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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 1 of 7 | « Previous | | 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 A3065 Or G:A2061(O5') A3486, A3487, A3488, A3489 A:A2062, G:A2502, G:A2061 C:A2501, A:A2060 G:A2446, G:A2445
4tp7 A3102 Ob U:A2419(O4) A3661, A3662, A3663, 3101, 3102 A:A2418
4tp7 A3095 Ob U:A1440(O4) A3626, A3627, A3628, A3629 A:A1439 G:A1441, A:A1551
4tp7 A3133 Ob U:A2593(O4) A3782, A3783, A3784, A3785, C312 C:A2591 G:A2592, G:A2599
4tp7 A3023 Ob U:A746(O4) A3302, A3303, A3304, D301, D302 U:A744, U:A2580, C:A2611, C:A2610 G:A745
4tp7 A3073 Ob C:A2499(O2) A3525, A3526, A3527, A3528, A3529 G:A2032 C:A2055, G:A2454, A:A2453, G:A2032
4tp7 B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, G:B96, A:B94
4tp7 A3090 Ob G:A1125(O6) A3600, A3601, A3602, A3603, A3604 A:A1028 G:A1124
4tp7 A3046 2Nb G:A1358(N7), G:A1371(N7) A3396, A3397, A3398, A3399 G:A1358, C:A1357, C:A1370
4tp7 A3021 2Nb G:A733(N7), A:A761(N7) A3292, A3293, A3294, A3295 A:A761, G:A733, G:A760, C:A732
4tp7 A3004 Oph U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A123, G:A121, G:A122
4tp7 A3079 Oph A:A299(OP2) A3549, A3550, A3551, A3552, U201 U:A339, A:A300, G:A338
4tp7 B201 Oph A:B58(OP2) B301, B302, B303, B304 G:B56, A:B57 A:B58, U:B22, G:B23
4tp7 A3054 Oph A:A1678(OP2) A3432, A3433, A3434, A3435, A3436 A:A1678, A:A1679
4tp7 A3008 Oph U:A419(OP1) A3233, A3234, A3235, A3236, A3237 G:A230
4tp7 A3034 Oph·Pout A:A945(OP1) A3345, A3346, A3347, A3348, A3349 G:A831 G:A831, U:A832
4tp7 A3078 Oph·Pout A:A14(OP2) A3545, A3546, A3547, A3548 G:A15
4tp7 A3069 Oph·Pout G:A2269(OP1) A3505, A3506, A3507, A3508 A:A2268 G:A2271, A:A2267
4tp7 A3061 Oph·Pout C:A2025(OP2) A3467, A3468, A3469, A3470, A3471 U:A2034 A:A2033 U:A1130
4tp7 A3051 Oph·Pout A:A1664(OP2) A3417, A3418, A3419, A3420, A3421 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666, G:A1663

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>