Zinc in PDB 6y5n: Ring-Dtc Domain of DELTEX1

All present enzymatic activity of Ring-Dtc Domain of DELTEX1:
2.3.2.27;

The structure of Ring-Dtc Domain of DELTEX1, PDB code: 6y5n 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)	36.01 / 1.88
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.490, 86.550, 129.830, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 21.1

The structure of Ring-Dtc Domain of DELTEX1 also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Ring-Dtc Domain of DELTEX1 (pdb code 6y5n). 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 Domain of DELTEX1, PDB code: 6y5n:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Ring-Dtc Domain of DELTEX1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Ring-Dtc Domain of DELTEX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn701 b:54.8 occ:1.00 ND1 A:HIS449 2.2 30.8 1.0 SG A:CYS452 2.4 32.0 1.0 SG A:CYS411 2.4 32.4 1.0 SG A:CYS414 2.5 20.9 1.0 HB3 A:CYS411 2.7 30.6 1.0 HB2 A:HIS449 2.8 33.8 1.0 HB3 A:CYS414 2.9 26.0 1.0 H A:CYS414 3.0 37.3 1.0 CB A:CYS411 3.0 25.4 1.0 CE1 A:HIS449 3.1 22.5 1.0 CG A:HIS449 3.1 30.1 1.0 HB2 A:CYS411 3.1 30.6 1.0 HB2 A:CYS452 3.2 32.1 1.0 CB A:CYS414 3.2 21.5 1.0 H A:HIS449 3.3 36.2 1.0 HE1 A:HIS449 3.3 27.2 1.0 CB A:CYS452 3.3 26.6 1.0 CB A:HIS449 3.4 28.1 1.0 HA A:SER422 3.5 32.2 1.0 HB3 A:CYS452 3.5 32.1 1.0 N A:CYS414 3.7 30.9 1.0 HB A:ILE413 3.9 29.1 1.0 H A:GLY423 3.9 33.0 1.0 HB2 A:CYS414 4.0 26.0 1.0 N A:HIS449 4.0 30.0 1.0 CA A:CYS414 4.0 25.5 1.0 HB3 A:HIS449 4.1 33.8 1.0 NE2 A:HIS449 4.2 31.1 1.0 HB2 A:SER422 4.3 32.9 1.0 CD2 A:HIS449 4.3 29.2 1.0 CA A:HIS449 4.3 29.2 1.0 H A:GLU416 4.4 39.5 1.0 CA A:SER422 4.4 26.7 1.0 H A:ILE413 4.4 30.7 1.0 CA A:CYS411 4.5 24.5 1.0 OG A:SER422 4.5 28.3 1.0 HB2 A:GLU416 4.6 37.3 1.0 H A:CYS452 4.6 27.2 1.0 CB A:SER422 4.6 27.2 1.0 H A:MET415 4.6 24.9 1.0 N A:GLY423 4.7 27.4 1.0 CA A:CYS452 4.7 20.2 1.0 HD23 A:LEU418 4.8 35.0 1.0 CB A:ILE413 4.8 24.1 1.0 HA A:CYS414 4.8 30.7 1.0 C A:CYS414 4.8 27.4 1.0 C A:ILE413 4.8 24.7 1.0 O A:CYS411 4.8 27.8 1.0 C A:CYS411 4.9 29.3 1.0 HA A:TYR448 4.9 34.4 1.0 HA A:CYS411 4.9 29.6 1.0 HG A:SER422 4.9 34.1 1.0 HB3 A:TYR448 5.0 31.9 1.0 N A:MET415 5.0 20.6 1.0 HA A:CYS452 5.0 23.5 1.0 O A:GLU416 5.0 29.9 1.0 O A:HIS449 5.0 25.2 1.0

Zinc binding site 2 out of 4 in the Ring-Dtc Domain of DELTEX1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Ring-Dtc Domain of DELTEX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:39.6 occ:1.00 ND1 A:HIS446 2.0 34.8 1.0 SG A:CYS471 2.4 42.6 1.0 SG A:CYS444 2.4 46.7 1.0 SG A:CYS468 2.4 41.2 1.0 HB2 A:CYS444 2.8 37.5 1.0 CE1 A:HIS446 2.9 31.5 1.0 HB2 A:HIS446 3.0 33.6 1.0 HE1 A:HIS446 3.0 37.9 1.0 CB A:CYS444 3.1 31.1 1.0 H A:CYS471 3.1 36.1 1.0 HB3 A:CYS471 3.1 33.6 1.0 CG A:HIS446 3.1 32.5 1.0 HB3 A:CYS468 3.1 36.2 1.0 CB A:CYS468 3.2 30.0 1.0 HB2 A:CYS468 3.2 36.2 1.0 HB3 A:CYS444 3.3 37.5 1.0 CB A:CYS471 3.3 27.9 1.0 CB A:HIS446 3.6 27.9 1.0 HB A:THR470 3.6 33.2 1.0 N A:CYS471 3.7 29.9 1.0 H A:HIS446 3.8 32.2 1.0 NE2 A:HIS446 4.1 40.7 1.0 HH A:TYR475 4.1 50.7 1.0 HH A:TYR448 4.1 29.6 1.0 CA A:CYS471 4.1 32.6 1.0 HB2 A:CYS471 4.1 33.6 1.0 HB3 A:HIS446 4.2 33.6 1.0 CD2 A:HIS446 4.2 31.9 1.0 HB1 A:ALA473 4.2 34.2 1.0 H A:ALA473 4.4 33.0 1.0 N A:HIS446 4.5 26.7 1.0 HD23 A:LEU441 4.5 37.1 1.0 H A:THR470 4.5 31.5 1.0 CA A:CYS444 4.5 21.5 1.0 CB A:THR470 4.6 27.6 1.0 H A:LYS472 4.6 34.3 1.0 HG22 A:THR470 4.7 43.3 1.0 CA A:CYS468 4.7 19.5 1.0 CA A:HIS446 4.7 23.1 1.0 O A:HOH1094 4.7 39.0 1.0 HE2 A:TYR475 4.8 32.6 1.0 C A:CYS444 4.8 26.9 1.0 C A:CYS471 4.8 28.9 1.0 C A:THR470 4.8 26.8 1.0 HE2 A:HIS446 4.8 49.0 1.0 OH A:TYR448 4.8 24.5 1.0 OH A:TYR475 4.9 42.1 1.0 HB3 A:ALA473 4.9 34.2 1.0 HA A:CYS471 4.9 39.2 1.0 N A:LYS472 4.9 28.5 1.0 H A:CYS444 5.0 29.0 1.0 HA A:CYS468 5.0 23.5 1.0

Zinc binding site 3 out of 4 in the Ring-Dtc Domain of DELTEX1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Ring-Dtc Domain of DELTEX1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn701 b:55.5 occ:1.00 ND1 B:HIS446 2.1 59.1 1.0 SG B:CYS444 2.2 69.5 1.0 SG B:CYS468 2.3 51.0 1.0 SG B:CYS471 2.3 68.0 1.0 HB2 B:CYS444 2.7 67.9 1.0 HB2 B:HIS446 2.9 56.1 1.0 CE1 B:HIS446 3.0 55.0 1.0 CB B:CYS444 3.0 56.5 1.0 CG B:HIS446 3.1 56.0 1.0 H B:CYS471 3.1 66.7 1.0 HB3 B:CYS468 3.2 54.4 1.0 HE1 B:HIS446 3.2 66.2 1.0 CB B:CYS468 3.2 45.2 1.0 HB3 B:CYS471 3.3 59.7 1.0 HB2 B:CYS468 3.3 54.4 1.0 HB3 B:CYS444 3.3 67.9 1.0 CB B:CYS471 3.4 49.6 1.0 CB B:HIS446 3.4 46.6 1.0 HB B:THR470 3.6 58.2 1.0 N B:CYS471 3.8 55.5 1.0 H B:HIS446 3.9 60.1 1.0 HB3 B:HIS446 4.0 56.1 1.0 HB3 B:ALA473 4.0 51.6 1.0 HH B:TYR448 4.1 55.0 1.0 NE2 B:HIS446 4.1 59.9 1.0 CD2 B:HIS446 4.2 56.6 1.0 CA B:CYS471 4.2 51.9 1.0 HB2 B:CYS471 4.2 59.7 1.0 HH B:TYR475 4.2 70.9 1.0 HD12 B:LEU441 4.3 54.7 1.0 H B:ALA473 4.3 54.8 1.0 CA B:CYS444 4.4 55.2 1.0 H B:THR470 4.4 60.7 1.0 N B:HIS446 4.5 50.0 1.0 CB B:THR470 4.6 48.4 1.0 HB2 B:ALA473 4.6 51.6 1.0 CA B:CYS468 4.6 37.2 1.0 CA B:HIS446 4.6 50.8 1.0 HD13 B:LEU441 4.7 54.7 1.0 C B:CYS444 4.7 59.1 1.0 CB B:ALA473 4.8 42.9 1.0 H B:LYS472 4.8 61.6 1.0 HB2 B:LEU441 4.8 56.8 1.0 HE1 B:TYR475 4.8 55.4 1.0 C B:CYS471 4.8 54.8 1.0 OH B:TYR448 4.8 45.7 1.0 O B:CYS444 4.9 63.6 1.0 C B:THR470 4.9 61.2 1.0 HE2 B:HIS446 4.9 72.0 1.0 HG22 B:THR470 4.9 64.1 1.0 HA B:CYS468 4.9 44.9 1.0 CD1 B:LEU441 5.0 45.4 1.0 HA B:CYS444 5.0 66.4 1.0 H B:CYS444 5.0 79.7 1.0 HA B:CYS471 5.0 62.4 1.0 HE2 B:TYR448 5.0 52.8 1.0

Zinc binding site 4 out of 4 in the Ring-Dtc Domain of DELTEX1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Ring-Dtc Domain of DELTEX1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:80.8 occ:1.00 HG B:CYS452 1.2 66.4 1.0 SG B:CYS411 2.1 50.1 1.0 ND1 B:HIS449 2.2 58.5 1.0 SG B:CYS452 2.3 55.2 1.0 SG B:CYS414 2.4 56.9 1.0 HB2 B:HIS449 2.7 60.5 1.0 HB3 B:CYS411 2.9 61.4 1.0 H B:CYS414 3.0 50.5 1.0 HB3 B:CYS414 3.0 58.1 1.0 CB B:CYS411 3.1 51.0 1.0 CG B:HIS449 3.1 49.4 1.0 HB2 B:CYS452 3.1 65.7 1.0 CE1 B:HIS449 3.2 49.3 1.0 CB B:CYS452 3.2 54.6 1.0 H B:HIS449 3.2 68.3 1.0 CB B:CYS414 3.3 48.3 1.0 HB2 B:CYS411 3.3 61.4 1.0 CB B:HIS449 3.3 50.3 1.0 HB3 B:CYS452 3.4 65.7 1.0 HE1 B:HIS449 3.4 59.4 1.0 HA B:SER422 3.6 68.4 1.0 HG B:SER422 3.7 67.4 1.0 N B:CYS414 3.8 42.0 1.0 HB B:ILE413 3.8 48.7 1.0 H B:GLY423 3.9 66.8 1.0 N B:HIS449 4.0 56.8 1.0 HB3 B:HIS449 4.0 60.5 1.0 HB2 B:CYS414 4.1 58.1 1.0 CA B:CYS414 4.1 48.4 1.0 HB2 B:SER422 4.2 68.7 1.0 CD2 B:HIS449 4.2 58.0 1.0 NE2 B:HIS449 4.2 60.6 1.0 CA B:HIS449 4.3 49.2 1.0 H B:GLU416 4.4 60.2 1.0 H B:ILE413 4.4 59.2 1.0 CA B:SER422 4.5 56.8 1.0 OG B:SER422 4.5 56.0 1.0 CA B:CYS411 4.5 51.1 1.0 H B:CYS452 4.5 61.0 1.0 CB B:SER422 4.6 57.2 1.0 HB2 B:GLU416 4.6 64.2 1.0 CA B:CYS452 4.6 49.2 1.0 N B:GLY423 4.6 55.5 1.0 H B:MET415 4.7 57.5 1.0 CB B:ILE413 4.7 40.5 1.0 O B:CYS411 4.8 54.7 1.0 HB3 B:TYR448 4.8 51.4 1.0 HA B:CYS452 4.9 59.3 1.0 HD23 B:LEU418 4.9 57.3 1.0 C B:CYS411 4.9 48.0 1.0 HA B:CYS414 4.9 58.2 1.0 C B:ILE413 4.9 42.3 1.0 HA B:TYR448 4.9 54.3 1.0 C B:CYS414 4.9 50.7 1.0 HD21 A:LEU590 4.9 65.7 1.0 O B:HIS449 5.0 44.3 1.0 HA B:CYS411 5.0 61.4 1.0 O B:GLU416 5.0 57.0 1.0 HA B:HIS449 5.0 59.2 1.0 HG22 B:ILE413 5.0 46.9 1.0 N B:CYS452 5.0 50.8 1.0

C.Chatrin, M.Gabrielsen, L.Buetow, M.A.Nakasone, S.F.Ahmed, D.Sumpton, G.J.Sibbet, B.O.Smith, D.T.Huang. Structural Insights Into Adp-Ribosylation of Ubiquitin By Deltex Family E3 Ubiquitin Ligases. Sci Adv V. 6 2020.
ISSN: ESSN 2375-2548
PubMed: 32948590
DOI: 10.1126/SCIADV.ABC0418