Zinc in PDB 5b73: Crystal Structure of Human ZMYND8 Phd-Bromo-Pwwp Domain

The structure of Crystal Structure of Human ZMYND8 Phd-Bromo-Pwwp Domain, PDB code: 5b73 was solved by H.Li, Y.Li, X.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.50 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	67.083, 67.999, 70.309, 90.00, 90.00, 90.00
R / Rfree (%)	18.7 / 22.4

The binding sites of Zinc atom in the Crystal Structure of Human ZMYND8 Phd-Bromo-Pwwp Domain (pdb code 5b73). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of Human ZMYND8 Phd-Bromo-Pwwp Domain, PDB code: 5b73:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human ZMYND8 Phd-Bromo-Pwwp Domain


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 Human ZMYND8 Phd-Bromo-Pwwp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn501 b:29.5 occ:1.00 NE2 A:HIS298 2.1 28.9 1.0 SG A:CYS278 2.3 33.1 1.0 SG A:CYS294 2.3 30.1 1.0 SG A:CYS275 2.3 30.2 1.0 CD2 A:HIS298 3.0 29.4 1.0 CE1 A:HIS298 3.2 26.0 1.0 CB A:CYS275 3.3 27.1 1.0 CB A:CYS278 3.3 31.9 1.0 CB A:CYS294 3.4 36.4 1.0 N A:CYS278 3.5 25.5 1.0 CA A:CYS278 3.9 29.2 1.0 CG A:HIS298 4.2 26.8 1.0 ND1 A:HIS298 4.3 27.6 1.0 O A:HOH619 4.3 30.4 1.0 C A:GLU277 4.5 32.5 1.0 CB A:GLU277 4.6 31.7 1.0 CA A:CYS275 4.7 27.3 1.0 CA A:CYS294 4.8 40.6 1.0 O A:CYS275 4.9 29.9 1.0 CA A:GLU277 5.0 31.7 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human ZMYND8 Phd-Bromo-Pwwp Domain


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 Human ZMYND8 Phd-Bromo-Pwwp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn502 b:28.5 occ:1.00 ND1 A:HIS131 2.1 29.1 1.0 SG A:CYS134 2.3 30.7 1.0 SG A:CYS111 2.3 27.3 1.0 SG A:CYS114 2.4 29.0 1.0 CE1 A:HIS131 2.9 26.2 1.0 CB A:CYS111 3.0 24.7 1.0 CG A:HIS131 3.1 28.3 1.0 CB A:CYS114 3.3 32.2 1.0 CB A:CYS134 3.4 31.4 1.0 CB A:HIS131 3.5 29.8 1.0 N A:CYS114 3.8 27.2 1.0 N A:HIS131 4.1 28.8 1.0 NE2 A:HIS131 4.1 27.9 1.0 CA A:CYS114 4.1 28.6 1.0 CD2 A:HIS131 4.2 31.5 1.0 CA A:HIS131 4.4 26.6 1.0 CA A:CYS111 4.5 23.2 1.0 CB A:VAL113 4.5 26.6 1.0 CA A:CYS134 4.7 29.3 1.0 C A:VAL113 4.8 29.9 1.0 C A:CYS114 4.9 29.9 1.0 N A:CYS134 5.0 28.0 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human ZMYND8 Phd-Bromo-Pwwp Domain


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 Human ZMYND8 Phd-Bromo-Pwwp Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn503 b:35.4 occ:1.00 SG A:CYS147 2.1 36.9 1.0 SG A:CYS123 2.3 38.1 1.0 SG A:CYS150 2.3 36.8 1.0 SG A:CYS126 2.4 32.4 1.0 CB A:CYS123 3.2 32.4 1.0 CB A:CYS150 3.3 40.8 1.0 CB A:CYS147 3.4 40.5 1.0 CB A:CYS126 3.4 37.3 1.0 N A:CYS126 3.8 38.4 1.0 N A:CYS147 3.9 51.9 1.0 CA A:CYS126 4.1 36.4 1.0 N A:CYS150 4.1 39.5 1.0 CA A:CYS147 4.2 41.7 1.0 CA A:CYS150 4.3 40.5 1.0 C A:LEU125 4.5 46.2 1.0 CB A:LEU125 4.5 46.0 1.0 NH1 A:ARG128 4.6 30.8 1.0 C A:CYS126 4.7 35.9 1.0 CA A:CYS123 4.7 38.3 1.0 C A:CYS147 4.8 45.7 1.0 CB A:ARG128 4.8 25.7 1.0 O A:CYS126 4.8 36.2 1.0 CA A:LEU125 4.9 37.2 1.0 N A:LEU125 4.9 47.6 1.0 O A:CYS147 4.9 47.2 1.0 CD A:ARG128 4.9 28.6 1.0

N.Li, Y.Li, J.Lv, X.Zheng, H.Wen, H.Shen, G.Zhu, T.Y.Chen, S.S.Dhar, P.Y.Kan, Z.Wang, R.Shiekhattar, X.Shi, F.Lan, K.Chen, W.Li, H.Li, M.G.Lee. ZMYND8 Reads the Dual Histone Mark H3K4ME1-H3K14AC to Antagonize the Expression of Metastasis-Linked Genes Mol.Cell V. 63 470 2016.
ISSN: ISSN 1097-2765
PubMed: 27477906
DOI: 10.1016/J.MOLCEL.2016.06.035