Chlorine in PDB 8k2e: Crystal Structure of YTHDC1 and Y3 Complex

The structure of Crystal Structure of YTHDC1 and Y3 Complex, PDB code: 8k2e was solved by H.L.Zhang, S.Y.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.71 / 1.60
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.644, 103.515, 41.815, 90, 102.43, 90
R / Rfree (%)	18.6 / 22.4

The structure of Crystal Structure of YTHDC1 and Y3 Complex also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 and Y3 Complex (pdb code 8k2e). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of YTHDC1 and Y3 Complex, PDB code: 8k2e:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of YTHDC1 and Y3 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of YTHDC1 and Y3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:19.3 occ:1.00 CL1 B:VIM601 0.0 19.3 1.0 C1 B:VIM601 1.8 11.3 1.0 C2 B:VIM601 2.7 12.1 1.0 C6 B:VIM601 2.8 17.4 1.0 H061 B:VIM601 2.8 20.8 1.0 C15 B:VIM601 3.1 20.6 1.0 O B:HOH731 3.3 15.1 1.0 O17 B:VIM601 3.5 19.6 1.0 CB B:ASN367 3.5 10.4 1.0 O16 B:VIM601 3.7 14.2 1.0 NE1 B:TRP377 3.8 11.1 1.0 CD1 B:TRP377 3.8 9.9 1.0 C B:ASN367 3.9 9.0 1.0 O B:ASN367 3.9 8.3 1.0 N B:VAL368 4.0 8.3 1.0 OG B:SER362 4.0 16.6 1.0 C5 B:VIM601 4.0 18.9 1.0 C3 B:VIM601 4.0 13.9 1.0 CG2 B:VAL368 4.1 9.7 1.0 CB B:SER362 4.2 11.7 1.0 CA B:ASN367 4.4 8.7 1.0 CA B:VAL368 4.4 9.8 1.0 C4 B:VIM601 4.5 16.3 1.0 CG B:ASN367 4.7 12.9 1.0 H051 B:VIM601 4.8 22.6 1.0 CE2 B:PHE401 4.8 11.2 1.0 CZ3 B:TRP428 4.8 14.1 1.0 O B:ASN364 4.9 11.9 1.0 O B:HOH720 4.9 20.8 1.0 ND2 B:ASN367 5.0 15.2 1.0 CB B:VAL368 5.0 10.4 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of YTHDC1 and Y3 Complex


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of YTHDC1 and Y3 Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:29.8 occ:1.00 CL1 A:VIM601 0.0 29.8 1.0 C1 A:VIM601 1.8 17.1 1.0 C6 A:VIM601 2.8 17.7 1.0 C2 A:VIM601 2.8 21.8 1.0 H061 A:VIM601 2.8 21.1 1.0 C15 A:VIM601 3.2 25.1 1.0 O A:HOH775 3.4 18.2 1.0 CB A:ASN367 3.5 18.1 1.0 O16 A:VIM601 3.7 25.1 1.0 C A:ASN367 3.7 14.1 1.0 O17 A:VIM601 3.8 22.2 1.0 CD1 A:TRP377 3.8 12.1 1.0 O A:ASN367 3.8 13.6 1.0 NE1 A:TRP377 3.9 11.6 1.0 N A:VAL368 3.9 13.1 1.0 C5 A:VIM601 4.1 17.7 1.0 C3 A:VIM601 4.1 23.3 1.0 OG A:SER362 4.1 19.5 1.0 CG2 A:VAL368 4.2 14.9 1.0 CA A:ASN367 4.2 19.1 1.0 CA A:VAL368 4.3 11.9 1.0 CB A:SER362 4.4 15.3 1.0 C4 A:VIM601 4.6 19.4 1.0 CZ3 A:TRP428 4.6 20.6 1.0 CG A:ASN367 4.7 14.8 1.0 H051 A:VIM601 4.8 21.1 1.0 CB A:VAL368 4.9 12.5 1.0 CB A:ALA371 4.9 11.6 1.0 O A:HOH708 5.0 22.4 1.0 CE3 A:TRP428 5.0 23.1 1.0

Y.Jiang, G.Zhang, J.You, H.Zhang, R.Yao, H.Xie, L.Zhang, Z.Xia, M.Dai, Y.Wu, L.Li, S.Yang. Pocketflow Is A Data-and-Knowledge-Driven Structure-Based Molecular Generative Model Nat. Mach. Intell. V. 6 326 2024.
DOI: 10.1038/S42256-024-00808-8