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

©Jiří Černý & Bohdan Schneider

RNA polymerase II elongation complex with unnatural base dTPT3, rNaMTP bound to E-site

Results of the assignment of 39 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
017kee_R_A1_U2AAAAA08140.43AA08
027kee_R_U2_C3AAAAA00720.20AA00
037kee_R_C3_G4AAAAA08630.32AA08
047kee_R_G4_A5AAAAA08180.35AA08
057kee_R_A5_G6AAAAA08450.24AA08
067kee_R_G6_A7AAAAA00410.30AA00
077kee_R_A7_G8AAwAA01770.20AA01
087kee_R_G8_G9AAAAA00720.13AA00
097kee_T_DC5_DG6NANNANT00.65BB07
107kee_T_DG6_DA7B-ABA10260.58BA10
117kee_T_DA7_DT8NANNANT00.77AA10
127kee_T_DT8_DA9A-BAB05680.28AB05
137kee_T_DA9_DA10miBBB13660.37BB13
147kee_T_DA10_DG11NANNANT00.65BB13
157kee_T_DG11_DC12NANNANT00.74BB17
167kee_T_DC12_DA13NANNANT00.58BA16
177kee_T_DA13_DG14NANNANT00.43AA10
187kee_T_DG14_DA15NANNANT00.82IC04
197kee_T_DA15_DC16NANNANT00.95BB11
207kee_T_DC16_DG17NANNANT00.66BB02
217kee_T_DT19_DC20AAwAA11160.49AA11
227kee_T_DC20_DC21AAAAA08350.39AA08
237kee_T_DC21_DT22NANNANT00.59AB02
247kee_T_DT22_DC23NANNANT00.39AA10
257kee_T_DC23_DT24A-BAB04210.34AB04
267kee_T_DT24_DC25BBBBB00410.34BB00
277kee_T_DC25_DG26BBBBB00160.18BB00
287kee_T_DG26_DA27miBBB10510.35BB10
297kee_T_DA27_DT28NANNANT01.37OP24
307kee_N_DT3_DC4NANNANT00.88IC04
317kee_N_DC4_DT5NANNANT00.53BB17
327kee_N_DT5_DG6A-BAB02190.56AB02
337kee_N_DG6_DC7NANNANT00.65BB13
347kee_N_DC7_DT8NANNANT00.48AA01
357kee_N_DT8_DT9BBBBB00720.39BB00
367kee_N_DT9_DA10B12BB04790.23BB04
377kee_N_DA10_DT11BB2BB07570.39BB07
387kee_N_DT11_DC12BBBBB00760.32BB00
397kee_N_DC12_DG13miBBB10440.23BB10

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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