Sodium in PDB 9gbf: X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2

All present enzymatic activity of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2:
2.1.1.357;

The structure of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2, PDB code: 9gbf was solved by G.Musco, P.Cocomazzi, A.Berardi, S.Knapp, A.Kramer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	4.97 / 1.76
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.131, 45.249, 60.646, 90, 99.65, 90
R / Rfree (%)	18.8 / 22.8

The structure of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Sodium atom in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 (pdb code 9gbf). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2, PDB code: 9gbf:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1405 b:24.0 occ:1.00 OD1 A:ASP1286 2.3 32.5 1.0 O A:PRO1281 2.4 17.4 1.0 O A:HIS1284 2.5 16.9 1.0 OG A:SER1302 2.6 16.3 1.0 O A:PRO1300 2.7 21.2 1.0 H A:SER1302 2.9 23.7 1.0 HG A:SER1302 3.0 19.9 1.0 N A:SER1302 3.4 19.4 1.0 HA A:ASN1301 3.4 24.2 1.0 C A:PRO1281 3.5 16.5 1.0 HA A:TRP1282 3.5 21.5 1.0 CG A:ASP1286 3.5 31.1 1.0 O A:SER1302 3.6 19.3 1.0 H A:HIS1284 3.6 23.6 1.0 C A:HIS1284 3.7 16.6 1.0 CB A:SER1302 3.8 14.6 1.0 H A:ASP1286 3.8 25.9 1.0 HG A:SER1292 3.8 25.3 1.0 C A:PRO1300 3.8 17.7 1.0 C A:ASN1301 4.0 21.6 1.0 CA A:SER1302 4.0 17.9 1.0 N A:ASP1286 4.0 21.2 1.0 CA A:ASN1301 4.0 19.8 1.0 HB3 A:SER1302 4.0 17.9 1.0 HB2 A:PRO1281 4.1 28.4 1.0 CA A:TRP1282 4.1 17.6 1.0 HA A:ASP1286 4.1 28.7 1.0 C A:SER1302 4.2 21.2 1.0 N A:TRP1282 4.2 14.4 1.0 OD2 A:ASP1286 4.2 50.1 1.0 C A:TRP1282 4.2 15.5 1.0 O A:TRP1282 4.3 19.9 1.0 N A:HIS1284 4.3 19.4 1.0 HB3 A:PRO1281 4.4 28.4 1.0 HB2 A:PRO1300 4.4 27.4 1.0 N A:ASN1301 4.4 20.3 1.0 HA A:CYS1285 4.4 21.5 1.0 CA A:ASP1286 4.4 23.6 1.0 C A:CYS1285 4.4 17.2 1.0 CA A:PRO1281 4.5 24.3 1.0 CB A:PRO1281 4.5 23.4 1.0 HB2 A:SER1302 4.5 17.9 1.0 CB A:ASP1286 4.5 26.0 1.0 OG A:SER1292 4.6 20.8 1.0 HA A:PRO1281 4.6 29.6 1.0 HD1 A:TRP1282 4.6 21.6 1.0 CA A:HIS1284 4.7 20.2 1.0 N A:CYS1285 4.7 20.1 1.0 CA A:CYS1285 4.7 17.6 1.0 HD1 A:HIS1284 4.9 37.9 1.0 O A:ASN1301 4.9 16.7 1.0 N A:HIS1283 4.9 15.7 1.0 HB2 A:ASP1286 4.9 31.6 1.0 HA A:SER1302 4.9 21.9 1.0 CA A:PRO1300 5.0 20.6 1.0

Sodium binding site 2 out of 2 in the X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of X-Ray Structure of PHDVC5HCH Tandem Domain of NSD2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1405 b:22.8 occ:1.00 O B:PRO1281 2.4 16.0 1.0 OG B:SER1302 2.4 14.2 1.0 O B:HIS1284 2.4 15.0 1.0 OD1 B:ASP1286 2.5 23.7 1.0 O B:PRO1300 2.7 18.1 1.0 H B:SER1302 2.9 17.9 1.0 N B:SER1302 3.3 14.6 1.0 HA B:TRP1282 3.4 18.8 1.0 C B:PRO1281 3.5 15.4 1.0 O B:SER1302 3.5 13.0 1.0 CB B:SER1302 3.5 14.5 1.0 CG B:ASP1286 3.5 21.9 1.0 C B:HIS1284 3.6 14.6 1.0 HG B:SER1292 3.6 21.4 1.0 H B:HIS1284 3.6 21.1 1.0 HA B:ASN1301 3.7 20.7 1.0 H B:ASP1286 3.7 17.9 1.0 CA B:SER1302 3.8 17.8 1.0 HB3 B:SER1302 3.8 17.8 1.0 C B:PRO1300 3.9 15.5 1.0 N B:ASP1286 4.0 14.6 1.0 CA B:TRP1282 4.0 15.3 1.0 C B:SER1302 4.0 15.8 1.0 C B:ASN1301 4.0 14.7 1.0 O B:TRP1282 4.0 15.1 1.0 C B:TRP1282 4.1 14.6 1.0 O B:HOH1506 4.1 26.3 1.0 HA B:CYS1285 4.1 24.5 1.0 N B:TRP1282 4.1 13.1 1.0 O B:HOH1539 4.2 31.3 1.0 OD2 B:ASP1286 4.2 28.1 1.0 N B:HIS1284 4.2 17.2 1.0 CA B:ASN1301 4.2 16.9 1.0 HB2 B:SER1302 4.2 17.8 1.0 HB2 B:PRO1281 4.3 25.7 1.0 OG B:SER1292 4.3 17.5 1.0 HA B:ASP1286 4.4 23.3 1.0 C B:CYS1285 4.4 11.7 1.0 HB3 B:PRO1281 4.4 25.7 1.0 N B:ASN1301 4.5 17.2 1.0 HB2 B:PRO1300 4.5 24.5 1.0 CA B:HIS1284 4.5 17.0 1.0 CA B:PRO1281 4.5 14.4 1.0 N B:CYS1285 4.5 14.1 1.0 CA B:CYS1285 4.6 20.1 1.0 CA B:ASP1286 4.6 19.1 1.0 CB B:PRO1281 4.6 21.1 1.0 HD1 B:TRP1282 4.6 15.9 1.0 HA B:PRO1281 4.6 17.6 1.0 CB B:ASP1286 4.7 19.1 1.0 HA B:SER1302 4.7 21.7 1.0 O B:ASN1301 4.8 18.5 1.0 N B:HIS1283 4.8 14.0 1.0 HB2 B:HIS1284 4.9 22.5 1.0 H B:TRP1282 5.0 16.1 1.0

A.Berardi, C.L.Kaestner, M.Ghitti, G.Quilici, P.Cocomazzi, J.Li, F.Ballabio, C.Zucchelli, S.Knapp, J.D.Licht, G.Musco. The C-Terminal PHDVC5HCH Tandem Domain of NSD2 Is A Combinatorial Reader of Unmodified H3K4 and Tri-Methylated H3K27 That Regulates Transcription of Cell Adhesion Genes in Multiple Myeloma Nucleic Acids Res. 2024.
ISSN: ESSN 1362-4962
DOI: 10.1093/NAR/GKAE1121