Zinc in PDB 9c0o: Crystal Structure of DMCFP1 Phd Finger Bound to H3K4ME3

The structure of Crystal Structure of DMCFP1 Phd Finger Bound to H3K4ME3, PDB code: 9c0o was solved by S.Gregoire, J.F.Couture, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	31.95 / 1.53
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	33.27, 43.12, 47.56, 90, 90, 90
R / Rfree (%)	15.6 / 19.4

The binding sites of Zinc atom in the Crystal Structure of DMCFP1 Phd Finger Bound to H3K4ME3 (pdb code 9c0o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the Crystal Structure of DMCFP1 Phd Finger Bound to H3K4ME3, PDB code: 9c0o:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of DMCFP1 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 DMCFP1 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn202 b:18.3 occ:1.00 NE2 A:HIS85 2.2 15.1 1.0 SG A:CYS70 2.3 17.5 1.0 SG A:CYS65 2.3 18.8 1.0 CB A:CYS70 2.9 17.5 1.0 CB A:CYS65 3.1 17.6 1.0 CE1 A:HIS85 3.1 17.1 1.0 CD2 A:HIS85 3.2 14.8 1.0 CE A:MET74 3.8 19.6 0.6 CA A:CYS65 4.1 19.1 1.0 ND1 A:HIS85 4.3 18.0 1.0 CD A:ARG72 4.3 14.3 1.0 CG A:HIS85 4.3 14.9 1.0 CE A:MET74 4.4 17.6 0.4 CA A:CYS70 4.4 19.7 1.0 SD A:MET74 4.4 24.2 0.4 CB A:SER67 4.5 38.9 1.0 O A:HOH364 4.7 39.2 1.0 O A:HOH343 4.7 32.8 1.0 NH1 A:ARG72 4.8 12.5 1.0 CB A:ARG72 4.8 12.1 1.0 OG A:SER67 4.9 41.7 1.0 CG A:ARG72 5.0 13.8 1.0 C A:CYS65 5.0 22.5 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of DMCFP1 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 DMCFP1 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn203 b:16.5 occ:1.00 SG A:CYS107 2.3 17.3 1.0 SG A:CYS77 2.3 15.4 1.0 SG A:CYS104 2.3 14.6 1.0 SG A:CYS80 2.3 15.6 1.0 CB A:CYS80 3.3 16.6 1.0 CB A:CYS107 3.3 16.9 1.0 CB A:CYS77 3.3 15.5 1.0 CB A:CYS104 3.4 13.9 1.0 N A:CYS80 3.5 15.7 1.0 N A:CYS104 3.9 13.1 1.0 O A:HOH310 4.0 28.1 1.0 CA A:CYS80 4.0 16.3 1.0 C A:GLY79 4.2 15.8 1.0 N A:CYS107 4.2 14.6 1.0 CA A:CYS104 4.2 14.2 1.0 CA A:CYS107 4.3 16.1 1.0 OH A:TYR84 4.3 19.3 1.0 CE1 A:TYR84 4.4 14.7 1.0 CA A:GLY79 4.5 14.2 1.0 N A:GLY79 4.6 16.4 1.0 CA A:CYS77 4.7 15.6 1.0 CZ A:TYR84 4.8 16.0 1.0 C A:CYS104 4.8 15.2 1.0 NH2 A:ARG106 4.8 28.4 1.0 O A:CYS104 4.8 13.7 1.0 C A:CYS80 4.9 17.9 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of DMCFP1 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 3 of Crystal Structure of DMCFP1 Phd Finger Bound to H3K4ME3 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn204 b:20.2 occ:0.82 OXT A:ARG119 1.9 21.7 1.0 ND1 A:HIS98 2.3 20.0 1.0 C A:ARG119 2.7 21.7 1.0 O A:ARG119 2.8 23.3 1.0 CE1 A:HIS98 3.2 19.3 1.0 CG A:HIS98 3.3 18.7 1.0 CB A:HIS98 3.5 16.3 1.0 CA A:HIS98 4.0 15.7 1.0 CA A:ARG119 4.1 21.1 1.0 CG A:ARG119 4.3 22.8 1.0 NE2 A:HIS98 4.3 19.8 1.0 CD2 A:HIS98 4.4 18.3 1.0 N A:ARG119 4.6 18.6 1.0 CB A:ARG119 4.7 22.5 1.0 O A:HIS98 4.8 17.0 1.0 C A:HIS98 4.9 15.8 1.0

S.Gregoire, J.Gregoire, Y.Yang, S.Capitani, M.Joshi, S.Sarvan, A.Zaker, Z.Ning, D.Figeys, K.Ulrich, J.S.Brunzelle, A.Mer, J.F.Couture. Structural Insights Into An Atypical Histone Binding Mechanism By A Phd Finger. To Be Published.