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MgRNA: Classification of Mg2+ binding sites in RNA crystal structures
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Representative site 3r8s:A2930, See in JSmolMgRNA representative site for type OP Click on the image to toggle views


Site type: Oph

Schematic drawing for
Oph
MgRNA type OP
List of all 588 Mg2+ binding sites with the site type Oph in RNA crystal structures in the benchmark dataset (switch to full dataset)
Sites in the table can be ordered by the following fields by clicking the column header: "PDB ID" or "Mg2+ ID"
Page 6 of 24 | | | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
2qox B2965 Oph U:B419(OP1) B3311, B3312, B3313, B3314, B3315
2qox B2947 Oph A:B1678(OP2) B3221, B3222, B3223, B3224, B3225 A:B1678, A:B1679
2qox B2922 Oph A:B800(OP1) B3099, B3100, B3101, B3102, B3103 G:B799 C:B192, A:B800, A:B191
2qoy A1591 Oph G:A100(OP2) A2132, A2133, A2134, A2135, A2136 G:A64
2qoy A1596 Oph C:A352(OP2) A2154, A2155, A2156, A2157, A2158 C:A330, G:A331, C:A352 A:A59, C:A330, G:A354
2qoz B2972 Oph A:B1678(OP2) B3826, B3827, B3828, B3829, B3830 A:B1679
2qoz B2930 Oph A:B945(OP1) B3631, B3632, B3633, B3634, B3635 G:B831
2qoz B2962 Oph A:B800(OP1) B3780, B3781, B3782, B3783, B3784 G:B799 C:B192, A:B800
2qoz B2934 Oph U:B419(OP1) B3649, B3650, B3651, B3652, B3653 C:B418 G:B230
2qp0 A1561 Oph A:A572(OP1) A1981, A1982, A1983, A1984, A1985 A:A819
2qp0 A1562 Oph G:A21(OP1) A1986, A1987, A1988, A1989, A1990 G:A568, G:A567 A:A573, G:A567
2qp0 A1586 Oph A:A937(OP2) A2093, A2094, A2095, A2096, A2097 A:A938, G:A939
2qp1 B2966 Oph U:B419(OP1) B3820, B3821, B3822, B3823, B3824 G:B230
2qp1 B2922 Oph A:B800(OP1) B3606, B3607, B3608, B3609, B3610 G:B799 C:B192, A:B800, A:B191
2z4k A1572 Oph G:A21(OP1) A1746, A1747, A1748, A1749, A1750 A:A563, A:A573, G:A567
2z4l B2963 Oph A:B800(OP1) B3288, B3289, B3290, B3291, B3292 G:B799, A:B203 A:B191
2z4l B2935 Oph U:B419(OP1) B3155, B3156, B3157, B3158, B3159 G:B230
2z4l B2977 Oph A:B2033(OP1) B3354, B3355, B3356, B3357 U:B2028
2z4m A1586 Oph A:A608(OP2) A1814, A1815, A1816, A1817, A1818 A:A630, A:A609, C:A631, U:A610
2z4m A1565 Oph A:A937(OP2) A1704, A1705, A1706, A1707, A1708 G:A939, A:A937, A:A938
2z4n B2967 Oph U:B419(OP1) B3315, B3316, B3317, B3318, B3319 G:B230
2z4n B2948 Oph A:B1678(OP2) B3223, B3224, B3225, B3226, B3227 A:B1678, A:B1679
2z4n B2923 Oph A:B800(OP1) B3101, B3102, B3103, B3104, B3105 A:B802, G:B799 C:B192, A:B800
3df1 A2176 Oph G:A21(OP1) A4177, A4178, A4179, A4180, A4181 G:A567, A:A573
3df1 A2064 Oph A:A937(OP2) A4065, A4066, A4067, A4068, A4069 A:A938, G:A939

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>