Zinc in PDB 8vlf: Crystal Structure of ASH1L Phd Finger in Complex with Histone H3K4ME3

The structure of Crystal Structure of ASH1L Phd Finger in Complex with Histone H3K4ME3, PDB code: 8vlf was solved by K.R.Vann, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.07 / 1.34
Space group	P 43
Cell size a, b, c (Å), α, β, γ (°)	49.8, 49.8, 46.29, 90, 90, 90
R / Rfree (%)	15.5 / 18.8

The binding sites of Zinc atom in the Crystal Structure of ASH1L Phd Finger in Complex with Histone H3K4ME3 (pdb code 8vlf). 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 ASH1L Phd Finger in Complex with Histone H3K4ME3, PDB code: 8vlf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of ASH1L Phd Finger in Complex with Histone 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 ASH1L Phd Finger in Complex with Histone H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:25.3 occ:1.00 SG A:CYS25 2.3 23.4 0.9 SG A:CYS48 2.3 27.4 1.0 SG A:CYS45 2.3 21.2 1.0 SG A:CYS22 2.3 25.3 1.0 CB A:CYS25 3.3 23.3 1.0 CB A:CYS22 3.3 24.5 1.0 CB A:CYS48 3.3 27.4 1.0 CB A:CYS45 3.4 21.7 1.0 N A:CYS25 3.8 26.0 1.0 N A:CYS45 3.9 23.3 1.0 CA A:CYS25 4.1 24.9 1.0 N A:CYS48 4.1 25.5 1.0 CA A:CYS45 4.2 22.9 0.9 CA A:CYS48 4.3 27.3 1.0 O A:HOH223 4.3 20.2 1.0 O B:HOH233 4.4 46.4 1.0 CG2 A:VAL27 4.7 19.2 1.0 CA A:CYS22 4.7 24.1 1.0 O B:HOH204 4.7 71.5 1.0 C A:CYS25 4.8 24.1 1.0 C A:CYS45 4.8 22.5 1.0 C A:LYS24 4.9 26.7 1.0 N A:MET26 5.0 23.5 1.0 CB A:LYS24 5.0 27.9 1.0 O A:CYS45 5.0 24.7 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of ASH1L Phd Finger in Complex with Histone 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 ASH1L Phd Finger in Complex with Histone H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:16.2 occ:0.86 ND1 A:HIS30 2.1 16.0 1.0 SG A:CYS33 2.3 17.3 0.8 SG A:CYS10 2.3 18.0 1.0 SG A:CYS8 2.3 15.2 0.9 CE1 A:HIS30 3.0 16.3 0.9 CG A:HIS30 3.1 16.4 1.0 CB A:CYS8 3.1 15.0 1.0 CB A:CYS33 3.2 18.8 1.0 CB A:CYS10 3.2 19.2 0.9 CB A:HIS30 3.4 16.7 1.0 N A:CYS10 3.9 19.4 1.0 CA A:CYS10 4.2 19.7 0.8 NE2 A:HIS30 4.2 17.2 0.9 N A:HIS30 4.2 15.9 1.0 CD2 A:HIS30 4.2 17.0 0.9 CA A:HIS30 4.4 16.7 1.0 CA A:CYS8 4.5 16.1 1.0 CA A:CYS33 4.6 19.9 0.8 N A:ILE9 4.7 17.7 1.0 C A:CYS8 4.7 17.4 0.9 O A:HIS30 4.9 16.5 0.8 N A:CYS33 5.0 19.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of ASH1L Phd Finger in Complex with Histone 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 ASH1L Phd Finger in Complex with Histone H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn101 b:16.5 occ:0.90 ND1 B:HIS30 2.1 15.9 1.0 SG B:CYS33 2.3 19.3 1.0 SG B:CYS10 2.3 18.1 1.0 SG B:CYS8 2.3 16.5 1.0 CE1 B:HIS30 3.0 16.5 0.9 CG B:HIS30 3.1 16.5 1.0 CB B:CYS8 3.1 15.6 1.0 CB B:CYS33 3.2 20.2 1.0 CB B:CYS10 3.2 19.3 1.0 CB B:HIS30 3.4 16.8 1.0 N B:CYS10 3.9 19.1 1.0 CA B:CYS10 4.2 19.5 0.8 NE2 B:HIS30 4.2 16.9 0.9 N B:HIS30 4.2 16.0 1.0 CD2 B:HIS30 4.2 16.6 0.9 CA B:HIS30 4.4 17.3 1.0 CA B:CYS8 4.5 16.1 1.0 CA B:CYS33 4.6 20.6 0.9 N B:ILE9 4.7 18.0 1.0 C B:CYS8 4.8 17.0 1.0 O B:HIS30 4.9 16.4 0.8 N B:CYS33 5.0 20.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of ASH1L Phd Finger in Complex with Histone 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 ASH1L Phd Finger in Complex with Histone H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn102 b:25.5 occ:1.00 SG B:CYS25 2.3 23.5 1.0 SG B:CYS48 2.3 27.5 1.0 SG B:CYS45 2.3 21.4 1.0 SG B:CYS22 2.3 25.7 1.0 CB B:CYS25 3.3 23.6 1.0 CB B:CYS48 3.3 26.7 1.0 CB B:CYS22 3.3 24.4 1.0 CB B:CYS45 3.4 21.8 1.0 N B:CYS25 3.8 25.2 1.0 N B:CYS45 3.9 23.6 1.0 CA B:CYS25 4.1 24.4 1.0 N B:CYS48 4.1 25.0 1.0 CA B:CYS45 4.2 22.9 1.0 CA B:CYS48 4.3 26.7 1.0 O B:HOH229 4.3 20.2 1.0 O A:HOH238 4.4 43.3 1.0 O A:HOH204 4.6 70.1 1.0 CG2 B:VAL27 4.7 19.1 1.0 CA B:CYS22 4.8 24.2 1.0 C B:CYS45 4.8 22.5 1.0 C B:CYS25 4.8 24.0 1.0 C B:LYS24 4.9 26.5 1.0 O B:CYS45 4.9 24.1 1.0 CB B:LYS24 4.9 28.7 1.0 N B:MET26 5.0 24.4 1.0

K.R.Vann, R.Sharma, C.C.Hsu, M.Devoucoux, A.H.Tencer, L.Zeng, K.Lin, L.Zhu, Q.Li, C.Lachance, R.R.Ospina, Q.Tong, K.L.Cheung, S.Yang, S.Biswas, H.Xuan, J.Gatchalian, L.Alamillo, J.Wang, S.M.Jang, B.J.Klein, Y.Lu, P.Ernst, B.D.Strahl, S.B.Rothbart, M.J.Walsh, M.L.Cleary, J.Cote, X.Shi, M.M.Zhou, T.G.Kutateladze. Structure-Function Relationship of ASH1L and Histone H3K36 and H3K4 Methylation. Nat Commun V. 16 2235 2025.
ISSN: ESSN 2041-1723
PubMed: 40044670
DOI: 10.1038/S41467-025-57556-5