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Zinc in PDB 4ybs: Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-6-[3-(2-Methylpropoxy)Phenoxy]-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1,2-Dimethyl-1H-Imidazole-4-Sulfonamide (7G)

Protein crystallography data

The structure of Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-6-[3-(2-Methylpropoxy)Phenoxy]-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1,2-Dimethyl-1H-Imidazole-4-Sulfonamide (7G), PDB code: 4ybs 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) 61.32 / 1.83
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.735, 36.238, 65.935, 90.00, 111.56, 90.00
R / Rfree (%) 16.7 / 23.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-6-[3-(2-Methylpropoxy)Phenoxy]-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1,2-Dimethyl-1H-Imidazole-4-Sulfonamide (7G) (pdb code 4ybs). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-6-[3-(2-Methylpropoxy)Phenoxy]-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1,2-Dimethyl-1H-Imidazole-4-Sulfonamide (7G), PDB code: 4ybs:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4ybs

Go back to Zinc Binding Sites List in 4ybs
Zinc binding site 1 out of 2 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-6-[3-(2-Methylpropoxy)Phenoxy]-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1,2-Dimethyl-1H-Imidazole-4-Sulfonamide (7G)


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-6-[3-(2-Methylpropoxy)Phenoxy]-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1,2-Dimethyl-1H-Imidazole-4-Sulfonamide (7G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1101

b:33.3
occ:1.00
SG A:CYS829 2.2 31.3 1.0
ND1 A:HIS849 2.2 31.7 1.0
SG A:CYS852 2.2 31.9 1.0
SG A:CYS832 2.4 31.1 1.0
CE1 A:HIS849 3.1 33.4 1.0
CB A:CYS852 3.1 30.6 1.0
CB A:CYS829 3.2 27.7 1.0
CG A:HIS849 3.2 32.4 1.0
CB A:CYS832 3.4 29.9 1.0
CB A:HIS849 3.6 32.0 1.0
N A:CYS832 3.9 29.1 1.0
N A:HIS849 4.1 26.6 1.0
CA A:CYS832 4.2 32.4 1.0
NE2 A:HIS849 4.3 32.6 1.0
CD2 A:HIS849 4.3 29.8 1.0
CA A:HIS849 4.4 29.5 1.0
O A:HOH1247 4.5 61.5 1.0
CA A:CYS829 4.6 27.3 1.0
CA A:CYS852 4.6 32.9 1.0
CB A:VAL831 4.6 33.6 1.0
C A:VAL831 4.8 33.9 1.0
C A:CYS832 4.9 32.2 1.0

Zinc binding site 2 out of 2 in 4ybs

Go back to Zinc Binding Sites List in 4ybs
Zinc binding site 2 out of 2 in the Crystal Structure of TRIM24 Phd-Bromodomain Complexed with N-{1,3- Dimethyl-6-[3-(2-Methylpropoxy)Phenoxy]-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1,2-Dimethyl-1H-Imidazole-4-Sulfonamide (7G)


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-6-[3-(2-Methylpropoxy)Phenoxy]-2-Oxo-2,3-Dihydro-1H-1,3- Benzodiazol-5-Yl}-1,2-Dimethyl-1H-Imidazole-4-Sulfonamide (7G) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1102

b:31.3
occ:1.00
SG A:CYS870 2.2 30.4 1.0
SG A:CYS844 2.4 32.1 1.0
SG A:CYS867 2.4 27.2 1.0
SG A:CYS841 2.4 30.6 1.0
CB A:CYS841 3.3 30.9 1.0
CB A:CYS844 3.3 31.4 1.0
CB A:CYS870 3.3 31.1 1.0
CB A:CYS867 3.5 26.3 1.0
N A:CYS844 3.8 33.6 1.0
N A:CYS867 4.0 26.9 1.0
CA A:CYS844 4.1 37.4 1.0
N A:CYS870 4.1 27.5 1.0
CA A:CYS867 4.3 27.6 1.0
CA A:CYS870 4.4 29.1 1.0
C A:LYS843 4.5 33.3 1.0
CB A:PHE869 4.7 24.6 1.0
O A:CYS867 4.7 21.9 1.0
CB A:LYS843 4.7 38.2 1.0
C A:CYS844 4.7 37.8 1.0
C A:CYS867 4.7 23.7 1.0
CA A:CYS841 4.7 33.7 1.0
O A:HOH1253 4.8 48.1 1.0
O A:CYS844 4.8 36.9 1.0
N A:LYS843 4.9 31.1 1.0
CA A:LYS843 4.9 32.0 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 05:56:20 2020

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