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Conformers: ABBIImiBZICOPNSYNN See the J(S)mol wiki for description of applet controls.

©Jiří Černý & Bohdan Schneider

Complex Between Neomycin B and the 16S-RRNA A-Site

Results of the assignment of 40 detected steps in 1 model(s), can be also downloaded as csv or json file. Average confal 0, percentile 0.

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Click a row in table or a step in JSmol for analysis of results. Click column headers to sort data.
step numberStep nameCANANtCconfalrmsd
012et4_A_G2_C3AAAAA00650.18AA00
022et4_A_C3_G4AAAAA00680.20AA00
032et4_A_G4_U5AAwAA01660.41AA01
042et4_A_U5_C6AAAAA00190.64AA00
052et4_A_C6_A7AAAAA00710.24AA00
062et4_A_A7_C8AAAAA00880.17AA00
072et4_A_C8_A9AAAAA00880.12AA00
082et4_A_A9_C10AAAAA00640.24AA00
092et4_A_C10_C11AAAAA00860.20AA00
102et4_A_C11_G12AAAAA00860.15AA00
112et4_A_G12_G13AAAAA00950.16AA00
122et4_A_G13_U14AAAAA00910.14AA00
132et4_A_U14_G15AAAAA00750.20AA00
142et4_A_G15_A16NANNANT01.50OP17
152et4_A_A16_A17AAAAA00590.34AA00
162et4_A_A17_G18NANNANT00.90OP11
172et4_A_G18_U19AAAAA00360.36AA00
182et4_A_U19_C20AAAAA00910.15AA00
192et4_A_C20_G21AAAAA00900.11AA00
202et4_A_G21_C22AAAAA00700.25AA00
212et4_B_G25_C26AAAAA00710.26AA00
222et4_B_C26_G27AAAAA00910.14AA00
232et4_B_G27_U28NANNANT00.48AA10
242et4_B_U28_C29AAwAA01150.52AA01
252et4_B_C29_A30AAAAA08730.25AA08
262et4_B_A30_C31AAAAA00830.20AA00
272et4_B_C31_A32AAAAA00930.11AA00
282et4_B_A32_C33AAAAA00960.09AA00
292et4_B_C33_C34AAAAA00810.17AA00
302et4_B_C34_G35AAAAA04840.22AA04
312et4_B_G35_G36AAAAA00840.20AA00
322et4_B_G36_U37AAAAA00930.12AA00
332et4_B_U37_G38AAAAA00960.18AA00
342et4_B_G38_A39NANNANT00.93OP14
352et4_B_A39_A40AAAAA09840.21AA09
362et4_B_A40_G41NANNANT00.76OP11
372et4_B_G41_U42AAAAA00470.33AA00
382et4_B_U42_C43AAwAA01780.29AA01
392et4_B_C43_G44AAAAA08880.25AA08
402et4_B_G44_C45AAAAA00800.25AA00

Steps with non-standard or missing atoms have not been assigned, description of conformers is defined in the table.
Definition of torsion angles
step:
Table of conformers

δ1ε1ζ1α2β2γ2δ2χ1χ2μNNCC
step_torsions
ntC_average
Δ torsions
torsion scores

commentsstep confal = NaN
cartesian RMSD = NaN Å
pseudorotation: NA
details: NA

Similarity of step to class averages

Download

Results as csv or json file.
Restraints file for Phenix (steps with RMSD <= 0.5Å)
Restraints file for REFMAC (steps with RMSD <= 0.5Å)
Commands file for MMB (steps with RMSD <= 0.5Å)
Best NtC fitted to input structure.

Definitions

Average parameters (csv), esd values (csv), and Cartesian coordinates of conformers.

Download the papers

Description of DNATCO server:
Černý et al., Nucleic Acids Research, 44, W284 (2016).
Definition of conformers:
Schneider et al., Acta Cryst D, 74, 52-64 (2018).
Example of application:
Schneider et al., Genes, 8(10), 278, (2017).

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