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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 4tp5



4TP5 (2.9Å) -- RIBOSOME : Crystal structure of the e. coli ribosome bound to virginiamycin m1. this file contains the 50s subunit of the first 70s ribosome with virginiamycin m1 bound.
List of all 73 Mg2+ binding sites in the PDB structure 4tp5 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 4 | « Previous | | 1 | 2 | 3 | 4
Mg2+ ion Site type Inner-sphere ligands Outer-sphere ligands
PDB ID Mg2+ ID Oph Or Ob+Nb Water Other Pout Rout Bout
4tp5 A3133 Ob U:A2593(O4) A3793, A3794, C304, C305, C306 G:A2592, C:A2591 G:A2592
4tp5 A3022 Ob U:A746(O4) A3304, A3305, A3306, A3307, A3308 C:A2610, C:A2611, U:A744 G:A745
4tp5 A3072 Ob C:A2499(O2) A3531, A3532, A3533, A3534, A3535 G:A2032 C:A2055, U:A2500, G:A2454, G:A2032
4tp5 B202 Ob U:B95(O4) B305, B306, B307, B308, V101 U:B80, G:B96, A:B94
4tp5 A3115 Ob U:A1602(O4) A3718, A3719, A3720, A3721 A:A1342
4tp5 A3045 2Nb G:A1358(N7), G:A1371(N7) A3403, A3404, A3405, A3406 G:A1371, C:A1370 C:A1357
4tp5 A3078 Oph A:A299(OP2) A3557, A3558, A3559, A3560, A3561 U:A339, A:A299, G:A338
4tp5 A3075 Oph G:A2588(OP2) A3545, A3546, A3547, A3548, C302 G:A2588, A:A2589
4tp5 A3008 Oph U:A419(OP1) A3233, A3234, A3235, A3236, A3237 G:A230
4tp5 A3100 Oph·Pout U:A2022(OP1) A3665, A3666, A3667, A3668, A3669 C:A2023 C:A2021, A:A529 A:A529
4tp5 A3053 Oph·Pout A:A1678(OP2) A3439, A3440, A3441, A3442, A3443 A:A1679 A:A1678, A:A1679
4tp5 A3050 Oph·Pout A:A1664(OP2) A3424, A3425, A3426, A3427, A3428 G:A1992 G:A1667, A:A1664, G:A1992, A:A1665, G:A1666
4tp5 A3049 Oph·Pout U:A1647(OP2) A3419, A3420, A3421, A3422, A3423 U:A1325 C:A1646, A:A1616 A:A1616
4tp5 A3128 Oph·Pout A:A1676(OP2) A3770, A3771, A3772, A3773, A3774 C:A1675 G:A1674 A:A1677, A:A1676
4tp5 A3036 Oph·Pout A:A1156(OP2) A3364, A3365, A3366, A3367, A3368 A:A1155 G:A997
4tp5 A3033 Oph·Pout A:A945(OP1) A3352, A3353, A3354, A3355, A3356 G:A831 G:A831, U:A832
4tp5 A3005 Oph·Pout U:A120(OP1) A3218, A3219, A3220, A3221, A3222 G:A123 G:A124, G:A123
4tp5 A3135 Oph·Pout A:A943(OP2) A3799, A3800, L303, L304, L305 U:A832
4tp5 A3004 Oph·Pout U:A120(OP2) A3213, A3214, A3215, A3216, A3217 G:A121 G:A122, G:A123
4tp5 A3042 Oph·2Pout U:A1313(OP1) A3388, A3389, A3390, A3391, T101 G:A1333, G:A1334

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>