Zinc in PDB 4l7x: Crystal Structure of the Dido Phd Finger in Complex with H3K4ME3

The structure of Crystal Structure of the Dido Phd Finger in Complex with H3K4ME3, PDB code: 4l7x was solved by Q.Tong, J.Gatchalian, T.G.Kutateladze, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.68 / 1.35
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	40.820, 40.820, 80.620, 90.00, 90.00, 90.00
R / Rfree (%)	13.2 / 14.2

The binding sites of Zinc atom in the Crystal Structure of the Dido Phd Finger in Complex with H3K4ME3 (pdb code 4l7x). 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 Dido Phd Finger in Complex with H3K4ME3, PDB code: 4l7x:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of the Dido 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 Dido Phd Finger in Complex with H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn101 b:15.8 occ:1.00 SG A:CYS57 2.3 21.2 0.8 SG A:CYS26 2.3 18.1 0.8 SG A:CYS23 2.4 17.3 0.8 SG A:CYS54 2.4 18.6 0.8 HB2 A:CYS57 2.8 26.3 0.8 HB3 A:CYS26 3.0 22.5 0.8 H A:CYS26 3.1 21.5 0.8 HB3 A:CYS23 3.1 18.4 0.8 CB A:CYS57 3.2 21.9 0.8 CB A:CYS23 3.2 15.3 0.8 CB A:CYS26 3.2 18.8 0.8 HB3 A:CYS54 3.2 22.7 0.9 HB2 A:CYS23 3.3 18.4 0.8 H A:CYS54 3.3 22.6 0.9 CB A:CYS54 3.4 18.9 0.9 N A:CYS26 3.6 17.9 0.8 HB3 A:ARG25 3.7 28.8 0.8 H A:CYS57 3.7 25.6 0.7 HB3 A:CYS57 3.8 26.3 0.8 HE1 A:PHE30 3.8 18.1 0.7 HZ A:PHE30 4.0 20.9 0.8 HB2 A:CYS26 4.0 22.5 0.8 CA A:CYS26 4.0 19.7 0.8 N A:CYS54 4.0 18.8 0.9 HB2 A:ASN56 4.0 36.0 0.7 HB2 A:CYS54 4.2 22.7 0.9 N A:CYS57 4.2 21.3 0.7 CA A:CYS54 4.2 19.2 0.9 CA A:CYS57 4.3 22.2 0.9 H A:ARG25 4.3 24.0 0.8 O A:HOH231 4.3 33.5 1.0 CE1 A:PHE30 4.4 15.1 0.7 CZ A:PHE30 4.5 17.4 0.8 CB A:ARG25 4.6 24.0 0.8 C A:ARG25 4.6 20.0 0.8 CA A:CYS23 4.6 16.1 1.0 HA A:CYS57 4.6 26.7 0.9 HB3 A:GLU28 4.7 18.9 0.8 H A:GLU27 4.7 19.5 0.8 H A:GLU28 4.7 16.4 0.7 HG2 A:ARG25 4.7 36.0 0.7 HA A:ILE53 4.8 23.9 0.8 C A:CYS54 4.8 19.0 0.8 HA A:CYS26 4.8 23.6 0.8 O A:CYS54 4.8 18.1 0.7 C A:CYS26 4.9 15.8 0.8 HG23 A:ILE53 4.9 29.3 0.8 CA A:ARG25 4.9 18.7 0.8 HD21 A:ASN56 4.9 32.8 0.6 N A:ARG25 4.9 20.0 0.9 HA A:CYS23 5.0 19.3 1.0 H A:ASN56 5.0 31.2 0.8 CB A:ASN56 5.0 30.0 0.7

Zinc binding site 2 out of 2 in the Crystal Structure of the Dido 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 Dido Phd Finger in Complex with H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn102 b:15.4 occ:1.00 ND1 A:HIS31 2.2 17.2 0.9 SG A:CYS9 2.3 17.2 0.8 SG A:CYS34 2.3 19.2 0.7 SG A:CYS11 2.3 19.6 0.8 HB3 A:CYS9 2.9 21.1 0.9 HB2 A:HIS31 2.9 18.3 0.9 CB A:CYS9 3.1 17.6 0.9 CE1 A:HIS31 3.1 15.6 0.8 HB2 A:CYS34 3.2 21.9 0.8 HB3 A:CYS11 3.2 27.1 0.8 CG A:HIS31 3.2 15.3 0.9 CB A:CYS34 3.2 18.2 0.8 H A:HIS31 3.2 16.3 0.8 HE1 A:HIS31 3.3 18.7 0.8 H A:CYS11 3.3 25.3 0.7 CB A:CYS11 3.4 22.5 0.8 HB2 A:CYS9 3.4 21.1 0.9 HB3 A:CYS34 3.4 21.9 0.8 CB A:HIS31 3.5 15.2 0.9 O A:HOH210 3.7 26.9 0.8 HH22 A:ARG18 4.0 22.8 0.7 N A:HIS31 4.0 13.6 0.8 N A:CYS11 4.1 21.1 0.7 HB2 A:CYS11 4.1 27.1 0.8 H A:ILE10 4.2 25.2 0.8 HB3 A:HIS31 4.3 18.3 0.9 NE2 A:HIS31 4.3 15.8 0.8 CD2 A:HIS31 4.3 15.0 0.8 CA A:CYS11 4.4 21.3 0.7 HH12 A:ARG18 4.4 23.2 0.8 CA A:HIS31 4.4 14.7 0.9 NH2 A:ARG18 4.5 19.0 0.7 CA A:CYS9 4.5 16.7 0.8 N A:ILE10 4.6 21.0 0.8 H A:CYS34 4.6 21.5 0.6 CA A:CYS34 4.7 21.8 0.9 HB2 A:GLN13 4.7 27.8 0.8 HA A:PHE30 4.7 15.0 0.9 NH1 A:ARG18 4.8 19.4 0.8 HB A:ILE10 4.9 29.1 0.9 HH21 A:ARG18 4.9 22.8 0.7 O A:HIS31 4.9 15.3 0.8 C A:CYS9 4.9 19.1 0.8 HA A:CYS34 4.9 26.1 0.9 CZ A:ARG18 4.9 18.4 0.9 HA A:CYS9 4.9 20.1 0.8 H A:ARG12 5.0 25.6 0.8

J.Gatchalian, A.Futterer, S.B.Rothbart, Q.Tong, H.Rincon-Arano, A.Sanchez De Diego, M.Groudine, B.D.Strahl, C.Martinez-A, K.H.Van Wely, T.G.Kutateladze. DIDO3 Phd Modulates Cell Differentiation and Division. Cell Rep V. 4 148 2013.
ISSN: ESSN 2211-1247
PubMed: 23831028
DOI: 10.1016/J.CELREP.2013.06.014