Zinc in PDB 5y20: Crystal Structure of AL1 Phd Finger Bound to H3K4ME3

The structure of Crystal Structure of AL1 Phd Finger Bound to H3K4ME3, PDB code: 5y20 was solved by S.Zhao, B.Zhang, H.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.57 / 2.41
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	46.168, 46.168, 70.164, 90.00, 90.00, 90.00
R / Rfree (%)	16.1 / 21.5

The binding sites of Zinc atom in the Crystal Structure of AL1 Phd Finger Bound to H3K4ME3 (pdb code 5y20). 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 AL1 Phd Finger Bound to H3K4ME3, PDB code: 5y20:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of AL1 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 AL1 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:26.4 occ:1.00 ND1 A:HIS31 2.1 22.0 1.0 SG A:CYS34 2.3 23.4 1.0 SG A:CYS7 2.3 23.2 1.0 SG A:CYS10 2.4 23.5 1.0 CG A:HIS31 3.0 22.9 1.0 CB A:CYS7 3.1 22.8 1.0 CE1 A:HIS31 3.2 21.8 1.0 CB A:HIS31 3.2 24.1 1.0 CB A:CYS34 3.4 23.6 1.0 CB A:CYS10 3.5 21.5 1.0 N A:CYS10 3.8 25.6 1.0 N A:HIS31 4.1 23.1 1.0 CA A:CYS10 4.2 24.0 1.0 CD2 A:HIS31 4.2 23.1 1.0 CA A:HIS31 4.2 23.3 1.0 NE2 A:HIS31 4.3 24.1 1.0 CB A:SER9 4.3 24.3 1.0 CA A:CYS7 4.6 21.2 1.0 CA A:CYS34 4.7 24.8 1.0 C A:SER9 4.8 27.3 1.0 N A:CYS34 4.9 24.1 1.0 CA A:SER9 4.9 24.5 1.0 N A:GLY12 4.9 24.8 1.0 N A:SER9 5.0 25.6 1.0 C A:CYS10 5.0 23.9 1.0 OG A:SER9 5.0 29.2 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of AL1 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 AL1 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:25.6 occ:1.00 SG A:CYS26 2.2 27.5 1.0 SG A:CYS53 2.3 24.8 1.0 SG A:CYS23 2.3 29.4 1.0 SG A:CYS50 2.3 25.8 1.0 CB A:CYS23 3.1 23.5 1.0 CB A:CYS26 3.2 27.6 1.0 CB A:CYS53 3.3 31.2 1.0 CB A:CYS50 3.4 25.9 1.0 N A:CYS26 3.6 29.4 1.0 CA A:CYS26 3.9 27.9 1.0 N A:CYS50 4.0 29.3 1.0 N A:CYS53 4.2 38.0 1.0 CA A:CYS50 4.2 27.8 1.0 CA A:CYS53 4.3 35.8 1.0 OH A:TYR30 4.4 26.5 1.0 CB A:VAL25 4.6 27.5 1.0 CA A:CYS23 4.6 24.8 1.0 NH2 A:ARG28 4.6 36.1 1.0 O A:CYS50 4.7 33.0 1.0 C A:CYS26 4.7 28.8 1.0 C A:VAL25 4.7 29.7 1.0 C A:CYS50 4.8 33.3 1.0 CE2 A:TYR30 4.8 24.2 1.0 N A:GLU27 4.8 30.8 1.0

S.Zhao, B.Zhang, H.Li. Crystal Structure of AL1 Phd Finger Bound to H3K4ME3 Cell Rep 2018.
ISSN: ESSN 2211-1247
DOI: 10.1016/J.CELREP.2017.12.099