Chlorine in PDB 6ym8: Crystal Structure of YTHDC1 with Compound YLI_DC1_002

The structure of Crystal Structure of YTHDC1 with Compound YLI_DC1_002, PDB code: 6ym8 was solved by R.K.Bedi, Y.Li, L.Wiedmer, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.33 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.81, 103.6, 42.03, 90, 105.66, 90
R / Rfree (%)	18.6 / 21.7

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 with Compound YLI_DC1_002 (pdb code 6ym8). 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 with Compound YLI_DC1_002, PDB code: 6ym8:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of YTHDC1 with Compound YLI_DC1_002


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 with Compound YLI_DC1_002 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:27.4 occ:1.00 CL1 A:OYN601 0.0 27.4 1.0 C02 A:OYN601 1.8 23.4 1.0 N03 A:OYN601 2.6 25.3 1.0 N12 A:OYN601 2.7 22.9 1.0 ND2 A:ASN364 3.0 32.5 1.0 ND2 A:ASN367 3.1 23.7 1.0 N A:ASN363 3.4 24.3 1.0 CG A:ASN364 3.4 25.3 1.0 CB A:ASN363 3.5 31.1 1.0 N A:ASN364 3.5 20.4 1.0 OG A:SER362 3.6 21.8 1.0 OD1 A:ASN364 3.6 25.3 1.0 CG A:PRO431 3.7 41.9 1.0 CA A:ASN363 3.8 25.6 1.0 O A:VAL429 3.9 34.2 1.0 C09 A:OYN601 3.9 21.4 1.0 C04 A:OYN601 3.9 27.6 1.0 CD A:PRO431 4.0 38.4 1.0 CG A:ASN367 4.0 27.3 1.0 C A:ASN363 4.0 24.7 1.0 CB A:ASN364 4.3 24.2 1.0 C A:SER362 4.4 21.5 1.0 CB A:ASN367 4.4 23.9 1.0 C08 A:OYN601 4.4 23.7 1.0 CA A:ASN364 4.5 22.2 1.0 OD1 A:ASN363 4.5 43.5 1.0 CG A:ASN363 4.5 39.1 1.0 CA A:SER362 4.7 18.0 1.0 CB A:SER362 4.7 20.6 1.0 O A:ASN364 4.7 21.2 1.0 OD1 A:ASN367 4.9 26.1 1.0 N A:PRO431 5.0 43.6 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of YTHDC1 with Compound YLI_DC1_002


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 with Compound YLI_DC1_002 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:21.0 occ:1.00 CL1 B:OYN601 0.0 21.0 1.0 C02 B:OYN601 1.8 18.4 1.0 N03 B:OYN601 2.6 18.8 1.0 N12 B:OYN601 2.7 18.6 1.0 ND2 B:ASN364 3.1 21.3 1.0 ND2 B:ASN367 3.3 18.2 1.0 CG B:ASN364 3.3 20.9 1.0 CG B:PRO431 3.5 32.0 1.0 OD1 B:ASN364 3.5 21.9 1.0 N B:ASN364 3.5 20.3 1.0 OG B:SER362 3.6 20.1 1.0 N B:ASN363 3.6 18.9 1.0 CB B:ASN363 3.7 21.7 1.0 CD B:PRO431 3.9 27.8 1.0 C04 B:OYN601 3.9 20.8 1.0 C09 B:OYN601 3.9 19.3 1.0 CA B:ASN363 4.0 22.3 1.0 C B:ASN363 4.1 23.3 1.0 CG B:ASN367 4.2 20.0 1.0 O B:VAL429 4.2 21.7 1.0 CB B:ASN364 4.2 22.5 1.0 CA B:ASN364 4.4 20.1 1.0 C08 B:OYN601 4.4 17.4 1.0 CB B:ASN367 4.4 16.2 1.0 C B:SER362 4.5 15.1 1.0 CB B:SER362 4.7 17.4 1.0 CG B:ASN363 4.7 25.4 1.0 CA B:SER362 4.7 16.8 1.0 O B:ASN364 4.7 20.1 1.0 CB B:PRO431 4.9 30.8 1.0 C B:ASN364 5.0 20.1 1.0

R.K.Bedi, Y.Li, L.Wiedmer, A.Caflisch. Crystal Structure of YTHDC1 with Compound YLI_DC1_002 To Be Published.