Zinc in PDB 4iut: Crystal Structure of SHH1 Sawadee Domain in Complex with H3K9ME2 Peptide

The structure of Crystal Structure of SHH1 Sawadee Domain in Complex with H3K9ME2 Peptide, PDB code: 4iut was solved by J.Du, D.J.Patel, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.87 / 2.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	53.391, 56.706, 59.057, 90.00, 93.22, 90.00
R / Rfree (%)	20.2 / 24.8

The binding sites of Zinc atom in the Crystal Structure of SHH1 Sawadee Domain in Complex with H3K9ME2 Peptide (pdb code 4iut). 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 SHH1 Sawadee Domain in Complex with H3K9ME2 Peptide, PDB code: 4iut:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of SHH1 Sawadee Domain in Complex with H3K9ME2 Peptide


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 SHH1 Sawadee Domain in Complex with H3K9ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn301 b:25.0 occ:1.00 NE2 A:HIS225 2.3 31.6 1.0 SG A:CYS191 2.5 25.4 1.0 SG A:CYS232 2.6 32.1 1.0 SG A:CYS230 2.6 26.7 1.0 CB A:CYS191 3.0 31.1 1.0 CE1 A:HIS225 3.2 30.9 1.0 CD2 A:HIS225 3.3 25.5 1.0 CB A:CYS232 3.3 25.3 1.0 CB A:CYS230 3.7 32.7 1.0 N A:CYS232 4.1 32.1 1.0 NH1 A:ARG222 4.3 37.9 1.0 ND1 A:HIS225 4.3 30.8 1.0 CA A:CYS232 4.3 31.7 1.0 CA A:CYS230 4.3 26.3 1.0 CG A:HIS225 4.4 31.1 1.0 CA A:CYS191 4.5 18.9 1.0 N A:ASN231 4.6 36.0 1.0 O A:PRO188 4.7 21.7 1.0 O A:HOH441 4.8 33.0 1.0 C A:CYS230 4.8 27.5 1.0 C A:CYS191 4.9 19.5 1.0 O A:CYS191 5.0 22.6 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of SHH1 Sawadee Domain in Complex with H3K9ME2 Peptide


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 SHH1 Sawadee Domain in Complex with H3K9ME2 Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn301 b:36.6 occ:1.00 NE2 B:HIS225 2.3 52.8 1.0 SG B:CYS232 2.5 40.5 1.0 SG B:CYS191 2.6 43.8 1.0 SG B:CYS230 2.6 30.0 1.0 CD2 B:HIS225 2.9 51.6 1.0 CE1 B:HIS225 3.3 56.1 1.0 CB B:CYS232 3.4 28.6 1.0 CB B:CYS191 3.4 32.9 1.0 CB B:CYS230 3.5 49.4 1.0 N B:CYS232 3.7 31.0 1.0 CA B:CYS230 4.0 50.2 1.0 N B:ASN231 4.0 32.6 1.0 CG B:HIS225 4.1 57.0 1.0 CA B:CYS232 4.1 31.0 1.0 ND1 B:HIS225 4.2 61.5 1.0 C B:CYS230 4.4 46.9 1.0 NH1 B:ARG222 4.5 37.3 1.0 C B:ASN231 4.7 30.9 1.0 OD1 B:ASN231 4.8 35.6 1.0 O B:GLY223 4.8 31.7 1.0 O B:PRO188 4.8 43.8 1.0 CA B:CYS191 4.9 30.2 1.0 N B:GLY223 4.9 29.3 1.0 CA B:ASN231 5.0 33.1 1.0

J.A.Law, J.Du, C.J.Hale, S.Feng, K.Krajewski, A.M.Palanca, B.D.Strahl, D.J.Patel, S.E.Jacobsen. Polymerase IV Occupancy at Rna-Directed Dna Methylation Sites Requires SHH1. Nature V. 498 385 2013.
ISSN: ISSN 0028-0836
PubMed: 23636332
DOI: 10.1038/NATURE12178