Zinc in PDB 5wle: Crystal Structure of the Pps Phd Finger in Complex with H3K4ME3

The structure of Crystal Structure of the Pps Phd Finger in Complex with H3K4ME3, PDB code: 5wle was solved by B.J.Klein, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.20 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	22.972, 44.223, 31.308, 90.00, 94.77, 90.00
R / Rfree (%)	14.5 / 18.6

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

Zinc binding site 1 out of 2 in the Crystal Structure of the Pps Phd Finger in Complex with 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 the Pps Phd Finger in Complex with H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1001 b:6.3 occ:1.00 ND1 A:HIS935 2.2 5.8 1.0 SG A:CYS915 2.2 4.2 1.0 SG A:CYS913 2.3 4.1 1.0 SG A:CYS938 2.3 4.8 1.0 CB A:CYS913 3.1 3.4 1.0 CG A:HIS935 3.1 2.3 1.0 CE1 A:HIS935 3.2 3.2 1.0 CB A:CYS915 3.3 6.6 1.0 CB A:CYS938 3.3 3.5 1.0 CB A:HIS935 3.4 2.7 1.0 O A:HOH1143 3.8 9.1 1.0 N A:CYS915 3.8 5.5 1.0 N A:HIS935 4.1 2.3 1.0 CA A:CYS915 4.2 5.9 1.0 NE2 A:HIS935 4.3 4.3 1.0 CD2 A:HIS935 4.3 3.6 1.0 CA A:HIS935 4.3 3.3 1.0 N A:ILE914 4.5 6.6 1.0 CA A:CYS913 4.5 6.2 1.0 CA A:CYS938 4.7 5.8 1.0 C A:CYS913 4.8 8.5 1.0 O A:HIS935 4.8 3.8 1.0 N A:CYS938 4.9 4.5 1.0 NH2 A:ARG922 4.9 5.0 1.0 O A:TRP912 4.9 6.0 1.0 C A:ILE914 5.0 8.1 1.0 NH1 A:ARG922 5.0 7.0 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of the Pps Phd Finger in Complex with 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 the Pps Phd Finger in Complex with H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1002 b:9.0 occ:1.00 SG A:CYS927 2.3 5.5 1.0 SG A:CYS930 2.3 5.5 1.0 SG A:CYS958 2.4 7.3 1.0 SG A:CYS961 2.4 7.0 1.0 CB A:CYS961 3.1 9.7 1.0 CB A:CYS927 3.1 6.4 1.0 CB A:CYS930 3.3 7.4 1.0 CB A:CYS958 3.4 8.9 1.0 N A:CYS930 3.7 4.4 1.0 N A:CYS958 3.9 7.7 1.0 CA A:CYS930 4.1 4.5 1.0 N A:CYS961 4.2 9.2 1.0 CA A:CYS958 4.2 11.1 1.0 CA A:CYS961 4.2 12.8 1.0 CE1 A:PHE934 4.3 5.4 1.0 CZ A:PHE934 4.4 5.7 1.0 NZ A:LYS960 4.4 28.3 1.0 O A:HOH1144 4.5 13.8 1.0 CA A:CYS927 4.6 4.5 1.0 C A:LEU929 4.8 5.2 1.0 C A:CYS958 4.8 8.3 1.0 O A:CYS958 4.8 8.5 1.0 CB A:LEU929 4.8 4.8 1.0 CE A:LYS960 4.9 21.9 1.0 C A:CYS930 5.0 4.6 1.0 N A:LEU929 5.0 4.9 1.0

A.H.Tencer, J.Gatchalian, B.J.Klein, A.Khan, Y.Zhang, B.D.Strahl, K.H.M.Van Wely, T.G.Kutateladze. A Unique pH-Dependent Recognition of Methylated Histone H3K4 By Pps and Dido. Structure V. 25 1530 2017.
ISSN: ISSN 1878-4186
PubMed: 28919441
DOI: 10.1016/J.STR.2017.08.009