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Zinc in PDB 4yat: Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B)

Protein crystallography data

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B), PDB code: 4yat 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) 62.10 / 2.18
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.990, 49.236, 65.770, 107.78, 90.00, 112.06
R / Rfree (%) 11.2 / 16.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B) (pdb code 4yat). 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-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B), PDB code: 4yat:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4yat

Go back to Zinc Binding Sites List in 4yat
Zinc binding site 1 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B)


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-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:28.7
occ:1.00
SG A:CYS852 2.2 26.6 1.0
SG A:CYS829 2.2 24.4 1.0
SG A:CYS832 2.3 32.4 1.0
ND1 A:HIS849 2.4 28.1 1.0
CB A:CYS829 2.9 27.0 1.0
CB A:CYS852 3.1 23.7 1.0
CB A:CYS832 3.3 33.0 1.0
CE1 A:HIS849 3.3 29.6 1.0
CG A:HIS849 3.4 29.6 1.0
N A:CYS832 3.7 35.4 1.0
CB A:HIS849 3.7 25.9 1.0
CA A:CYS832 4.0 36.1 1.0
N A:HIS849 4.0 25.4 1.0
CA A:CYS829 4.4 30.0 1.0
CB A:VAL831 4.5 33.6 1.0
NE2 A:HIS849 4.5 31.8 1.0
CA A:HIS849 4.5 24.9 1.0
CD2 A:HIS849 4.5 29.8 1.0
CA A:CYS852 4.6 26.0 1.0
C A:VAL831 4.8 37.0 1.0
C A:CYS832 4.8 35.7 1.0
N A:VAL831 4.9 32.3 1.0
CA A:VAL831 4.9 34.1 1.0
C A:CYS829 4.9 31.4 1.0
O A:HOH1336 5.0 30.1 1.0

Zinc binding site 2 out of 4 in 4yat

Go back to Zinc Binding Sites List in 4yat
Zinc binding site 2 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B)


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-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:37.4
occ:1.00
SG A:CYS841 2.3 31.9 1.0
SG A:CYS870 2.3 33.0 1.0
SG A:CYS867 2.4 29.3 1.0
SG A:CYS844 2.4 31.1 1.0
CB A:CYS870 3.1 29.4 1.0
CB A:CYS844 3.3 36.0 1.0
CB A:CYS841 3.4 39.1 1.0
CB A:CYS867 3.5 29.6 1.0
N A:CYS844 3.8 36.8 1.0
N A:CYS867 3.9 31.5 1.0
N A:CYS870 4.1 28.9 1.0
CA A:CYS844 4.1 36.6 1.0
CA A:CYS867 4.2 31.6 1.0
CA A:CYS870 4.2 29.8 1.0
O A:CYS867 4.6 31.2 1.0
C A:LYS843 4.6 39.7 1.0
C A:CYS867 4.6 28.2 1.0
CB A:PHE869 4.7 25.5 1.0
CB A:LYS843 4.8 47.1 1.0
C A:CYS844 4.8 35.0 1.0
CA A:CYS841 4.8 40.7 1.0
O A:CYS844 4.8 36.8 1.0
N A:LYS843 4.9 43.5 1.0
C A:PHE869 4.9 28.6 1.0
CA A:LYS843 5.0 42.6 1.0

Zinc binding site 3 out of 4 in 4yat

Go back to Zinc Binding Sites List in 4yat
Zinc binding site 3 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B)


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-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1101

b:30.7
occ:1.00
SG B:CYS852 2.2 30.6 1.0
ND1 B:HIS849 2.2 37.1 1.0
SG B:CYS829 2.3 30.2 1.0
SG B:CYS832 2.4 28.1 1.0
CB B:CYS829 3.0 30.5 1.0
CB B:CYS852 3.1 27.5 1.0
CE1 B:HIS849 3.2 38.5 1.0
CG B:HIS849 3.2 35.2 1.0
CB B:CYS832 3.4 23.9 1.0
CB B:HIS849 3.6 33.2 1.0
N B:CYS832 3.9 27.3 1.0
N B:HIS849 3.9 33.2 1.0
CA B:CYS832 4.2 26.7 1.0
NE2 B:HIS849 4.3 38.7 1.0
CA B:HIS849 4.4 30.6 1.0
CD2 B:HIS849 4.4 39.3 1.0
CA B:CYS829 4.5 31.9 1.0
CA B:CYS852 4.6 28.4 1.0
CB B:VAL831 4.7 23.4 1.0
C B:CYS832 4.9 26.4 1.0
C B:VAL831 5.0 24.1 1.0

Zinc binding site 4 out of 4 in 4yat

Go back to Zinc Binding Sites List in 4yat
Zinc binding site 4 out of 4 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B)


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-(1,3- Dimethyl-2-Oxo-2,3-Dihydro-1H-1,3-Benzodiazol-5-Yl)-4-Methoxybenzene- 1-Sulfonamide (5B) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1102

b:28.9
occ:1.00
SG B:CYS841 2.2 26.3 1.0
SG B:CYS870 2.4 31.7 1.0
SG B:CYS844 2.4 33.2 1.0
SG B:CYS867 2.5 23.8 1.0
CB B:CYS870 3.2 25.8 1.0
CB B:CYS844 3.2 33.5 1.0
CB B:CYS841 3.2 29.7 1.0
CB B:CYS867 3.5 23.9 1.0
N B:CYS844 3.7 36.2 1.0
N B:CYS867 3.9 26.2 1.0
CA B:CYS844 4.0 36.7 1.0
CA B:CYS867 4.2 25.7 1.0
N B:CYS870 4.3 26.4 1.0
O B:HOH1333 4.3 38.2 1.0
CA B:CYS870 4.4 27.8 1.0
C B:LYS843 4.5 39.4 1.0
C B:CYS844 4.7 36.9 1.0
CA B:CYS841 4.7 33.8 1.0
C B:CYS867 4.7 24.5 1.0
O B:CYS867 4.7 24.3 1.0
CB B:LYS843 4.7 39.9 1.0
O B:CYS844 4.8 37.1 1.0
CB B:PHE869 4.8 26.5 1.0
N B:LYS843 4.8 36.3 1.0
CA B:LYS843 4.9 38.2 1.0

Reference:

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
Page generated: Wed Dec 16 05:56:15 2020

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