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Zinc in PDB 5h1u: Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 2

Protein crystallography data

The structure of Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 2, PDB code: 5h1u was solved by J.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 33.55 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.560, 48.568, 123.374, 86.72, 81.46, 67.90
R / Rfree (%) 22.5 / 26.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 2 (pdb code 5h1u). 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 2, PDB code: 5h1u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5h1u

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1102

b:27.5
occ:1.00
SG B:CYS841 2.2 24.6 1.0
SG B:CYS870 2.3 29.0 1.0
SG B:CYS844 2.4 29.8 1.0
SG B:CYS867 2.5 23.5 1.0
CB B:CYS844 3.2 25.1 1.0
CB B:CYS870 3.3 25.5 1.0
CB B:CYS841 3.4 30.8 1.0
CB B:CYS867 3.5 23.9 1.0
N B:CYS844 3.8 34.5 1.0
CA B:CYS844 4.1 33.2 1.0
N B:CYS870 4.1 19.2 1.0
N B:CYS867 4.1 26.7 1.0
CA B:CYS870 4.3 27.3 1.0
CA B:CYS867 4.3 27.9 1.0
C B:LYS843 4.5 36.1 1.0
CB B:PHE869 4.5 28.5 1.0
O B:CYS867 4.7 22.4 1.0
C B:CYS844 4.7 33.6 1.0
C B:CYS867 4.7 20.1 1.0
CA B:CYS841 4.8 35.2 1.0
O B:CYS844 4.8 33.0 1.0
CB B:LYS843 4.9 29.4 1.0
N B:LYS843 4.9 31.4 1.0
C B:PHE869 4.9 19.6 1.0
CA B:LYS843 5.0 26.9 1.0

Zinc binding site 2 out of 8 in 5h1u

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1103

b:26.8
occ:1.00
ND1 B:HIS849 2.1 20.2 1.0
SG B:CYS829 2.3 26.0 1.0
SG B:CYS852 2.3 27.4 1.0
SG B:CYS832 2.4 27.8 1.0
CE1 B:HIS849 3.0 26.9 1.0
CB B:CYS829 3.0 24.4 1.0
CG B:HIS849 3.2 28.3 1.0
CB B:CYS852 3.2 27.5 1.0
CB B:CYS832 3.3 17.6 1.0
CB B:HIS849 3.5 30.4 1.0
N B:CYS832 3.9 29.1 1.0
O B:HOH1252 3.9 37.1 1.0
N B:HIS849 4.0 29.9 1.0
CA B:CYS832 4.2 26.6 1.0
NE2 B:HIS849 4.2 24.6 1.0
CD2 B:HIS849 4.3 24.8 1.0
CA B:HIS849 4.4 25.4 1.0
CA B:CYS829 4.5 21.8 1.0
CB B:VAL831 4.6 24.9 1.0
CA B:CYS852 4.6 22.4 1.0
C B:VAL831 4.9 29.5 1.0
C B:CYS832 4.9 31.8 1.0
CG1 B:VAL831 5.0 24.2 1.0

Zinc binding site 3 out of 8 in 5h1u

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Zinc binding site 3 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:28.8
occ:1.00
SG A:CYS841 2.2 26.5 1.0
SG A:CYS870 2.4 29.1 1.0
SG A:CYS844 2.4 27.4 1.0
SG A:CYS867 2.5 24.7 1.0
CB A:CYS844 3.2 25.0 1.0
CB A:CYS841 3.3 32.3 1.0
CB A:CYS870 3.4 30.5 1.0
CB A:CYS867 3.5 26.6 1.0
N A:CYS844 3.8 30.4 1.0
N A:CYS867 4.0 26.9 1.0
CA A:CYS844 4.0 28.1 1.0
N A:CYS870 4.2 16.2 1.0
CA A:CYS867 4.2 27.7 1.0
CA A:CYS870 4.4 28.6 1.0
C A:LYS843 4.5 35.4 1.0
C A:CYS844 4.6 33.2 1.0
O A:CYS867 4.7 26.6 1.0
C A:CYS867 4.7 21.4 1.0
CB A:PHE869 4.7 26.3 1.0
O A:CYS844 4.7 39.5 1.0
CA A:CYS841 4.7 31.7 1.0
N A:LYS843 4.8 27.5 1.0
CB A:LYS843 4.8 31.2 1.0
CA A:LYS843 4.9 27.2 1.0

Zinc binding site 4 out of 8 in 5h1u

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Zinc binding site 4 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1103

b:27.8
occ:1.00
ND1 A:HIS849 2.1 32.4 1.0
SG A:CYS829 2.2 30.7 1.0
SG A:CYS852 2.4 29.1 1.0
SG A:CYS832 2.4 27.6 1.0
CE1 A:HIS849 3.0 39.0 1.0
CB A:CYS829 3.0 31.2 1.0
CG A:HIS849 3.1 33.3 1.0
CB A:CYS852 3.2 32.9 1.0
CB A:CYS832 3.3 17.0 1.0
CB A:HIS849 3.5 30.1 1.0
N A:CYS832 3.8 28.4 1.0
N A:HIS849 4.0 29.5 1.0
NE2 A:HIS849 4.1 38.9 1.0
CA A:CYS832 4.2 27.2 1.0
CD2 A:HIS849 4.2 37.1 1.0
CA A:HIS849 4.4 27.4 1.0
CA A:CYS829 4.5 27.4 1.0
CB A:VAL831 4.6 23.7 1.0
CA A:CYS852 4.6 22.8 1.0
C A:CYS832 4.9 30.6 1.0
C A:VAL831 4.9 25.0 1.0
CG1 A:VAL831 5.0 23.2 1.0

Zinc binding site 5 out of 8 in 5h1u

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Zinc binding site 5 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1102

b:36.5
occ:1.00
SG C:CYS870 2.3 36.1 1.0
SG C:CYS841 2.4 36.8 1.0
SG C:CYS867 2.4 28.2 1.0
SG C:CYS844 2.5 36.4 1.0
CB C:CYS844 3.3 33.4 1.0
CB C:CYS870 3.3 24.0 1.0
CB C:CYS841 3.4 40.1 1.0
CB C:CYS867 3.5 28.4 1.0
N C:CYS844 3.8 41.7 1.0
N C:CYS867 4.0 33.7 1.0
N C:CYS870 4.1 21.4 1.0
CA C:CYS844 4.1 35.4 1.0
CA C:CYS867 4.3 30.0 1.0
CA C:CYS870 4.3 24.9 1.0
C C:LYS843 4.5 42.8 1.0
O C:CYS867 4.7 27.8 1.0
CB C:PHE869 4.7 28.4 1.0
C C:CYS867 4.7 30.6 1.0
C C:CYS844 4.7 42.5 1.0
CA C:CYS841 4.8 43.9 1.0
O C:CYS844 4.9 42.6 1.0
N C:LYS843 4.9 45.1 1.0
C C:PHE869 5.0 27.2 1.0

Zinc binding site 6 out of 8 in 5h1u

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Zinc binding site 6 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1103

b:32.2
occ:1.00
ND1 C:HIS849 2.0 18.3 1.0
SG C:CYS852 2.3 30.1 1.0
SG C:CYS829 2.3 30.7 1.0
SG C:CYS832 2.4 34.0 1.0
CE1 C:HIS849 2.9 31.6 1.0
CB C:CYS829 3.1 34.0 1.0
CG C:HIS849 3.1 35.2 1.0
CB C:CYS852 3.2 21.9 1.0
CB C:CYS832 3.4 37.0 1.0
CB C:HIS849 3.6 38.2 1.0
N C:CYS832 3.8 30.0 1.0
N C:HIS849 4.0 27.8 1.0
NE2 C:HIS849 4.0 30.4 1.0
CA C:CYS832 4.1 31.5 1.0
CD2 C:HIS849 4.2 29.4 1.0
CA C:HIS849 4.4 33.9 1.0
CA C:CYS829 4.6 39.7 1.0
CA C:CYS852 4.6 24.0 1.0
CB C:VAL831 4.6 31.4 1.0
C C:VAL831 4.8 31.0 1.0
C C:CYS832 4.8 36.4 1.0
N C:VAL831 4.9 26.9 1.0
N C:GLN833 5.0 37.8 1.0

Zinc binding site 7 out of 8 in 5h1u

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Zinc binding site 7 out of 8 in the Complex Structure of TRIM24 Phd-Bromodomain and Inhibitor 2


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1102

b:38.8
occ:1.00
SG D:CYS841 2.3 37.1 1.0
SG D:CYS870 2.3 36.0 1.0
SG D:CYS844 2.5 35.5 1.0
SG D:CYS867 2.5 27.8 1.0
CB D:CYS841 3.2 38.3 1.0
CB D:CYS844 3.2 27.4 1.0
CB D:CYS870 3.3 28.2 1.0
CB D:CYS867 3.5 30.7 1.0
N D:CYS844 3.7 37.2 1.0
CA D:CYS844 4.0 30.1 1.0
N D:CYS867 4.1 35.2 1.0
N D:CYS870 4.2 22.6 1.0
CA D:CYS867 4.3 33.3 1.0
CA D:CYS870 4.4 30.1 1.0
C D:LYS843 4.4 41.8 1.0
C D:CYS844 4.6 38.7 1.0
CA D:CYS841 4.6 43.1 1.0
N D:LYS843 4.7 46.3 1.0
CB D:LYS843 4.7 37.4 1.0
O D:CYS844 4.8 36.2 1.0
C D:CYS867 4.8 29.0 1.0
CB D:PHE869 4.8 33.2 1.0
O D:CYS867 4.8 32.9 1.0
CA D:LYS843 4.8 35.5 1.0

Zinc binding site 8 out of 8 in 5h1u

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


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 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1103

b:31.1
occ:1.00
ND1 D:HIS849 1.9 20.3 1.0
SG D:CYS852 2.3 33.9 1.0
SG D:CYS832 2.3 29.5 1.0
SG D:CYS829 2.4 32.4 1.0
CE1 D:HIS849 2.8 39.0 1.0
CG D:HIS849 3.0 39.5 1.0
CB D:CYS829 3.1 34.5 1.0
CB D:CYS852 3.2 23.3 1.0
CB D:CYS832 3.3 32.3 1.0
CB D:HIS849 3.4 39.1 1.0
N D:CYS832 3.8 28.5 1.0
NE2 D:HIS849 4.0 28.6 1.0
N D:HIS849 4.0 31.2 1.0
CD2 D:HIS849 4.1 28.0 1.0
CA D:CYS832 4.1 29.0 1.0
CA D:HIS849 4.4 35.8 1.0
CA D:CYS829 4.6 42.6 1.0
CA D:CYS852 4.6 28.1 1.0
CB D:VAL831 4.6 32.4 1.0
C D:CYS832 4.8 38.3 1.0
C D:VAL831 4.9 29.2 1.0
N D:GLN833 4.9 38.7 1.0

Reference:

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
Page generated: Wed Dec 16 06:19:55 2020

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