Zinc in PDB 5yc3: Crystal Structure of AL3 Phd Finger Bound to H3K4ME2

The structure of Crystal Structure of AL3 Phd Finger Bound to H3K4ME2, PDB code: 5yc3 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)	39.26 / 2.60
Space group	P 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	30.921, 30.921, 157.029, 90.00, 90.00, 90.00
R / Rfree (%)	19.1 / 24.1

The binding sites of Zinc atom in the Crystal Structure of AL3 Phd Finger Bound to H3K4ME2 (pdb code 5yc3). 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 AL3 Phd Finger Bound to H3K4ME2, PDB code: 5yc3:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of AL3 Phd Finger Bound to H3K4ME2


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 AL3 Phd Finger Bound to H3K4ME2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:32.8 occ:1.00 ND1 A:HIS31 2.1 32.1 1.0 SG A:CYS7 2.3 28.1 1.0 SG A:CYS34 2.3 30.3 1.0 SG A:CYS10 2.4 28.7 1.0 CG A:HIS31 3.0 28.5 1.0 CB A:CYS7 3.0 26.0 1.0 CE1 A:HIS31 3.1 28.9 1.0 CB A:HIS31 3.2 28.0 1.0 CB A:CYS34 3.4 31.9 1.0 CB A:CYS10 3.4 31.1 1.0 N A:CYS10 3.9 35.5 1.0 N A:HIS31 4.0 30.0 1.0 CD2 A:HIS31 4.1 30.1 1.0 NE2 A:HIS31 4.2 31.3 1.0 CA A:HIS31 4.2 29.2 1.0 CA A:CYS10 4.2 32.0 1.0 CA A:CYS7 4.5 26.6 1.0 CB A:ALA9 4.7 26.9 1.0 CA A:CYS34 4.8 33.0 1.0 N A:GLY11 4.9 33.1 1.0 C A:CYS10 5.0 33.0 1.0 C A:ALA9 5.0 36.9 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of AL3 Phd Finger Bound to H3K4ME2


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 AL3 Phd Finger Bound to H3K4ME2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:30.2 occ:1.00 SG A:CYS50 2.3 29.9 1.0 SG A:CYS53 2.4 36.5 1.0 SG A:CYS26 2.4 28.9 1.0 SG A:CYS23 2.4 25.7 1.0 CB A:CYS26 3.2 26.4 1.0 CB A:CYS23 3.3 22.2 1.0 CB A:CYS53 3.3 32.6 1.0 CB A:CYS50 3.4 24.1 1.0 N A:CYS26 3.7 26.5 1.0 N A:CYS50 4.0 29.8 1.0 CA A:CYS26 4.0 28.5 1.0 CA A:CYS50 4.2 29.7 1.0 N A:CYS53 4.3 38.2 1.0 CA A:CYS53 4.4 35.6 1.0 CB A:LEU25 4.7 33.2 1.0 CA A:CYS23 4.7 29.5 1.0 C A:LEU25 4.7 30.4 1.0 O A:CYS50 4.8 36.8 1.0 C A:CYS26 4.8 31.2 1.0 C A:CYS50 4.8 33.5 1.0 N A:GLU27 4.9 32.7 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