Chlorine 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:

Zinc

(Zn)

4 atoms

The binding sites of Chlorine atom in the Ring-Dtc Domain of DELTEX1 (pdb code 6y5n). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Ring-Dtc Domain of DELTEX1, PDB code: 6y5n:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Ring-Dtc Domain of DELTEX1


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Ring-Dtc Domain of DELTEX1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl705 b:91.4 occ:1.00 HH22 A:ARG534 2.3 39.7 1.0 HA A:VAL576 2.7 35.2 1.0 H A:TRP577 2.8 35.8 1.0 HD1 A:TRP577 3.1 45.2 1.0 NH2 A:ARG534 3.1 33.0 1.0 HB A:VAL576 3.4 40.0 1.0 HG12 A:VAL576 3.4 45.9 1.0 HH12 A:ARG534 3.5 64.9 1.0 HH21 A:ARG534 3.5 39.7 1.0 CA A:VAL576 3.5 29.2 1.0 O A:HOH1032 3.5 59.2 1.0 N A:TRP577 3.6 29.7 1.0 CD1 A:TRP577 3.6 37.5 1.0 CB A:VAL576 3.8 33.2 1.0 CZ A:ARG534 4.0 47.4 1.0 NH1 A:ARG534 4.0 54.0 1.0 O A:VAL575 4.1 33.9 1.0 C A:VAL576 4.1 28.9 1.0 CG1 A:VAL576 4.1 38.2 1.0 NE1 A:TRP577 4.3 35.4 1.0 HE1 A:TRP577 4.3 42.6 1.0 O A:HOH1042 4.3 63.1 1.0 CG A:TRP577 4.4 28.9 1.0 HB2 A:TRP577 4.4 38.3 1.0 HG11 A:VAL576 4.6 45.9 1.0 N A:VAL576 4.7 30.9 1.0 HA A:SER566 4.7 60.0 1.0 CB A:TRP577 4.7 31.8 1.0 CA A:TRP577 4.7 33.5 1.0 HG13 A:VAL576 4.8 45.9 1.0 HB2 A:SER566 4.8 61.2 1.0 C A:VAL575 4.8 30.3 1.0 HH11 A:ARG534 4.9 64.9 1.0 OG A:SER566 5.0 62.2 1.0

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


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Ring-Dtc Domain of DELTEX1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl703 b:53.4 occ:1.00 HH12 B:ARG534 2.3 35.7 1.0 HA B:VAL576 2.7 30.2 1.0 H B:TRP577 2.9 30.0 1.0 HH22 B:ARG534 2.9 39.6 1.0 O B:HOH924 3.0 37.3 1.0 O B:HOH934 3.0 46.7 1.0 NH1 B:ARG534 3.1 29.6 1.0 HD1 B:TRP577 3.1 39.1 1.0 O B:HOH930 3.2 35.6 1.0 HG12 B:VAL576 3.3 43.6 1.0 HB B:VAL576 3.4 34.6 1.0 CA B:VAL576 3.5 25.0 1.0 NH2 B:ARG534 3.6 32.9 1.0 N B:TRP577 3.6 24.9 1.0 CD1 B:TRP577 3.6 32.5 1.0 HH11 B:ARG534 3.7 35.7 1.0 CZ B:ARG534 3.8 32.9 1.0 CB B:VAL576 3.8 28.7 1.0 O B:VAL575 3.9 29.8 1.0 CG1 B:VAL576 4.0 36.2 1.0 C B:VAL576 4.1 27.4 1.0 NE1 B:TRP577 4.3 30.3 1.0 HE1 B:TRP577 4.3 36.5 1.0 HH21 B:ARG534 4.3 39.6 1.0 HA B:SER566 4.4 33.0 1.0 CG B:TRP577 4.4 28.1 1.0 HB2 B:TRP577 4.5 33.3 1.0 HG11 B:VAL576 4.5 43.6 1.0 N B:VAL576 4.6 26.1 1.0 HG13 B:VAL576 4.6 43.6 1.0 HB2 B:SER566 4.6 32.9 1.0 C B:VAL575 4.7 23.1 1.0 H B:ASN567 4.7 40.9 1.0 CB B:TRP577 4.8 27.6 1.0 CA B:TRP577 4.8 25.4 1.0 OG B:SER566 4.9 33.1 1.0 O B:HOH856 5.0 35.1 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