Chlorine in PDB 8q2q: Crystal Structure of YTHDC1 in Complex with Compound 2B (YL_32)

The structure of Crystal Structure of YTHDC1 in Complex with Compound 2B (YL_32), PDB code: 8q2q was solved by R.K.Bedi, Y.Li, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.75 / 1.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.98, 103.41, 42.39, 90, 106, 90
R / Rfree (%)	21.6 / 22.7

The binding sites of Chlorine atom in the Crystal Structure of YTHDC1 in Complex with Compound 2B (YL_32) (pdb code 8q2q). 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 in Complex with Compound 2B (YL_32), PDB code: 8q2q:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of YTHDC1 in Complex with Compound 2B (YL_32)


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 in Complex with Compound 2B (YL_32) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl601 b:36.6 occ:1.00 CL12 A:IT6601 0.0 36.6 1.0 C11 A:IT6601 1.8 33.4 1.0 ND2 A:ASN364 2.7 41.2 1.0 N10 A:IT6601 2.7 34.1 1.0 N13 A:IT6601 2.9 29.9 1.0 CG A:ASN364 3.2 35.3 1.0 N A:ASN363 3.2 31.2 1.0 ND2 A:ASN367 3.3 33.4 1.0 N A:ASN364 3.3 29.9 1.0 CB A:ASN363 3.5 34.1 1.0 OD1 A:ASN364 3.6 35.6 1.0 CA A:ASN363 3.6 29.3 1.0 OG A:SER362 3.6 28.4 1.0 C A:ASN363 3.8 29.8 1.0 O A:VAL429 3.9 44.8 1.0 CD A:PRO431 3.9 42.5 1.0 CG A:PRO431 4.0 45.5 1.0 C09 A:IT6601 4.1 34.3 1.0 C03 A:IT6601 4.2 25.0 1.0 CB A:ASN364 4.2 36.8 1.0 CG A:ASN367 4.2 35.8 1.0 C A:SER362 4.3 29.7 1.0 CA A:ASN364 4.3 31.5 1.0 CG A:ASN363 4.5 38.8 1.0 CB A:ASN367 4.6 29.7 1.0 CA A:SER362 4.6 27.4 1.0 O A:ASN364 4.6 27.3 1.0 C04 A:IT6601 4.7 28.7 1.0 O A:HOH830 4.7 44.9 1.0 ND2 A:ASN363 4.7 39.5 1.0 CB A:SER362 4.7 27.0 1.0 O A:ASN363 4.8 31.4 1.0 C A:ASN364 4.9 31.9 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of YTHDC1 in Complex with Compound 2B (YL_32)


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 in Complex with Compound 2B (YL_32) within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl601 b:27.7 occ:1.00 CL12 B:IT6601 0.0 27.7 1.0 C11 B:IT6601 1.8 25.4 1.0 N10 B:IT6601 2.7 25.3 1.0 N13 B:IT6601 2.8 24.1 1.0 ND2 B:ASN364 3.1 26.8 1.0 CG B:ASN364 3.3 24.1 1.0 CG B:PRO431 3.3 40.6 1.0 N B:ASN364 3.4 22.8 1.0 N B:ASN363 3.5 21.5 1.0 ND2 B:ASN367 3.5 23.0 1.0 OD1 B:ASN364 3.6 24.4 1.0 OG B:SER362 3.7 21.3 1.0 CD B:PRO431 3.7 37.6 1.0 CB B:ASN363 3.9 28.3 1.0 C B:ASN363 3.9 23.4 1.0 CA B:ASN363 3.9 23.7 1.0 CB B:ASN364 4.0 22.8 1.0 C03 B:IT6601 4.1 23.7 1.0 C09 B:IT6601 4.1 26.8 1.0 O B:VAL429 4.1 28.4 1.0 CA B:ASN364 4.2 25.1 1.0 CG B:ASN367 4.3 22.9 1.0 C B:SER362 4.5 17.7 1.0 CB B:ASN367 4.5 18.4 1.0 C04 B:IT6601 4.6 22.5 1.0 O B:ASN364 4.6 21.4 1.0 CB B:PRO431 4.7 42.1 1.0 CA B:SER362 4.8 18.9 1.0 C B:ASN364 4.8 22.8 1.0 CB B:SER362 4.8 19.7 1.0 O B:ASN363 4.9 27.5 1.0 N B:PRO431 4.9 42.7 1.0 CG B:ASN363 4.9 27.3 1.0

R.K.Bedi, Y.Li, A.Caflisch. Crystal Structure of YTHDC1 in Complex with Compound 2B (YL_32) To Be Published.