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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 2qp1




2QP1 (3.5Å) -- RIBOSOME : Crystal structure of the bacterial ribosome from escherichia coli in complex with spectinomycin and neomycin. this file contains the 50s subunit of the second 70s ribosome, with neomycin bound. the entire crystal structure contains two 70s ribosomes.
List of all 105 Mg2+ binding sites in the PDB structure 2qp1 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
2qp1 B2984 Ob C:B2499(O2) B3905, B3906, B3907, B3908, B3909 G:B2032 C:B2055, U:B2500, G:B2032, G:B2454, A:B2453
2qp1 B2972 Ob U:B746(O4) B3853, B3854, B3855, B3856, D408 U:B744, C:B2610, C:B2611
2qp1 B2941 2Nb G:B1358(N7), G:B1371(N7) B3702, B3703, B3704, B3705 G:B1371, G:B1358, C:B1357, C:B1370
2qp1 B2922 Oph A:B800(OP1) B3606, B3607, B3608, B3609, B3610 G:B799 C:B192, A:B800, A:B191
2qp1 B2966 Oph U:B419(OP1) B3820, B3821, B3822, B3823, B3824 G:B230
2qp1 B2931 Oph·Pout A:B945(OP1) B3651, B3652, B3653, B3654, B3655 G:B831 U:B832, G:B831
2qp1 B2926 Oph·Pout A:B1156(OP2) B3625, B3626, B3627, B3628, B3629 A:B1155 U:B999, G:B1157, G:B997
2qp1 B2913 Oph·Pout A:B1664(OP2) B3564, B3565, B3566, B3567, B3568 G:B1992 A:B1664, A:B1665, G:B1667, G:B1992, G:B1666
2qp1 B3010 Oph·Pout A:B1676(OP2) B4000, B4001, B4002, B4003, B4004 C:B1675 A:B1677, A:B1676
2qp1 B3002 Oph·Pout A:B1938(OP2) B3970, B3971, B3972, B3973, B3974 C:B1958
2qp1 B2947 Oph·Pout A:B1678(OP2) B3727, B3728, B3729, B3730, B3731 A:B1679 A:B1678, A:B1679
2qp1 B2943 Oph·Pout G:B536(OP2) B3709, B3710, B3711, B3712, B3713 G:B535 G:B536, G:B537
2qp1 B2914 Oph·2Pout U:B567(OP1) B3569, B3570, B3571, B3572, B3573 G:B809, G:B808 U:B810, G:B809
2qp1 B2912 Oph·2Pout G:B1776(OP2) B3559, B3560, B3561, B3562, B3563 U:B1775, A:B1981 G:B1776
2qp1 B2911 Oph·2Pout A:B1970(OP2) B3554, B3555, B3556, B3557, B3558 G:B1835, A:B1900 U:B1834 G:B1835
2qp1 B2946 Oph·2Pout U:B120(OP2) B3722, B3723, B3724, B3725, B3726 G:B122, G:B121 G:B122, G:B123, G:B121
2qp1 B2945 Oph·2Pout A:B574(OP2) B3717, B3718, B3719, B3720, B3721 U:B573, U:B576 U:B576, G:B577
2qp1 B2940 Oph·2Pout A:B2270(OP2) B3697, B3698, B3699, B3700, B3701 A:B2267, G:B2271 G:B2271
2qp1 B2929 Oph·2Pout A:B2062(OP2) B3640, B3641, B3642, B3643, B3644 G:B2444, C:B2443 G:B2445, G:B2444
2qp1 B2928 Oph·2Pout C:B2025(OP2) B3635, B3636, B3637, B3638, B3639 G:B2024, U:B2034 U:B1130

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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