835
2qao B3008 Oph·2Pout C:B1774(OP1) B3625, B3626, B3627, B3628, B3629 U:B1775, A:B1786 A:B1772, G:B1776

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/)
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