Zinc in PDB 5h1t: Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1

The structure of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1, PDB code: 5h1t was solved by J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.40 / 1.95
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	36.725, 48.612, 123.454, 86.56, 81.47, 67.81
R / Rfree (%)	17.7 / 22

The binding sites of Zinc atom in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 (pdb code 5h1t). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1, PDB code: 5h1t:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1101 b:35.0 occ:1.00 ND1 A:HIS849 2.1 34.6 1.0 SG A:CYS832 2.3 38.8 1.0 SG A:CYS829 2.4 32.0 1.0 SG A:CYS852 2.4 37.2 1.0 CB A:CYS829 3.0 33.9 1.0 CE1 A:HIS849 3.1 32.6 1.0 CG A:HIS849 3.2 43.2 1.0 CB A:CYS852 3.2 26.8 1.0 CB A:CYS832 3.4 37.6 1.0 CB A:HIS849 3.5 38.0 1.0 N A:CYS832 3.8 36.2 1.0 N A:HIS849 4.0 25.6 1.0 CA A:CYS832 4.1 36.7 1.0 NE2 A:HIS849 4.2 40.6 1.0 CD2 A:HIS849 4.3 42.9 1.0 CA A:HIS849 4.4 34.7 1.0 CA A:CYS829 4.5 34.2 1.0 CB A:VAL831 4.6 36.8 1.0 CA A:CYS852 4.7 32.5 1.0 C A:CYS832 4.8 44.5 1.0 C A:VAL831 4.8 39.6 1.0 N A:GLN833 4.9 42.2 1.0 N A:VAL831 5.0 36.6 1.0

Zinc binding site 2 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1102 b:39.0 occ:1.00 SG A:CYS870 2.2 35.3 1.0 SG A:CYS841 2.3 38.9 1.0 SG A:CYS844 2.4 41.0 1.0 SG A:CYS867 2.5 31.3 1.0 CB A:CYS841 3.3 37.8 1.0 CB A:CYS870 3.3 32.7 1.0 CB A:CYS844 3.3 41.4 1.0 CB A:CYS867 3.4 37.3 1.0 N A:CYS844 3.8 44.8 1.0 N A:CYS867 3.9 36.9 1.0 N A:CYS870 4.1 32.5 1.0 CA A:CYS844 4.1 41.9 1.0 CA A:CYS867 4.2 35.1 1.0 CA A:CYS870 4.3 32.6 1.0 C A:LYS843 4.4 50.9 1.0 CB A:LYS843 4.6 47.2 1.0 C A:CYS867 4.7 28.9 1.0 O A:CYS867 4.7 30.3 1.0 CA A:CYS841 4.7 39.6 1.0 C A:CYS844 4.8 42.0 1.0 CB A:PHE869 4.8 30.7 1.0 N A:LYS843 4.9 48.9 1.0 O A:CYS844 4.9 40.0 1.0 CA A:LYS843 4.9 44.8 1.0

Zinc binding site 3 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1101 b:28.0 occ:1.00 SG B:CYS852 2.3 27.1 1.0 ND1 B:HIS849 2.3 35.5 1.0 SG B:CYS829 2.3 26.9 1.0 SG B:CYS832 2.3 27.0 1.0 CB B:CYS829 3.1 29.3 1.0 CG B:HIS849 3.2 32.1 1.0 CB B:CYS852 3.2 23.5 1.0 CE1 B:HIS849 3.2 32.8 1.0 CB B:CYS832 3.3 26.5 1.0 CB B:HIS849 3.4 30.8 1.0 N B:CYS832 3.8 34.3 1.0 N B:HIS849 4.0 29.3 1.0 CA B:CYS832 4.2 28.2 1.0 CD2 B:HIS849 4.3 35.8 1.0 NE2 B:HIS849 4.3 31.0 1.0 CA B:HIS849 4.3 27.2 1.0 CA B:CYS829 4.5 34.2 1.0 CB B:VAL831 4.6 27.7 1.0 CA B:CYS852 4.6 26.3 1.0 C B:VAL831 4.9 33.1 1.0 C B:CYS832 4.9 29.3 1.0

Zinc binding site 4 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1102 b:30.1 occ:1.00 SG B:CYS870 2.2 31.5 1.0 SG B:CYS844 2.3 30.8 1.0 SG B:CYS841 2.3 30.9 1.0 SG B:CYS867 2.4 25.1 1.0 CB B:CYS844 3.3 30.7 1.0 CB B:CYS841 3.3 32.8 1.0 CB B:CYS870 3.3 26.7 1.0 CB B:CYS867 3.6 19.4 1.0 N B:CYS844 3.7 38.1 1.0 CA B:CYS844 4.0 38.2 1.0 N B:CYS867 4.0 23.7 1.0 N B:CYS870 4.1 20.9 1.0 O B:HOH1263 4.2 34.8 1.0 CA B:CYS867 4.3 20.5 1.0 CA B:CYS870 4.3 26.6 1.0 C B:LYS843 4.5 38.9 1.0 C B:CYS844 4.6 37.4 1.0 O B:CYS844 4.7 33.2 1.0 CA B:CYS841 4.7 33.6 1.0 C B:CYS867 4.8 23.1 1.0 O B:CYS867 4.8 23.8 1.0 CB B:PHE869 4.8 21.8 1.0 N B:LYS843 4.8 30.4 1.0 CB B:LYS843 4.9 38.8 1.0 CA B:LYS843 5.0 36.6 1.0

Zinc binding site 5 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1101 b:30.7 occ:1.00 SG C:CYS870 2.2 29.9 1.0 SG C:CYS841 2.4 32.6 1.0 SG C:CYS844 2.4 31.2 1.0 SG C:CYS867 2.4 24.9 1.0 CB C:CYS844 3.3 33.9 1.0 CB C:CYS870 3.3 24.4 1.0 CB C:CYS841 3.3 24.7 1.0 CB C:CYS867 3.5 19.5 1.0 N C:CYS844 3.8 40.3 1.0 N C:CYS867 4.0 24.0 1.0 CA C:CYS844 4.1 36.8 1.0 N C:CYS870 4.1 19.5 1.0 O C:HOH1261 4.2 37.7 1.0 CA C:CYS867 4.3 21.1 1.0 CA C:CYS870 4.3 23.6 1.0 C C:LYS843 4.5 38.5 1.0 CB C:PHE869 4.6 22.6 1.0 C C:CYS844 4.7 32.4 1.0 O C:CYS867 4.7 20.9 1.0 C C:CYS867 4.7 15.0 1.0 CA C:CYS841 4.8 31.8 1.0 O C:CYS844 4.8 32.9 1.0 CB C:LYS843 4.8 37.3 1.0 N C:LYS843 4.8 34.1 1.0 CA C:LYS843 5.0 35.4 1.0 C C:PHE869 5.0 29.3 1.0

Zinc binding site 6 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1102 b:28.7 occ:1.00 SG C:CYS829 2.2 29.6 1.0 SG C:CYS852 2.2 28.1 1.0 ND1 C:HIS849 2.3 37.4 1.0 SG C:CYS832 2.3 27.9 1.0 CB C:CYS829 3.0 30.2 1.0 CB C:CYS852 3.2 30.1 1.0 CE1 C:HIS849 3.2 38.4 1.0 CG C:HIS849 3.2 37.7 1.0 CB C:CYS832 3.3 27.4 1.0 CB C:HIS849 3.5 30.0 1.0 N C:CYS832 3.8 34.3 1.0 N C:HIS849 4.0 31.1 1.0 CA C:CYS832 4.1 23.7 1.0 NE2 C:HIS849 4.3 41.6 1.0 CD2 C:HIS849 4.3 42.1 1.0 CA C:HIS849 4.4 29.2 1.0 CA C:CYS829 4.5 29.0 1.0 CB C:VAL831 4.6 24.7 1.0 CA C:CYS852 4.6 25.9 1.0 C C:VAL831 4.9 30.9 1.0 C C:CYS832 4.9 26.0 1.0 O C:ASN834 4.9 30.0 1.0 CG1 C:VAL831 5.0 22.9 1.0

Zinc binding site 7 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1101 b:34.5 occ:1.00 ND1 D:HIS849 2.2 33.0 1.0 SG D:CYS832 2.3 37.1 1.0 SG D:CYS829 2.3 31.3 1.0 SG D:CYS852 2.4 33.1 1.0 CB D:CYS829 3.0 37.6 1.0 CE1 D:HIS849 3.2 37.0 1.0 CG D:HIS849 3.2 41.3 1.0 CB D:CYS852 3.2 24.8 1.0 CB D:CYS832 3.3 42.8 1.0 CB D:HIS849 3.5 36.5 1.0 N D:CYS832 3.8 39.8 1.0 N D:HIS849 4.0 29.2 1.0 CA D:CYS832 4.2 38.5 1.0 NE2 D:HIS849 4.3 42.2 1.0 CD2 D:HIS849 4.3 42.6 1.0 CA D:HIS849 4.4 32.4 1.0 CA D:CYS829 4.5 35.0 1.0 CB D:VAL831 4.6 34.6 1.0 CA D:CYS852 4.7 33.5 1.0 C D:CYS832 4.9 40.1 1.0 C D:VAL831 4.9 37.5 1.0

Zinc binding site 8 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 1 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1102 b:39.7 occ:1.00 SG D:CYS870 2.3 35.3 1.0 SG D:CYS841 2.3 44.3 1.0 SG D:CYS844 2.3 38.9 1.0 SG D:CYS867 2.4 30.1 1.0 CB D:CYS870 3.3 30.7 1.0 CB D:CYS844 3.3 41.0 1.0 CB D:CYS841 3.3 42.1 1.0 CB D:CYS867 3.4 36.3 1.0 N D:CYS844 3.8 43.1 1.0 N D:CYS867 3.9 37.7 1.0 CA D:CYS844 4.1 42.0 1.0 N D:CYS870 4.1 29.4 1.0 CA D:CYS867 4.2 34.0 1.0 CA D:CYS870 4.3 32.6 1.0 C D:LYS843 4.5 48.1 1.0 CB D:LYS843 4.7 47.3 1.0 C D:CYS844 4.7 43.1 1.0 C D:CYS867 4.7 32.8 1.0 O D:CYS867 4.8 28.2 1.0 CA D:CYS841 4.8 44.6 1.0 O D:CYS844 4.8 42.2 1.0 N D:LYS843 4.9 53.1 1.0 CB D:PHE869 4.9 28.9 1.0 CA D:LYS843 4.9 48.9 1.0

J.Liu, F.Li, H.Bao, Y.Jiang, S.Zhang, R.Ma, J.Gao, J.Wu, K.Ruan. The Polar Warhead of A TRIM24 Bromodomain Inhibitor Rearranges A Water-Mediated Interaction Network Febs J. V. 284 1082 2017.
ISSN: ISSN 1742-4658
PubMed: 28207202
DOI: 10.1111/FEBS.14041