Zinc in PDB 6y2x: Ring-Dtc Domains of Deltex 2, Form 2

All present enzymatic activity of Ring-Dtc Domains of Deltex 2, Form 2:
2.3.2.27;

The structure of Ring-Dtc Domains of Deltex 2, Form 2, PDB code: 6y2x was solved by M.Gabrielsen, L.Buetow, D.T.Huang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.41 / 1.77
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	41.756, 219.585, 120.822, 90.00, 90.00, 90.00
R / Rfree (%)	24.2 / 27.4

The binding sites of Zinc atom in the Ring-Dtc Domains of Deltex 2, Form 2 (pdb code 6y2x). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Ring-Dtc Domains of Deltex 2, Form 2, PDB code: 6y2x:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Ring-Dtc Domains of Deltex 2, Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ring-Dtc Domains of Deltex 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:66.6 occ:1.00 SG A:CYS453 2.1 72.1 1.0 ND1 A:HIS450 2.2 76.9 1.0 SG A:CYS412 2.4 67.5 1.0 SG A:CYS415 2.5 80.2 1.0 CB A:CYS412 3.2 73.9 1.0 CE1 A:HIS450 3.2 77.1 1.0 CG A:HIS450 3.2 74.6 1.0 CB A:CYS415 3.3 80.7 1.0 CB A:CYS453 3.3 69.0 1.0 CB A:HIS450 3.5 66.8 1.0 N A:CYS415 3.7 77.7 1.0 CA A:CYS415 4.1 82.5 1.0 N A:HIS450 4.1 62.1 1.0 NE2 A:HIS450 4.3 77.2 1.0 CD2 A:HIS450 4.3 69.8 1.0 OG A:SER423 4.4 83.4 1.0 CA A:HIS450 4.4 65.7 1.0 CB A:ILE414 4.4 70.8 1.0 N A:GLY424 4.5 82.7 1.0 CA A:CYS412 4.5 75.6 1.0 CA A:SER423 4.5 80.6 1.0 O A:CYS412 4.6 78.8 1.0 C A:ILE414 4.6 78.1 1.0 CB A:SER423 4.6 79.1 1.0 CA A:CYS453 4.7 69.3 1.0 C A:CYS412 4.8 76.8 1.0 CA A:ILE414 4.8 75.0 1.0 N A:ILE414 4.9 71.4 1.0 C A:CYS415 4.9 87.8 1.0 O A:HIS450 5.0 62.0 1.0 O A:GLU417 5.0 0.0 1.0

Zinc binding site 2 out of 4 in the Ring-Dtc Domains of Deltex 2, Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ring-Dtc Domains of Deltex 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:46.4 occ:1.00 ND1 A:HIS447 1.9 51.2 1.0 SG A:CYS469 2.2 50.1 1.0 SG A:CYS472 2.3 45.0 1.0 SG A:CYS445 2.4 41.6 1.0 CE1 A:HIS447 2.8 47.9 1.0 CG A:HIS447 3.0 47.3 1.0 CB A:CYS469 3.2 50.1 1.0 CB A:CYS445 3.2 39.0 1.0 CB A:HIS447 3.4 51.0 1.0 CB A:CYS472 3.5 47.7 1.0 N A:CYS472 3.7 58.9 1.0 NE2 A:HIS447 3.9 52.5 1.0 CD2 A:HIS447 4.0 48.6 1.0 CA A:CYS472 4.2 54.2 1.0 CB A:SER471 4.3 69.2 1.0 N A:HIS447 4.5 43.4 1.0 CA A:CYS445 4.5 36.6 1.0 CA A:HIS447 4.6 46.5 1.0 CA A:CYS469 4.6 52.6 1.0 CD1 A:LEU442 4.7 47.4 1.0 O A:CYS445 4.7 39.0 1.0 C A:CYS445 4.7 41.0 1.0 C A:SER471 4.7 75.1 1.0 OG A:SER471 4.8 77.1 1.0 CB A:THR474 4.8 50.4 1.0 OG1 A:THR474 4.8 45.1 1.0 C A:CYS472 4.9 53.5 1.0 CA A:SER471 4.9 66.0 1.0 N A:SER471 5.0 59.8 1.0

Zinc binding site 3 out of 4 in the Ring-Dtc Domains of Deltex 2, Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ring-Dtc Domains of Deltex 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:86.1 occ:1.00 SG B:CYS445 2.3 87.2 1.0 SG B:CYS469 2.3 86.2 1.0 ND1 B:HIS447 2.3 95.2 1.0 SG B:CYS472 2.5 88.6 1.0 CG B:HIS447 3.1 92.0 1.0 CB B:CYS469 3.2 84.9 1.0 CE1 B:HIS447 3.3 90.5 1.0 CB B:HIS447 3.3 92.8 1.0 CB B:CYS445 3.9 97.0 1.0 CB B:CYS472 4.0 95.8 1.0 N B:CYS472 4.0 98.3 1.0 CD2 B:HIS447 4.2 93.1 1.0 NE2 B:HIS447 4.2 94.9 1.0 CB B:SER471 4.3 0.5 1.0 N B:HIS447 4.5 99.3 1.0 CA B:HIS447 4.5 87.6 1.0 CA B:CYS472 4.6 95.6 1.0 CA B:CYS469 4.6 86.8 1.0 C B:SER471 4.9 0.9 1.0 OG1 B:THR474 4.9 0.0 1.0 N B:SER471 4.9 0.7 1.0 CA B:SER471 4.9 0.6 1.0

Zinc binding site 4 out of 4 in the Ring-Dtc Domains of Deltex 2, Form 2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ring-Dtc Domains of Deltex 2, Form 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:94.9 occ:1.00 SG B:CYS415 2.3 93.9 1.0 SG B:CYS453 2.5 81.8 1.0 ND1 B:HIS450 2.5 82.2 1.0 SG B:CYS412 2.8 0.3 1.0 CB B:CYS412 3.1 0.6 1.0 CB B:CYS453 3.3 81.2 1.0 CG B:HIS450 3.4 86.5 1.0 CE1 B:HIS450 3.5 83.1 1.0 CB B:HIS450 3.6 80.3 1.0 CB B:CYS415 3.7 0.2 1.0 N B:CYS415 3.8 86.5 1.0 N B:HIS450 3.8 81.4 1.0 CA B:HIS450 4.3 89.2 1.0 CA B:CYS415 4.3 87.0 1.0 CB B:SER423 4.4 82.6 1.0 CA B:SER423 4.4 0.1 1.0 CD2 B:HIS450 4.5 84.6 1.0 CA B:CYS412 4.5 97.1 1.0 NE2 B:HIS450 4.5 82.6 1.0 CB B:ILE414 4.5 84.4 1.0 O B:CYS412 4.6 93.2 1.0 CA B:CYS453 4.7 80.1 1.0 C B:CYS412 4.7 94.0 1.0 C B:ILE414 4.8 93.8 1.0 O B:HIS450 4.9 79.7 1.0 N B:ILE414 4.9 86.6 1.0 CA B:ILE414 5.0 86.0 1.0

S.F.Ahmed, L.Buetow, M.Gabrielsen, S.Lilla, C.Chatrin, G.J.Sibbet, S.Zanivan, D.T.Huang. DELTEX2 C-Terminal Domain Recognizes and Recruits Adp-Ribosylated Proteins For Ubiquitination. Sci Adv V. 6 2020.
ISSN: ESSN 2375-2548
PubMed: 32937373
DOI: 10.1126/SCIADV.ABC0629