Zinc in PDB 4yax: Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G)

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G), PDB code: 4yax 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)	120.67 / 2.25
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.040, 37.110, 128.750, 90.00, 110.41, 90.00
R / Rfree (%)	17 / 23.5

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G) (pdb code 4yax). 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 N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G), PDB code: 4yax:
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 N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G)


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 N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:17.7 occ:1.00 SG A:CYS870 2.1 20.6 1.0 SG A:CYS841 2.3 21.4 1.0 SG A:CYS844 2.4 20.1 1.0 SG A:CYS867 2.4 18.6 1.0 CB A:CYS841 3.2 24.7 1.0 CB A:CYS844 3.2 23.0 1.0 CB A:CYS870 3.3 18.2 1.0 CB A:CYS867 3.6 17.3 1.0 N A:CYS844 3.9 26.3 1.0 CA A:CYS844 4.1 25.1 1.0 N A:CYS867 4.1 19.2 1.0 O A:HOH1259 4.1 23.0 1.0 N A:CYS870 4.1 16.6 1.0 CA A:CYS867 4.3 17.9 1.0 CA A:CYS870 4.3 17.9 1.0 O A:HOH1283 4.6 38.3 1.0 C A:LYS843 4.6 30.4 1.0 CA A:CYS841 4.7 25.8 1.0 C A:CYS844 4.7 25.3 1.0 O A:CYS867 4.7 16.7 1.0 C A:CYS867 4.8 15.7 1.0 CB A:PHE869 4.8 13.7 1.0 N A:LYS843 4.9 32.4 1.0 O A:CYS844 4.9 30.1 1.0 CB A:LYS843 4.9 36.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G)


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 N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G) within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1103 b:15.6 occ:1.00 SG A:CYS852 2.1 13.9 1.0 SG A:CYS829 2.2 14.3 1.0 SG A:CYS832 2.3 15.1 1.0 ND1 A:HIS849 2.3 20.6 1.0 CB A:CYS829 2.9 16.8 1.0 CB A:CYS852 3.1 13.4 1.0 CB A:CYS832 3.2 17.0 1.0 CE1 A:HIS849 3.3 21.0 1.0 CG A:HIS849 3.4 20.6 1.0 CB A:HIS849 3.7 18.4 1.0 N A:CYS832 3.9 17.6 1.0 N A:HIS849 4.1 17.3 1.0 CA A:CYS832 4.1 17.9 1.0 CA A:CYS829 4.4 17.7 1.0 NE2 A:HIS849 4.4 21.6 1.0 CD2 A:HIS849 4.5 21.3 1.0 CA A:HIS849 4.5 17.9 1.0 O A:HOH1392 4.5 42.3 1.0 CA A:CYS852 4.5 13.6 1.0 CB A:VAL831 4.5 15.9 1.0 O A:HOH1339 4.7 35.1 1.0 C A:CYS829 4.9 17.4 1.0 C A:VAL831 4.9 17.1 1.0 O A:ASN834 4.9 27.1 1.0 C A:CYS832 5.0 20.9 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G)


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 N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:21.0 occ:1.00 ND1 B:HIS849 2.2 23.6 1.0 SG B:CYS852 2.2 19.3 1.0 SG B:CYS829 2.3 19.9 1.0 SG B:CYS832 2.3 19.8 1.0 CB B:CYS829 3.0 21.0 1.0 CE1 B:HIS849 3.0 23.0 1.0 CB B:CYS852 3.2 18.3 1.0 CG B:HIS849 3.3 23.0 1.0 CB B:CYS832 3.3 19.5 1.0 CB B:HIS849 3.7 22.0 1.0 N B:CYS832 3.7 19.7 1.0 N B:HIS849 4.1 20.0 1.0 CA B:CYS832 4.1 20.1 1.0 NE2 B:HIS849 4.2 23.1 1.0 O B:HOH1355 4.3 55.8 1.0 CD2 B:HIS849 4.3 22.3 1.0 CA B:CYS829 4.5 22.2 1.0 CA B:HIS849 4.5 21.1 1.0 CB B:VAL831 4.6 17.9 1.0 O B:HOH1377 4.6 46.8 1.0 CA B:CYS852 4.6 18.9 1.0 C B:CYS832 4.8 22.0 1.0 C B:VAL831 4.8 18.7 1.0 N B:VAL831 5.0 18.4 1.0 N B:GLN833 5.0 25.6 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G)


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 N-[6-(4- Methoxyphenoxy)-1,3-Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5- Yl]Benzenesulfonamide (5G) within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:25.6 occ:1.00 SG B:CYS841 2.1 28.4 1.0 SG B:CYS870 2.3 29.1 1.0 SG B:CYS844 2.3 25.7 1.0 SG B:CYS867 2.4 24.3 1.0 CB B:CYS841 3.1 32.0 1.0 CB B:CYS870 3.1 26.3 1.0 CB B:CYS844 3.3 29.5 1.0 CB B:CYS867 3.5 24.9 1.0 N B:CYS844 3.8 33.0 1.0 N B:CYS867 4.0 26.5 1.0 O B:HOH1244 4.0 28.5 1.0 CA B:CYS844 4.1 30.5 1.0 N B:CYS870 4.2 23.6 1.0 CA B:CYS867 4.2 25.4 1.0 CA B:CYS870 4.3 25.3 1.0 O B:HOH1251 4.3 41.3 1.0 C B:LYS843 4.5 38.6 1.0 CA B:CYS841 4.5 34.9 1.0 C B:CYS844 4.7 30.7 1.0 C B:CYS867 4.7 23.6 1.0 O B:CYS867 4.7 24.3 1.0 O B:CYS844 4.8 30.6 1.0 CB B:LYS843 4.8 45.2 1.0 N B:LYS843 4.9 42.8 1.0 CB B:PHE869 4.9 23.3 1.0 CA B:LYS843 4.9 41.4 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