Zinc in PDB 4yad: Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B)

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B), PDB code: 4yad was solved by G.Poncet-Montange, W.Palmer, P.Jones, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	60.73 / 1.73
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.350, 36.950, 129.280, 90.00, 110.03, 90.00
R / Rfree (%)	17.6 / 20.8

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B) (pdb code 4yad). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B), PDB code: 4yad:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:17.9 occ:1.00 ND1 A:HIS849 2.2 20.0 1.0 SG A:CYS829 2.2 17.5 1.0 SG A:CYS852 2.3 19.1 1.0 SG A:CYS832 2.3 17.4 1.0 CE1 A:HIS849 3.0 20.8 1.0 CB A:CYS829 3.1 15.1 1.0 CB A:CYS852 3.2 17.2 1.0 CG A:HIS849 3.3 21.0 1.0 CB A:CYS832 3.3 18.0 1.0 CB A:HIS849 3.7 18.4 1.0 N A:CYS832 3.9 16.2 1.0 N A:HIS849 4.0 18.0 1.0 CA A:CYS832 4.1 16.1 1.0 NE2 A:HIS849 4.2 20.7 1.0 CD2 A:HIS849 4.4 21.5 1.0 CA A:HIS849 4.4 18.3 1.0 CA A:CYS829 4.5 17.9 1.0 CB A:VAL831 4.6 17.5 1.0 CA A:CYS852 4.6 17.9 1.0 O A:HOH1330 4.8 38.1 1.0 O A:HOH1323 4.8 34.6 1.0 C A:VAL831 4.9 18.5 1.0 C A:CYS832 4.9 17.2 1.0 CG1 A:VAL831 5.0 15.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:19.8 occ:1.00 SG A:CYS870 2.2 21.7 1.0 SG A:CYS841 2.4 20.7 1.0 SG A:CYS844 2.4 21.1 1.0 SG A:CYS867 2.4 17.5 1.0 CB A:CYS841 3.2 19.5 1.0 CB A:CYS844 3.2 23.4 1.0 CB A:CYS870 3.3 20.0 1.0 CB A:CYS867 3.5 16.5 1.0 N A:CYS844 3.8 23.7 1.0 N A:CYS867 4.0 17.0 1.0 CA A:CYS844 4.1 23.4 1.0 N A:CYS870 4.1 18.1 1.0 CA A:CYS867 4.3 17.1 1.0 O A:HOH1253 4.3 28.3 1.0 CA A:CYS870 4.3 18.4 1.0 C A:LYS843 4.5 28.6 1.0 O A:HOH1262 4.6 37.4 1.0 C A:CYS844 4.6 23.8 1.0 CA A:CYS841 4.7 22.4 1.0 O A:CYS844 4.7 28.4 1.0 C A:CYS867 4.7 16.1 1.0 CB A:PHE869 4.7 17.9 1.0 O A:CYS867 4.8 14.9 1.0 CB A:LYS843 4.8 31.4 1.0 N A:LYS843 4.8 28.5 1.0 CA A:LYS843 4.9 25.8 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:21.8 occ:1.00 ND1 B:HIS849 2.2 18.4 1.0 SG B:CYS829 2.2 21.6 1.0 SG B:CYS832 2.2 22.8 1.0 SG B:CYS852 2.3 21.4 1.0 CB B:CYS829 3.0 20.9 1.0 CE1 B:HIS849 3.1 20.9 1.0 CG B:HIS849 3.2 23.3 1.0 CB B:CYS852 3.3 18.8 1.0 CB B:CYS832 3.3 19.8 1.0 CB B:HIS849 3.5 22.8 1.0 N B:CYS832 3.8 20.5 1.0 N B:HIS849 4.1 22.6 1.0 CA B:CYS832 4.1 23.2 1.0 NE2 B:HIS849 4.3 19.7 1.0 CD2 B:HIS849 4.3 19.6 1.0 CA B:HIS849 4.4 22.9 1.0 CA B:CYS829 4.5 20.2 1.0 CB B:VAL831 4.6 23.7 1.0 CA B:CYS852 4.7 18.4 1.0 O B:HOH1322 4.8 41.9 1.0 C B:CYS832 4.9 23.8 1.0 C B:VAL831 4.9 21.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B)


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with 2,4- Dimethoxy-N-(1-Methyl-2-Oxo-1,2,3,4-Tetrahydroquinolin-6-Yl)Benzene- 1-Sulfonamide (3B) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:25.5 occ:1.00 SG B:CYS841 2.2 28.4 1.0 SG B:CYS844 2.3 29.5 1.0 SG B:CYS870 2.4 27.3 1.0 SG B:CYS867 2.4 20.5 1.0 CB B:CYS841 3.2 30.3 1.0 CB B:CYS870 3.3 25.1 1.0 CB B:CYS844 3.3 34.4 1.0 CB B:CYS867 3.5 22.5 1.0 N B:CYS844 3.7 33.2 1.0 N B:CYS867 4.0 24.5 1.0 CA B:CYS844 4.0 29.3 1.0 N B:CYS870 4.2 23.0 1.0 CA B:CYS867 4.3 21.3 1.0 CA B:CYS870 4.3 24.9 1.0 O B:HOH1233 4.3 37.0 1.0 O B:HOH1244 4.4 40.0 1.0 C B:LYS843 4.4 39.9 1.0 CA B:CYS841 4.6 31.0 1.0 C B:CYS844 4.7 30.5 1.0 CB B:LYS843 4.7 43.4 1.0 O B:CYS844 4.8 29.1 1.0 C B:CYS867 4.8 21.4 1.0 O B:CYS867 4.8 20.3 1.0 N B:LYS843 4.8 42.0 1.0 CA B:LYS843 4.9 38.4 1.0 CB B:PHE869 4.9 22.1 1.0

W.S.Palmer, G.Poncet-Montange, G.Liu, A.Petrocchi, N.Reyna, G.Subramanian, J.Theroff, A.Yau, M.Kost-Alimova, J.P.Bardenhagen, E.Leo, H.E.Shepard, T.N.Tieu, X.Shi, Y.Zhan, S.Zhao, M.C.Barton, G.Draetta, C.Toniatti, P.Jones, M.Geck Do, J.N.Andersen. Structure-Guided Design of Iacs-9571, A Selective High-Affinity Dual TRIM24-BRPF1 Bromodomain Inhibitor. J.Med.Chem. V. 59 1440 2016.
ISSN: ISSN 0022-2623
PubMed: 26061247
DOI: 10.1021/ACS.JMEDCHEM.5B00405