Zinc in PDB 7lky: Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641

The structure of Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641, PDB code: 7lky was solved by J.Liu, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.22 / 1.85
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	43.394, 45.345, 64.442, 90.02, 95.19, 90.07
R / Rfree (%)	23.3 / 28.1

The binding sites of Zinc atom in the Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641 (pdb code 7lky). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641, PDB code: 7lky:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in the Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641


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 PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:36.7 occ:1.00 N I:GLY1 1.9 19.3 1.0 OD2 A:ASP68 2.1 21.5 1.0 CG A:ASP68 2.7 19.2 1.0 OD1 A:ASP68 2.7 19.1 1.0 CA I:GLY1 2.9 20.3 1.0 CB A:ASP68 4.0 12.5 1.0 C I:GLY1 4.1 29.5 1.0 O I:GLY1 4.4 32.3 1.0

Zinc binding site 2 out of 6 in the Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641


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 PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:37.9 occ:1.00 N J:GLY1 2.0 30.7 1.0 OE2 A:GLU59 2.0 34.2 1.0 OD2 B:ASP68 2.2 32.2 1.0 CD A:GLU59 2.6 27.3 1.0 OE1 A:GLU59 2.6 28.4 1.0 CA J:GLY1 2.9 26.2 1.0 CG B:ASP68 3.0 27.7 1.0 OD1 B:ASP68 3.1 31.6 1.0 CG A:GLU59 3.9 21.6 1.0 C J:GLY1 4.2 26.6 1.0 CB B:ASP68 4.5 26.6 1.0 O J:GLY1 4.5 34.3 1.0

Zinc binding site 3 out of 6 in the Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641


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 PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641 within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn101 b:79.7 occ:1.00 OD1 C:ASP68 2.0 27.4 1.0 N K:GLY1 2.0 27.3 1.0 CG C:ASP68 2.6 30.8 1.0 OD2 C:ASP68 2.6 25.9 1.0 O K:HOH201 3.3 24.8 1.0 O C:HOH212 3.3 17.5 1.0 CA K:GLY1 3.4 32.6 1.0 CB C:ASP68 4.1 22.7 1.0 C K:GLY1 4.4 30.3 1.0 O K:GLY1 4.6 30.1 1.0 CA C:ASP68 4.7 20.1 1.0 NE2 C:GLN64 4.7 33.0 1.0 O C:HOH203 4.8 11.6 1.0 N C:ASP68 5.0 18.0 1.0

Zinc binding site 4 out of 6 in the Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641


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 PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641 within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn102 b:36.7 occ:1.00 N L:GLY1 1.9 15.5 1.0 OD1 D:ASP68 2.0 29.0 1.0 CG D:ASP68 2.6 34.4 1.0 OD2 D:ASP68 2.7 38.0 1.0 CA L:GLY1 2.9 29.8 1.0 O D:HOH229 3.2 23.9 1.0 O L:GLY1 3.6 41.6 1.0 C L:GLY1 3.7 38.3 1.0 CB D:ASP68 4.1 30.8 1.0 O D:GLU66 4.5 27.7 1.0 NE2 D:GLN64 4.5 10.9 1.0 CA D:ASP68 4.6 22.2 1.0 N D:ASP68 4.8 17.3 1.0 N L:GLY2 4.9 36.7 1.0

Zinc binding site 5 out of 6 in the Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641 within 5.0Å range: probe atom residue distance (Å) B Occ E:Zn102 b:27.1 occ:1.00 OD2 E:ASP68 1.8 30.6 1.0 N M:GLY1 1.9 27.5 1.0 OE1 H:GLU59 1.9 18.6 1.0 CG E:ASP68 2.7 29.5 1.0 CA M:GLY1 2.9 30.3 1.0 OD1 E:ASP68 2.9 27.6 1.0 CD H:GLU59 3.0 12.4 1.0 OE2 H:GLU59 3.5 16.8 1.0 CB E:ASP68 4.0 23.9 1.0 C M:GLY1 4.2 27.4 1.0 CG H:GLU59 4.2 12.2 1.0 O M:GLY1 4.6 29.2 1.0

Zinc binding site 6 out of 6 in the Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of PHF1 Tudor Domain in Complex with A Peptidomimetic Ligand UNC6641 within 5.0Å range: probe atom residue distance (Å) B Occ H:Zn101 b:45.9 occ:1.00 OD2 H:ASP68 2.0 31.9 1.0 N P:GLY1 2.1 35.4 1.0 CG H:ASP68 2.7 26.5 1.0 OD1 H:ASP68 2.8 28.3 1.0 CA P:GLY1 3.4 29.8 1.0 CB H:ASP68 4.2 22.8 1.0 O P:GLY1 4.3 46.3 1.0 C P:GLY1 4.4 35.2 1.0

I.A.Engelberg, J.Liu, J.L.Norris-Drouin, S.H.Cholensky, S.A.Ottavi, S.V.Frye, T.G.Kutateladze, L.I.James. Discovery of An H3K36ME3-Derived Peptidomimetic Ligand with Enhanced Affinity For Plant Homeodomain Finger Protein 1 (PHF1). J.Med.Chem. V. 64 8510 2021.
ISSN: ISSN 0022-2623
PubMed: 33999620
DOI: 10.1021/ACS.JMEDCHEM.1C00430