Zinc in PDB 5v21: Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam

All present enzymatic activity of Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam:
2.1.1.43;

The structure of Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam, PDB code: 5v21 was solved by Y.Zhang, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.53 / 2.42
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	58.493, 76.316, 77.179, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 26.9

The binding sites of Zinc atom in the Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam (pdb code 5v21). 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 Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam, PDB code: 5v21:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam


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 Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:30.3 occ:1.00 SG A:CYS1539 2.3 24.7 1.0 SG A:CYS1516 2.3 29.5 1.0 SG A:CYS1529 2.3 27.3 1.0 SG A:CYS1533 2.5 31.6 1.0 CB A:CYS1529 3.1 21.1 1.0 CB A:CYS1539 3.3 30.0 1.0 CB A:CYS1516 3.3 32.1 1.0 CB A:CYS1533 3.6 29.9 1.0 ZN A:ZN1802 3.6 38.3 1.0 SG A:CYS1499 4.2 34.5 1.0 CA A:CYS1539 4.2 32.4 1.0 CB A:ASN1541 4.3 30.4 1.0 CA A:CYS1529 4.6 24.2 1.0 SG A:CYS1520 4.7 37.1 1.0 CA A:CYS1516 4.7 33.0 1.0 CB A:ASN1535 4.8 34.0 1.0 ND2 A:ASN1535 4.9 39.3 1.0 CA A:CYS1533 4.9 35.6 1.0 ND2 A:ASN1541 5.0 26.2 1.0 N A:ASN1541 5.0 28.6 1.0

Zinc binding site 2 out of 3 in the Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam


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 Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:38.3 occ:1.00 SG A:CYS1499 2.2 34.5 1.0 SG A:CYS1501 2.3 49.9 1.0 SG A:CYS1516 2.4 29.5 1.0 SG A:CYS1520 2.4 37.1 1.0 CB A:CYS1501 3.1 39.0 1.0 CB A:CYS1520 3.2 36.5 1.0 CB A:CYS1516 3.3 32.1 1.0 CB A:CYS1499 3.3 45.8 1.0 ZN A:ZN1801 3.6 30.3 1.0 CA A:CYS1516 3.8 33.0 1.0 CA A:CYS1520 4.0 40.2 1.0 N A:CYS1501 4.2 48.0 1.0 SG A:CYS1529 4.2 27.3 1.0 CA A:CYS1501 4.2 43.2 1.0 N A:CYS1516 4.6 36.6 1.0 ND2 A:ASN1535 4.6 39.3 1.0 N A:LEU1521 4.7 38.2 1.0 CA A:CYS1499 4.7 46.2 1.0 SG A:CYS1533 4.7 31.6 1.0 C A:CYS1520 4.8 38.4 1.0 C A:CYS1516 5.0 34.5 1.0

Zinc binding site 3 out of 3 in the Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam


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 Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:33.2 occ:1.00 SG A:CYS1678 2.3 28.3 1.0 SG A:CYS1680 2.3 32.7 1.0 SG A:CYS1631 2.4 30.1 1.0 SG A:CYS1685 2.4 30.0 1.0 CB A:CYS1680 3.2 32.8 1.0 CB A:CYS1685 3.3 31.3 1.0 CB A:CYS1678 3.4 27.9 1.0 CB A:CYS1631 3.4 31.9 1.0 CA A:CYS1685 3.6 34.5 1.0 N A:ARG1686 3.9 33.6 1.0 N A:CYS1631 4.0 33.6 1.0 N A:CYS1680 4.1 27.8 1.0 CA A:CYS1680 4.2 30.3 1.0 C A:CYS1685 4.2 34.1 1.0 NE2 A:HIS1629 4.3 30.5 1.0 CA A:CYS1631 4.3 33.7 1.0 CD2 A:HIS1629 4.4 27.9 1.0 O A:CYS1678 4.5 29.0 1.0 C A:CYS1678 4.6 31.2 1.0 N A:GLY1687 4.6 33.5 1.0 CA A:CYS1678 4.6 27.1 1.0 N A:GLY1681 4.8 34.5 1.0 N A:CYS1685 4.9 36.4 1.0 C A:CYS1680 4.9 32.6 1.0 OG A:SER1682 5.0 39.1 1.0

Y.Zhang, C.M.Shan, J.Wang, K.Bao, L.Tong, S.Jia. Molecular Basis For the Role of Oncogenic Histone Mutations in Modulating H3K36 Methylation. Sci Rep V. 7 43906 2017.
ISSN: ESSN 2045-2322
PubMed: 28256625
DOI: 10.1038/SREP43906