Zinc in PDB 7o4f: The Dyw Domain of A. Thaliana OTP86 in Its Active State

The structure of The Dyw Domain of A. Thaliana OTP86 in Its Active State, PDB code: 7o4f was solved by G.Weber, G.J.Palm, M.Takenaka, T.Barthel, C.Feiler, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.03 / 1.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	117.599, 132.883, 30.633, 90, 90, 90
R / Rfree (%)	22.1 / 26.8

The binding sites of Zinc atom in the The Dyw Domain of A. Thaliana OTP86 in Its Active State (pdb code 7o4f). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the The Dyw Domain of A. Thaliana OTP86 in Its Active State, PDB code: 7o4f:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the The Dyw Domain of A. Thaliana OTP86 in Its Active State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Dyw Domain of A. Thaliana OTP86 in Its Active State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:15.2 occ:1.00 NE2 A:HIS924 2.0 17.2 1.0 ND1 A:HIS947 2.1 12.8 1.0 SG A:CYS956 2.3 16.6 1.0 SG A:CYS954 2.3 14.3 1.0 CE1 A:HIS947 2.9 15.2 1.0 CD2 A:HIS924 3.0 17.5 1.0 CE1 A:HIS924 3.0 18.1 1.0 CB A:CYS954 3.2 15.4 1.0 CG A:HIS947 3.2 18.1 1.0 CB A:CYS956 3.3 16.6 1.0 CB A:HIS947 3.6 17.1 1.0 N A:CYS956 4.1 13.9 1.0 NE2 A:HIS947 4.1 19.0 1.0 ND1 A:HIS924 4.2 15.5 1.0 CG A:HIS924 4.2 16.1 1.0 CD2 A:HIS947 4.2 16.6 1.0 CA A:CYS956 4.3 15.9 1.0 CA A:HIS947 4.3 17.4 1.0 CZ A:PHE949 4.3 13.4 1.0 CE1 A:PHE949 4.3 17.7 1.0 CA A:CYS954 4.6 12.9 1.0 CE3 A:TRP960 4.7 20.4 1.0 C A:CYS954 4.8 17.3 1.0 CD2 A:TRP960 4.9 15.1 1.0 C A:CYS956 4.9 16.0 1.0 N A:ASP958 5.0 20.3 1.0

Zinc binding site 2 out of 8 in the The Dyw Domain of A. Thaliana OTP86 in Its Active State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Dyw Domain of A. Thaliana OTP86 in Its Active State within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:19.2 occ:1.00 O A:HOH1107 2.1 16.7 1.0 ND1 A:HIS892 2.2 31.6 1.0 SG A:CYS923 2.3 19.9 1.0 SG A:CYS920 2.3 19.6 1.0 CB A:CYS923 3.1 15.2 1.0 CG A:HIS892 3.1 32.2 1.0 CE1 A:HIS892 3.2 32.4 1.0 CB A:HIS892 3.4 32.4 1.0 CB A:CYS920 3.4 16.7 1.0 OE1 A:GLU894 3.8 20.4 1.0 N A:CYS920 3.9 14.2 1.0 N A:CYS923 4.0 19.9 1.0 O A:HOH1149 4.1 36.0 1.0 CA A:CYS923 4.1 19.0 1.0 O A:HOH1153 4.1 28.9 1.0 CA A:CYS920 4.2 18.2 1.0 CD2 A:HIS892 4.3 35.2 1.0 NE2 A:HIS892 4.3 35.2 1.0 CD A:GLU894 4.3 16.4 1.0 OE2 A:GLU894 4.4 17.6 1.0 C A:CYS920 4.7 19.1 1.0 O A:CYS920 4.8 15.2 1.0 CA A:HIS892 4.9 34.8 1.0

Zinc binding site 3 out of 8 in the The Dyw Domain of A. Thaliana OTP86 in Its Active State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Dyw Domain of A. Thaliana OTP86 in Its Active State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1001 b:14.8 occ:1.00 NE2 B:HIS924 2.0 12.7 1.0 ND1 B:HIS947 2.1 12.1 1.0 SG B:CYS954 2.3 13.8 1.0 SG B:CYS956 2.3 17.6 1.0 CE1 B:HIS947 2.9 16.8 1.0 CD2 B:HIS924 3.0 16.6 1.0 CE1 B:HIS924 3.1 15.6 1.0 CG B:HIS947 3.2 15.1 1.0 CB B:CYS954 3.2 12.8 1.0 CB B:CYS956 3.3 19.8 1.0 CB B:HIS947 3.6 13.2 1.0 N B:CYS956 4.1 14.1 1.0 NE2 B:HIS947 4.1 18.5 1.0 CG B:HIS924 4.2 16.1 1.0 ND1 B:HIS924 4.2 16.6 1.0 CA B:CYS956 4.2 17.3 1.0 CA B:HIS947 4.2 11.8 1.0 CD2 B:HIS947 4.2 13.9 1.0 CE1 B:PHE949 4.2 15.7 1.0 CZ B:PHE949 4.3 14.6 1.0 CA B:CYS954 4.6 13.0 1.0 CE3 B:TRP960 4.6 19.1 1.0 CD2 B:TRP960 4.9 17.2 1.0 C B:CYS954 4.9 14.9 1.0 C B:CYS956 4.9 18.1 1.0 N B:ASP958 5.0 18.6 1.0

Zinc binding site 4 out of 8 in the The Dyw Domain of A. Thaliana OTP86 in Its Active State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Dyw Domain of A. Thaliana OTP86 in Its Active State within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1002 b:19.9 occ:1.00 O B:HOH1117 2.1 16.3 1.0 ND1 B:HIS892 2.1 27.7 1.0 SG B:CYS923 2.2 19.0 1.0 SG B:CYS920 2.3 18.2 1.0 CE1 B:HIS892 3.1 27.2 1.0 CB B:CYS923 3.1 17.2 1.0 CG B:HIS892 3.1 27.7 1.0 CB B:CYS920 3.4 18.0 1.0 CB B:HIS892 3.5 21.4 1.0 OE1 B:GLU894 3.7 18.7 1.0 N B:CYS920 3.9 15.9 1.0 N B:CYS923 4.0 18.6 1.0 CA B:CYS920 4.2 19.7 1.0 O B:HOH1163 4.2 33.8 1.0 CA B:CYS923 4.2 16.9 1.0 NE2 B:HIS892 4.2 29.8 1.0 O B:HOH1174 4.2 30.1 1.0 CD2 B:HIS892 4.3 29.3 1.0 CD B:GLU894 4.3 16.6 1.0 O B:HOH1184 4.4 38.6 1.0 OE2 B:GLU894 4.6 19.2 1.0 O B:CYS920 4.7 17.0 1.0 C B:CYS920 4.7 19.9 1.0 CA B:HIS892 4.9 24.6 1.0

Zinc binding site 5 out of 8 in the The Dyw Domain of A. Thaliana OTP86 in Its Active State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Dyw Domain of A. Thaliana OTP86 in Its Active State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1001 b:16.0 occ:1.00 NE2 D:HIS924 2.1 15.2 1.0 ND1 D:HIS947 2.1 12.7 1.0 SG D:CYS954 2.3 15.3 1.0 SG D:CYS956 2.3 17.4 1.0 CE1 D:HIS947 2.9 14.9 1.0 CD2 D:HIS924 3.0 18.7 1.0 CE1 D:HIS924 3.1 17.6 1.0 CB D:CYS954 3.1 16.1 1.0 CG D:HIS947 3.2 16.0 1.0 CB D:CYS956 3.3 19.5 1.0 CB D:HIS947 3.6 15.5 1.0 N D:CYS956 4.1 16.1 1.0 NE2 D:HIS947 4.1 20.0 1.0 CG D:HIS924 4.2 14.8 1.0 ND1 D:HIS924 4.2 14.0 1.0 CE1 D:PHE949 4.2 15.3 1.0 CD2 D:HIS947 4.2 16.1 1.0 CZ D:PHE949 4.2 15.2 1.0 CA D:HIS947 4.2 13.0 1.0 CA D:CYS956 4.2 17.6 1.0 CA D:CYS954 4.6 13.4 1.0 CE3 D:TRP960 4.6 18.9 1.0 C D:CYS954 4.8 16.8 1.0 CD2 D:TRP960 4.9 17.8 1.0 C D:CYS956 4.9 20.8 1.0 N D:ASP958 5.0 18.3 1.0

Zinc binding site 6 out of 8 in the The Dyw Domain of A. Thaliana OTP86 in Its Active State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Dyw Domain of A. Thaliana OTP86 in Its Active State within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1002 b:18.0 occ:1.00 O D:HOH1116 2.1 16.1 1.0 ND1 D:HIS892 2.2 23.8 1.0 SG D:CYS923 2.3 18.2 1.0 SG D:CYS920 2.3 16.0 1.0 CB D:CYS923 3.0 16.7 1.0 CG D:HIS892 3.1 23.1 1.0 CE1 D:HIS892 3.2 23.5 1.0 CB D:HIS892 3.4 23.9 1.0 CB D:CYS920 3.5 18.8 1.0 OE1 D:GLU894 3.7 17.0 1.0 N D:CYS920 3.9 12.7 1.0 N D:CYS923 4.0 15.8 1.0 O D:HOH1166 4.1 31.7 1.0 CA D:CYS923 4.1 16.1 1.0 O D:HOH1162 4.2 22.9 1.0 CA D:CYS920 4.2 19.5 1.0 CD2 D:HIS892 4.3 27.9 1.0 CD D:GLU894 4.3 19.6 1.0 NE2 D:HIS892 4.3 29.8 1.0 OE2 D:GLU894 4.5 17.9 1.0 C D:CYS920 4.8 19.7 1.0 O D:CYS920 4.8 15.8 1.0 CA D:HIS892 4.9 27.3 1.0

Zinc binding site 7 out of 8 in the The Dyw Domain of A. Thaliana OTP86 in Its Active State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Dyw Domain of A. Thaliana OTP86 in Its Active State within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1001 b:15.5 occ:1.00 NE2 G:HIS924 2.0 16.4 1.0 ND1 G:HIS947 2.1 13.7 1.0 SG G:CYS956 2.3 18.9 1.0 SG G:CYS954 2.3 16.8 1.0 CE1 G:HIS947 2.9 18.7 1.0 CD2 G:HIS924 3.0 15.1 1.0 CE1 G:HIS924 3.1 16.3 1.0 CG G:HIS947 3.1 13.9 1.0 CB G:CYS954 3.2 15.7 1.0 CB G:CYS956 3.3 17.8 1.0 CB G:HIS947 3.6 15.9 1.0 N G:CYS956 4.0 16.4 1.0 NE2 G:HIS947 4.1 17.7 1.0 ND1 G:HIS924 4.1 16.5 1.0 CG G:HIS924 4.2 15.6 1.0 CD2 G:HIS947 4.2 16.3 1.0 CA G:CYS956 4.2 17.3 1.0 CE1 G:PHE949 4.2 17.4 1.0 CA G:HIS947 4.3 14.1 1.0 CZ G:PHE949 4.3 14.8 1.0 CA G:CYS954 4.6 14.9 1.0 CE3 G:TRP960 4.7 20.3 1.0 C G:CYS954 4.9 19.0 1.0 C G:CYS956 4.9 18.0 1.0 CD2 G:TRP960 4.9 17.3 1.0 N G:ASP958 4.9 21.7 1.0

Zinc binding site 8 out of 8 in the The Dyw Domain of A. Thaliana OTP86 in Its Active State


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Dyw Domain of A. Thaliana OTP86 in Its Active State within 5.0Å range: probe atom residue distance (Å) B Occ G:Zn1002 b:21.9 occ:1.00 O G:HOH1116 2.0 17.0 1.0 ND1 G:HIS892 2.2 32.9 1.0 SG G:CYS920 2.3 19.9 1.0 SG G:CYS923 2.3 20.6 1.0 CE1 G:HIS892 3.1 34.2 1.0 CB G:CYS923 3.1 18.6 1.0 CG G:HIS892 3.2 35.9 1.0 CB G:CYS920 3.4 19.5 1.0 CB G:HIS892 3.5 39.0 1.0 OE1 G:GLU894 3.8 25.1 1.0 N G:CYS920 3.9 15.6 1.0 O G:HOH1168 4.0 32.5 1.0 N G:CYS923 4.0 19.7 1.0 CA G:CYS923 4.1 18.2 1.0 CA G:CYS920 4.2 16.8 1.0 O G:HOH1153 4.2 41.7 1.0 NE2 G:HIS892 4.2 34.0 1.0 CD2 G:HIS892 4.3 35.7 1.0 CD G:GLU894 4.3 18.8 1.0 O G:HOH1157 4.3 39.9 1.0 OE2 G:GLU894 4.6 19.4 1.0 C G:CYS920 4.7 20.8 1.0 O G:CYS920 4.7 17.6 1.0 CA G:HIS892 5.0 41.9 1.0

M.Takenaka, S.Takenaka, T.Barthel, B.Frink, S.Haag, D.Verbitskiy, B.Oldenkott, M.Schallenberg-Ruedinger, C.Feiler, M.S.Weiss, G.J.Palm, G.Weber. Dyw Domain Structures Imply An Unusual Regulation Principle in Plant Organellar Rna Editing Catalysis Nat Catal.
ISSN: ESSN 2520-1158
DOI: 10.1038/S41929-021-00633-X