Zinc in PDB 6kqp: NSD1 Set Domain in Complex with Sam

All present enzymatic activity of NSD1 Set Domain in Complex with Sam:
2.1.1.357;

The structure of NSD1 Set Domain in Complex with Sam, PDB code: 6kqp was solved by H.J.Cho, T.Cierpicki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.87 / 2.40
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	91.649, 91.649, 60.582, 90.00, 90.00, 90.00
R / Rfree (%)	19.4 / 24.7

The binding sites of Zinc atom in the NSD1 Set Domain in Complex with Sam (pdb code 6kqp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 3 binding sites of Zinc where determined in the NSD1 Set Domain in Complex with Sam, PDB code: 6kqp:
Jump to Zinc binding site number: 1; 2; 3;

Zinc binding site 1 out of 3 in the NSD1 Set Domain in Complex with Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of NSD1 Set Domain in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2102 b:50.5 occ:1.00 SG A:CYS2072 2.2 48.2 1.0 SG A:CYS2077 2.4 61.9 1.0 SG A:CYS2070 2.4 47.0 1.0 SG A:CYS2023 2.5 54.2 1.0 CB A:CYS2077 3.2 60.4 1.0 CB A:CYS2072 3.3 48.9 1.0 CB A:CYS2070 3.4 46.9 1.0 CB A:CYS2023 3.4 47.8 1.0 CA A:CYS2077 3.7 60.4 1.0 N A:CYS2023 3.8 49.9 1.0 NE2 A:HIS2021 4.1 38.2 1.0 N A:CYS2072 4.1 47.2 1.0 CA A:CYS2023 4.2 46.1 1.0 CA A:CYS2072 4.3 50.6 1.0 N A:SER2078 4.3 52.1 1.0 CD2 A:HIS2021 4.3 45.4 1.0 O A:HOH2213 4.3 41.7 1.0 C A:CYS2077 4.4 51.7 1.0 O A:PHE2080 4.5 45.6 1.0 N A:GLY2079 4.6 48.9 1.0 CA A:CYS2070 4.7 48.3 1.0 C A:CYS2022 4.8 46.3 1.0 C A:CYS2070 4.8 46.1 1.0 N A:CYS2077 4.9 58.8 1.0 CA A:CYS2022 4.9 47.5 1.0

Zinc binding site 2 out of 3 in the NSD1 Set Domain in Complex with Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of NSD1 Set Domain in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2103 b:38.0 occ:1.00 SG A:CYS1905 2.1 33.1 1.0 SG A:CYS1931 2.2 41.1 1.0 SG A:CYS1925 2.4 38.2 1.0 SG A:CYS1920 2.4 47.4 1.0 CB A:CYS1920 2.8 40.1 1.0 CB A:CYS1905 3.0 37.3 1.0 CB A:CYS1931 3.2 43.4 1.0 O A:HOH2244 3.3 9.3 1.0 CB A:CYS1925 3.6 35.0 1.0 ZN A:ZN2104 3.7 35.8 1.0 CA A:CYS1931 3.9 43.6 1.0 CB A:ASN1933 4.2 37.0 1.0 SG A:CYS1895 4.2 52.6 1.0 CA A:CYS1920 4.4 42.5 1.0 CA A:CYS1905 4.4 37.8 1.0 CB A:ALA1927 4.6 44.6 1.0 N A:ASN1933 4.6 38.1 1.0 C A:CYS1931 4.7 41.2 1.0 SG A:CYS1911 4.7 34.8 1.0 N A:GLN1932 4.7 42.2 1.0 CA A:CYS1925 4.9 38.6 1.0 CA A:ASN1933 4.9 39.5 1.0 N A:CYS1905 5.0 40.4 1.0

Zinc binding site 3 out of 3 in the NSD1 Set Domain in Complex with Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of NSD1 Set Domain in Complex with Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn2104 b:35.8 occ:1.00 SG A:CYS1895 2.1 52.6 1.0 SG A:CYS1911 2.3 34.8 1.0 SG A:CYS1905 2.3 33.1 1.0 SG A:CYS1897 2.4 38.5 1.0 CB A:CYS1911 3.0 33.4 1.0 CB A:CYS1895 3.1 42.5 1.0 CB A:CYS1905 3.3 37.3 1.0 CB A:CYS1897 3.3 43.0 1.0 SG A:CYS1920 3.5 47.4 1.0 CA A:CYS1905 3.6 37.8 1.0 ZN A:ZN2103 3.7 38.0 1.0 CA A:CYS1911 3.7 35.2 1.0 O A:HOH2244 4.0 9.3 1.0 N A:CYS1905 4.1 40.4 1.0 N A:CYS1897 4.2 40.9 1.0 CA A:CYS1897 4.4 41.9 1.0 SG A:CYS1925 4.4 38.2 1.0 CA A:CYS1895 4.5 42.4 1.0 C A:CYS1911 4.7 37.5 1.0 N A:CYS1911 4.8 38.9 1.0 N A:ASN1896 4.9 46.5 1.0 C A:CYS1905 4.9 36.9 1.0 N A:ILE1912 4.9 37.3 1.0 C A:CYS1895 4.9 48.5 1.0

H.Huang, C.A.Howard, S.Zari, H.J.Cho, S.Shukla, H.Li, J.Ndoj, P.Gonzalez-Alonso, C.Nikolaidis, J.Abbott, D.S.Rogawski, M.A.Potopnyk, K.Kempinska, H.Miao, T.Purohit, A.Henderson, A.Mapp, M.L.Sulis, A.Ferrando, J.Grembecka, T.Cierpicki. Covalent Inhibition of NSD1 Histone Methyltransferase. Nat.Chem.Biol. V. 16 1403 2020.
ISSN: ESSN 1552-4469
PubMed: 32868895
DOI: 10.1038/S41589-020-0626-6