Zinc in PDB 5wxh: Crystal Structure of TAF3 Phd Finger Bound to H3K4ME3

The structure of Crystal Structure of TAF3 Phd Finger Bound to H3K4ME3, PDB code: 5wxh was solved by S.Zhao, J.Huang, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.30 / 1.30
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	27.244, 35.138, 38.562, 82.96, 75.62, 73.49
R / Rfree (%)	15.3 / 17.5

The binding sites of Zinc atom in the Crystal Structure of TAF3 Phd Finger Bound to H3K4ME3 (pdb code 5wxh). 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 TAF3 Phd Finger Bound to H3K4ME3, PDB code: 5wxh:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of TAF3 Phd Finger Bound to H3K4ME3


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 TAF3 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:16.4 occ:1.00 SG A:CYS888 2.3 17.1 1.0 SG A:CYS914 2.3 19.4 1.0 SG A:CYS885 2.3 15.6 1.0 SG A:CYS911 2.3 17.1 1.0 CB A:CYS885 3.2 13.9 1.0 CB A:CYS888 3.2 19.1 1.0 CB A:CYS914 3.3 19.4 1.0 CB A:CYS911 3.4 16.7 1.0 N A:CYS888 3.6 17.8 1.0 N A:CYS911 4.0 15.5 1.0 CA A:CYS888 4.0 17.8 1.0 N A:CYS914 4.1 20.2 1.0 O A:HOH1105 4.1 20.4 1.0 NZ A:LYS913 4.2 44.5 1.0 CA A:CYS911 4.2 15.4 1.0 CA A:CYS914 4.3 20.0 1.0 CB A:ASP887 4.4 20.8 1.0 CE A:LYS913 4.6 44.4 1.0 CA A:CYS885 4.7 13.6 1.0 C A:CYS888 4.7 17.4 1.0 C A:ASP887 4.8 19.8 1.0 C A:CYS911 4.8 21.1 1.0 O A:CYS911 4.8 19.3 1.0 N A:ASP889 4.8 17.5 1.0 CA A:ASP887 5.0 17.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of TAF3 Phd Finger Bound to H3K4ME3


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 TAF3 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:15.5 occ:1.00 ND1 A:HIS893 2.1 14.6 1.0 SG A:CYS896 2.3 16.6 1.0 SG A:CYS873 2.3 16.7 1.0 SG A:CYS870 2.3 13.0 1.0 CE1 A:HIS893 3.0 15.3 1.0 CB A:CYS870 3.1 11.8 1.0 CG A:HIS893 3.2 14.8 1.0 CB A:CYS896 3.3 15.2 1.0 CB A:CYS873 3.3 18.0 1.0 CB A:HIS893 3.5 14.1 1.0 N A:CYS873 3.7 16.5 1.0 O A:HOH1176 4.1 38.0 1.0 N A:HIS893 4.1 12.8 1.0 CA A:CYS873 4.1 17.4 1.0 NE2 A:HIS893 4.2 14.4 1.0 CD2 A:HIS893 4.3 13.6 1.0 O A:HOH1165 4.3 36.8 1.0 CA A:HIS893 4.4 12.8 1.0 CA A:CYS870 4.5 11.7 1.0 C A:GLY872 4.5 20.6 1.0 CA A:CYS896 4.7 15.8 1.0 CA A:GLY872 4.7 17.5 1.0 O A:CYS870 4.8 13.1 1.0 N A:GLY872 4.8 14.4 1.0 C A:CYS870 4.8 12.1 1.0 O A:HIS893 4.9 14.7 1.0 C A:CYS873 4.9 15.5 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of TAF3 Phd Finger Bound to H3K4ME3


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 TAF3 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1001 b:19.1 occ:1.00 SG C:CYS914 2.2 26.8 1.0 SG C:CYS888 2.3 19.6 1.0 SG C:CYS911 2.4 23.5 1.0 SG C:CYS885 2.4 17.9 1.0 CB C:CYS888 3.2 22.6 1.0 CB C:CYS885 3.3 14.7 1.0 CB C:CYS914 3.3 27.1 1.0 CB C:CYS911 3.5 25.6 1.0 N C:CYS888 3.6 20.2 1.0 N C:CYS911 3.9 22.7 1.0 CA C:CYS888 4.0 19.2 1.0 N C:CYS914 4.1 32.7 1.0 CA C:CYS911 4.3 24.6 1.0 O C:HOH1103 4.3 20.7 1.0 CA C:CYS914 4.3 27.7 1.0 CB C:ASP887 4.6 27.6 1.0 C C:CYS888 4.7 18.2 1.0 O C:HOH1168 4.7 41.3 1.0 CA C:CYS885 4.7 13.6 1.0 C C:CYS911 4.8 27.0 1.0 N C:ASP889 4.8 15.5 1.0 O C:CYS911 4.8 26.8 1.0 C C:ASP887 4.8 25.0 1.0 CB C:LYS913 4.9 32.9 1.0 C C:LYS913 5.0 35.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of TAF3 Phd Finger Bound to H3K4ME3


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 TAF3 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1002 b:18.7 occ:1.00 ND1 C:HIS893 2.1 19.4 1.0 SG C:CYS896 2.3 22.7 1.0 SG C:CYS873 2.3 22.8 1.0 SG C:CYS870 2.4 17.6 1.0 CE1 C:HIS893 3.0 19.4 1.0 CB C:CYS870 3.1 17.4 1.0 CG C:HIS893 3.1 18.6 1.0 CB C:CYS873 3.2 21.9 1.0 CB C:CYS896 3.3 20.6 1.0 CB C:HIS893 3.4 17.2 1.0 N C:CYS873 3.7 23.4 1.0 N C:HIS893 4.1 15.8 1.0 CA C:CYS873 4.1 23.6 1.0 NE2 C:HIS893 4.2 21.1 1.0 CD2 C:HIS893 4.2 19.8 1.0 CA C:HIS893 4.4 18.1 1.0 C C:GLY872 4.5 23.9 1.0 CA C:CYS870 4.5 15.4 1.0 CA C:CYS896 4.7 21.7 1.0 O C:CYS870 4.7 18.0 1.0 CA C:GLY872 4.8 22.2 1.0 C C:CYS870 4.8 15.5 1.0 N C:GLY872 4.8 20.4 1.0 C C:CYS873 4.9 22.0 1.0 O C:HIS893 4.9 16.9 1.0

S.Zhao, M.Yang, W.Zhou, B.Zhang, Z.Cheng, J.Huang, M.Zhang, Z.Wang, R.Wang, Z.Chen, J.Zhu, H.Li. Kinetic and High-Throughput Profiling of Epigenetic Interactions By 3D-Carbene Chip-Based Surface Plasmon Resonance Imaging Technology Proc. Natl. Acad. Sci. V. 114 E7245 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28808021
DOI: 10.1073/PNAS.1704155114