Zinc in PDB 5v22: Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sah

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

The structure of Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sah, PDB code: 5v22 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)	40.00 / 2.40
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.287, 77.196, 76.527, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 25.7

The binding sites of Zinc atom in the Crystal Structure of Human SETD2 Set-Domain in Complex with H3K36M Peptide and Sah (pdb code 5v22). 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 Sah, PDB code: 5v22:
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 Sah


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1801 b:35.0 occ:1.00 SG A:CYS1539 2.3 32.7 1.0 SG A:CYS1516 2.3 37.2 1.0 SG A:CYS1529 2.4 33.0 1.0 SG A:CYS1533 2.4 36.0 1.0 CB A:CYS1529 3.1 29.8 1.0 CB A:CYS1516 3.3 38.8 1.0 CB A:CYS1539 3.3 34.8 1.0 CB A:CYS1533 3.4 31.0 1.0 ZN A:ZN1802 3.8 38.9 1.0 SG A:CYS1499 4.1 36.0 1.0 CA A:CYS1539 4.3 33.8 1.0 O A:HOH1966 4.3 31.1 1.0 CB A:ASN1541 4.3 34.1 1.0 CA A:CYS1529 4.6 30.7 1.0 CA A:CYS1533 4.7 39.0 1.0 SG A:CYS1520 4.8 38.7 1.0 CA A:CYS1516 4.8 42.0 1.0 ND2 A:ASN1541 5.0 24.5 1.0 CB A:ASN1535 5.0 40.7 1.0 ND2 A:ASN1535 5.0 43.1 1.0 N A:ASN1541 5.0 29.2 1.0

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


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1802 b:38.9 occ:1.00 SG A:CYS1499 2.3 36.0 1.0 SG A:CYS1501 2.3 42.7 1.0 SG A:CYS1520 2.4 38.7 1.0 SG A:CYS1516 2.5 37.2 1.0 CB A:CYS1501 3.1 40.5 1.0 CB A:CYS1520 3.2 35.9 1.0 CB A:CYS1499 3.2 45.9 1.0 CB A:CYS1516 3.3 38.8 1.0 ZN A:ZN1801 3.8 35.0 1.0 CA A:CYS1516 3.8 42.0 1.0 CA A:CYS1520 3.9 38.1 1.0 N A:CYS1501 4.2 43.5 1.0 SG A:CYS1529 4.2 33.0 1.0 CA A:CYS1501 4.3 41.1 1.0 O A:HOH1935 4.5 47.9 1.0 N A:CYS1516 4.7 41.1 1.0 CA A:CYS1499 4.7 45.1 1.0 C A:CYS1520 4.7 43.0 1.0 N A:LEU1521 4.7 39.8 1.0 ND2 A:ASN1535 4.8 43.1 1.0 SG A:CYS1533 4.9 36.0 1.0 C A:CYS1516 4.9 39.5 1.0

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


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 Sah within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1803 b:36.6 occ:1.00 SG A:CYS1678 2.3 34.6 1.0 SG A:CYS1680 2.3 34.5 1.0 SG A:CYS1631 2.4 32.9 1.0 SG A:CYS1685 2.5 39.3 1.0 CB A:CYS1685 3.2 39.3 1.0 CB A:CYS1680 3.4 39.4 1.0 CB A:CYS1678 3.4 33.5 1.0 CB A:CYS1631 3.5 37.9 1.0 CA A:CYS1685 3.6 38.9 1.0 N A:ARG1686 3.9 46.6 1.0 N A:CYS1631 3.9 36.9 1.0 N A:CYS1680 4.1 30.2 1.0 O A:HOH1930 4.1 38.9 1.0 C A:CYS1685 4.3 43.9 1.0 CA A:CYS1680 4.3 35.2 1.0 CA A:CYS1631 4.3 37.2 1.0 NE2 A:HIS1629 4.5 30.5 1.0 CD2 A:HIS1629 4.6 30.9 1.0 C A:CYS1678 4.6 35.5 1.0 O A:CYS1678 4.6 29.2 1.0 CA A:CYS1678 4.6 33.5 1.0 HN62 A:SAH1804 4.6 32.1 1.0 N A:GLY1681 4.7 41.2 1.0 N A:CYS1685 4.8 42.5 1.0 N A:GLY1687 4.8 39.1 1.0 C A:CYS1680 4.9 36.2 1.0 C A:SER1630 5.0 34.9 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