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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 4tp7



4TP7 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 50s subunit of the second 70s ribosome with virginiamycin m1 bound.
List of all 126 Mg2+ binding sites in the PDB structure 4tp7 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 5 of 7 | | | 1 | 2 | 3 | 4 | 5 | 6 | 7
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tp7 A3081 3Pout·4Bout A3557, A3558, A3559, A3560 A:A2406, G:A411, A:A2407 A:A2411, A:A2407, U:A2408, G:A2409
4tp7 A3082 Oph·Pout A:A572(OP1) A3561, A3562, A3563, A3564, A3565 A:A983 U:A573, A:A572
4tp7 A3083 2Pout·2Bout A3566, A3567, A3568, A3569, A3570, A3571 A:A574, C:A2055 G:A2035, U:A2034
4tp7 A3084 Oph·Ob G:A818(OP2) G:A1187(O6) A3572, A3573, A3574, A3575 C:A817, G:A1186 G:A818, G:A1186
4tp7 A3085 Pout·4Bout A3576, A3577, A3578, A3579, A3580, A3581 A:A933 U:A842, G:A843, U:A934, G:A841
4tp7 A3086 2Pout·2Bout A3582, A3583, A3584, A3585, A3586, A3587 G:A977, G:A976 G:A977, G:A978
4tp7 A3087 4Pout A3588, A3589, A3590, A3591, A3592 A:A981, G:A977, G:A978, C:A982
4tp7 A3088 mer-3Oph A:A990(OP2), C:A991(OP2), G:A1186(OP2) A3593, A3594, A3595 G:A989, G:A1186
4tp7 A3089 cis-2Oph C:A1013(OP2), A:A1014(OP2) A3596, A3597, A3598, A3599 A:A1143
4tp7 A3090 Ob G:A1125(O6) A3600, A3601, A3602, A3603, A3604 A:A1028 G:A1124
4tp7 A3091 Oph·2Pout A:A1327(OP2) A3605, A3606, A3607, A3608, A3609 U:A1326, A:A1328 G:A1324, A:A1328
4tp7 A3092 cis-2Oph A:A1359(OP1), G:A1360(OP2) A3610, A3611, A3612, A3613 G:A1361
4tp7 A3093 3Bout A3614, A3615, A3616, A3617, A3618, A3619 G:A1410, U:A1411, U:A1409
4tp7 A3094 Pout·4Bout A3620, A3621, A3622, A3623, A3624, A3625 A:A1572 G:A1423, G:A1424, C:A1574, G:A1425
4tp7 A3095 Ob U:A1440(O4) A3626, A3627, A3628, A3629 A:A1439 G:A1441, A:A1551
4tp7 A3096 4Bout A3630, A3631, A3632, A3633, A3634, A3635 G:A1464, G:A1445, C:A1446, G:A1465
4tp7 A3097 2Pout·2Rout·3Bout A3636, A3637, A3638, A3639, A3640, A3641 A:A1608, G:A1619 C:A1617, A:A1608 G:A1619, G:A1620, G:A1613
4tp7 A3098 Oph·5Pout U:A1636(OP2) A3642, A3643, A3644, A3645, A3646 A:A1301, A:A1635, A:A1637, G:A1299, G:A1300
4tp7 A3099 Oph·2Pout C:A1658(OP1) A3647, A3648, A3649, D303, D304 G:A1659, U:A744 A:A743
4tp7 A3100 2Bout A3650, A3651, A3652, A3653, A3654, A3655 G:A1823, G:A1824

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>