Calcium in PDB 6kqq: NSD1 Set Domain in Complex with BT3 and Sam

All present enzymatic activity of NSD1 Set Domain in Complex with BT3 and Sam:
2.1.1.43;

The structure of NSD1 Set Domain in Complex with BT3 and Sam, PDB code: 6kqq 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)	30.35 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	40.469, 60.811, 64.255, 101.18, 107.76, 93.59
R / Rfree (%)	16.3 / 20.1

The structure of NSD1 Set Domain in Complex with BT3 and Sam also contains other interesting chemical elements:

Zinc

(Zn)

6 atoms

The binding sites of Calcium atom in the NSD1 Set Domain in Complex with BT3 and Sam (pdb code 6kqq). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the NSD1 Set Domain in Complex with BT3 and Sam, PDB code: 6kqq:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the NSD1 Set Domain in Complex with BT3 and Sam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of NSD1 Set Domain in Complex with BT3 and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2107 b:27.8 occ:1.00 OE1 A:GLU1910 2.3 28.6 1.0 O A:HOH2282 2.5 32.1 1.0 CD A:GLU1910 3.3 33.9 1.0 OE2 A:GLU1910 3.6 42.2 1.0 O A:HOH2462 4.5 39.0 1.0 O A:HOH2244 4.6 30.2 1.0 CG A:GLU1910 4.6 28.4 1.0 CA A:GLU1910 4.8 29.2 1.0 O A:SER1909 4.8 30.1 1.0 CB A:GLU1910 4.9 32.0 1.0

Calcium binding site 2 out of 2 in the NSD1 Set Domain in Complex with BT3 and Sam


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of NSD1 Set Domain in Complex with BT3 and Sam within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca2108 b:15.9 occ:1.00 O A:HOH2401 2.3 32.6 1.0 O A:HOH2298 2.3 15.7 1.0 O A:LYS2003 2.4 16.9 1.0 OE2 A:GLU1978 2.4 12.9 1.0 O B:HOH2290 2.4 15.7 1.0 O B:HOH2216 2.5 26.4 1.0 OE1 A:GLU1978 2.6 17.3 1.0 CD A:GLU1978 2.8 17.7 1.0 C A:LYS2003 3.6 16.8 1.0 CA A:LYS2003 4.3 14.3 1.0 O A:HOH2344 4.3 24.5 1.0 CB A:LYS2003 4.3 16.2 1.0 CG A:GLU1978 4.4 11.4 1.0 O B:ARG1914 4.4 11.0 1.0 O B:HOH2253 4.4 32.5 1.0 N A:ASP2004 4.6 13.5 1.0 OD1 A:ASP2004 4.6 22.4 1.0 O B:HOH2321 4.7 24.3 1.0 O B:SER1909 4.7 15.4 1.0 CA A:ASP2004 4.8 15.5 1.0 O B:ILE1907 4.8 16.5 1.0 C B:ARG1914 4.8 10.0 1.0 O A:HOH2245 4.9 13.8 1.0 SD B:MET1915 4.9 15.3 1.0 CB B:ARG1914 4.9 13.3 1.0 O B:HOH2302 4.9 27.8 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