Iodine in PDB 6t10: Crystal Structure of YTHDC1 with Fragment 28 (DHU_DC1_176)

The structure of Crystal Structure of YTHDC1 with Fragment 28 (DHU_DC1_176), PDB code: 6t10 was solved by R.K.Bedi, D.Huang, P.Sledz, A.Caflisch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.61 / 1.48
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	39.742, 103.524, 42.189, 90.00, 105.74, 90.00
R / Rfree (%)	19 / 21

The binding sites of Iodine atom in the Crystal Structure of YTHDC1 with Fragment 28 (DHU_DC1_176) (pdb code 6t10). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 2 binding sites of Iodine where determined in the Crystal Structure of YTHDC1 with Fragment 28 (DHU_DC1_176), PDB code: 6t10:
Jump to Iodine binding site number: 1; 2;

Iodine binding site 1 out of 2 in the Crystal Structure of YTHDC1 with Fragment 28 (DHU_DC1_176)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Crystal Structure of YTHDC1 with Fragment 28 (DHU_DC1_176) within 5.0Å range: probe atom residue distance (Å) B Occ A:I601 b:59.8 occ:1.00 I10 A:M6Z601 0.0 59.8 1.0 C07 A:M6Z601 2.1 37.0 1.0 C08 A:M6Z601 3.0 33.4 1.0 C06 A:M6Z601 3.1 34.8 1.0 CE A:MET438 3.5 41.7 1.0 SD A:MET434 3.7 52.2 1.0 CG A:PRO431 3.9 38.4 1.0 CD A:PRO431 3.9 33.8 1.0 CE A:MET434 3.9 41.5 1.0 ND2 A:ASN363 4.0 32.5 1.0 CD2 A:LEU430 4.3 35.3 1.0 C09 A:M6Z601 4.4 31.1 1.0 C05 A:M6Z601 4.4 33.4 1.0 SD A:MET438 4.4 56.6 1.0 CB A:MET434 4.6 40.4 1.0 CG A:LEU430 4.7 35.5 1.0 CB A:LEU430 4.8 33.0 1.0 CG A:MET434 4.8 41.5 1.0 O A:HOH735 4.8 29.8 1.0 C11 A:M6Z601 4.9 31.0 1.0 N A:PRO431 4.9 36.8 1.0

Iodine binding site 2 out of 2 in the Crystal Structure of YTHDC1 with Fragment 28 (DHU_DC1_176)


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Crystal Structure of YTHDC1 with Fragment 28 (DHU_DC1_176) within 5.0Å range: probe atom residue distance (Å) B Occ B:I601 b:79.8 occ:1.00 I10 B:M6Z601 0.0 79.8 1.0 C07 B:M6Z601 2.1 43.1 1.0 C08 B:M6Z601 3.1 41.3 1.0 C06 B:M6Z601 3.1 40.0 1.0 C09 B:M6Z601 4.4 36.4 1.0 C05 B:M6Z601 4.4 37.9 1.0 CD2 B:LEU430 4.4 41.3 1.0 CB B:ASN363 4.9 30.1 1.0 C11 B:M6Z601 4.9 34.8 1.0 ND2 B:ASN363 5.0 44.4 1.0

R.K.Bedi, D.Huang, L.Wiedmer, Y.Li, A.Dolbois, J.A.Wojdyla, M.E.Sharpe, A.Caflisch, P.Sledz. Selectively Disrupting M6A-Dependent Protein-Rna Interactions with Fragments. Acs Chem.Biol. 2020.
ISSN: ESSN 1554-8937
PubMed: 32101404
DOI: 10.1021/ACSCHEMBIO.9B00894