Zinc in PDB 3g7l: Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide

The structure of Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide, PDB code: 3g7l was solved by T.Schalch, L.Joshua-Tor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.34 / 2.20
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	41.560, 41.560, 87.380, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 23.7

The binding sites of Zinc atom in the Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide (pdb code 3g7l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide, PDB code: 3g7l:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn76 b:50.9 occ:1.00 OD2 A:ASP51 2.2 53.1 1.0 ZN A:ZN2 2.8 80.7 0.9 CG A:ASP51 2.9 46.8 1.0 OD1 A:ASP51 3.0 50.4 1.0 HD1 A:TYR47 3.3 63.8 1.0 H A:ASP48 3.5 57.7 1.0 OD1 A:ASP48 3.5 43.4 1.0 CG A:ASP48 3.9 46.3 1.0 OD2 A:ASP48 4.0 49.0 1.0 O A:ACY1 4.0 62.7 1.0 CD1 A:TYR47 4.1 53.9 1.0 HB3 A:TYR47 4.2 51.1 1.0 HA A:TYR47 4.3 53.8 1.0 N A:ASP48 4.3 48.8 1.0 CB A:ASP51 4.3 47.0 1.0 HB2 A:ASP51 4.5 55.5 1.0 HB3 A:ASP51 4.7 55.5 1.0 HE1 A:TYR47 4.8 73.4 1.0 CB A:TYR47 4.8 43.2 1.0 CA A:TYR47 4.9 45.5 1.0 C A:ACY1 4.9 55.3 1.0 CE1 A:TYR47 4.9 61.8 1.0 OXT A:ACY1 5.0 46.7 1.0 CG A:TYR47 5.0 50.3 1.0 CB A:ASP48 5.0 41.4 1.0

Zinc binding site 2 out of 4 in the Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2 b:80.7 occ:0.89 OD1 A:ASP51 2.5 50.4 1.0 O A:ACY1 2.7 62.7 1.0 ZN A:ZN76 2.8 50.9 1.0 CG A:ASP51 3.3 46.8 1.0 OD2 A:ASP51 3.5 53.1 1.0 C A:ACY1 3.8 55.3 1.0 H1 A:ACY1 4.4 69.1 1.0 OD1 A:ASP48 4.4 43.4 1.0 HB2 A:TYR50 4.5 67.9 1.0 HA A:ASP51 4.6 52.4 1.0 OXT A:ACY1 4.6 46.7 1.0 CB A:ASP51 4.7 47.0 1.0 CH3 A:ACY1 4.7 58.2 1.0

Zinc binding site 3 out of 4 in the Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn3 b:91.2 occ:0.84 OD2 A:ASP30 2.5 47.2 1.0 HE1 A:TRP70 3.1 46.8 1.0 NE1 A:TRP70 3.4 39.7 1.0 CG A:ASP30 3.5 34.2 1.0 HZ2 A:TRP70 3.6 34.6 1.0 CE2 A:TRP70 3.8 46.0 1.0 CZ2 A:TRP70 3.9 29.5 1.0 OD1 A:ASP30 3.9 45.4 1.0 CD1 A:TRP70 4.3 36.8 1.0 HA A:LYS71 4.5 55.4 1.0 HD1 A:TRP70 4.6 43.4 1.0 O A:TRP70 4.6 47.9 1.0 O A:HOH92 4.7 42.7 1.0 HB3 A:ASP30 4.8 37.2 1.0 CD2 A:TRP70 4.8 43.4 1.0 CB A:ASP30 4.8 31.7 1.0 CH2 A:TRP70 4.9 35.7 1.0

Zinc binding site 4 out of 4 in the Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Chromodomain of CHP1 in Complex with Histone H3K9ME3 Peptide within 5.0Å range:

T.Schalch, G.Job, V.J.Noffsinger, S.Shanker, C.Kuscu, L.Joshua-Tor, J.F.Partridge. High-Affinity Binding of CHP1 Chromodomain to K9 Methylated Histone H3 Is Required to Establish Centromeric Heterochromatin Mol.Cell V. 34 36 2009.
ISSN: ISSN 1097-2765
PubMed: 19362535
DOI: 10.1016/J.MOLCEL.2009.02.024