Zinc in PDB 4gnf: Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15

All present enzymatic activity of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15:
2.1.1.43;

The structure of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15, PDB code: 4gnf was solved by F.Li, C.He, J.Wu, Y.Shi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	21.70 / 1.55
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	60.030, 62.710, 62.840, 90.00, 90.00, 90.00
R / Rfree (%)	16 / 20.5

The binding sites of Zinc atom in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15 (pdb code 4gnf). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15, PDB code: 4gnf:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15


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 NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1501 b:30.4 occ:1.00 ND1 A:HIS1346 2.1 27.4 1.0 SG A:CYS1349 2.3 36.2 1.0 SG A:CYS1324 2.3 27.0 1.0 SG A:CYS1327 2.4 32.8 1.0 CE1 A:HIS1346 3.0 28.8 1.0 CB A:CYS1324 3.1 24.3 1.0 CG A:HIS1346 3.1 26.1 1.0 CB A:CYS1327 3.3 33.5 1.0 CB A:CYS1349 3.3 32.6 1.0 CB A:HIS1346 3.5 25.1 1.0 N A:CYS1327 3.7 28.9 1.0 N A:HIS1346 4.1 25.3 1.0 CA A:CYS1327 4.1 30.2 1.0 NE2 A:HIS1346 4.2 29.4 1.0 CD2 A:HIS1346 4.2 27.9 1.0 CA A:HIS1346 4.4 25.5 1.0 CB A:GLN1326 4.5 29.7 1.0 CA A:CYS1324 4.6 21.7 1.0 CA A:CYS1349 4.6 31.2 1.0 C A:GLN1326 4.7 29.9 1.0 C A:CYS1327 4.8 30.6 1.0 N A:GLY1328 4.9 27.5 1.0 N A:CYS1349 5.0 34.3 1.0 CA A:GLN1326 5.0 28.3 1.0 N A:GLN1326 5.0 23.9 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15


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 NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1502 b:20.7 occ:1.00 NE2 A:HIS1365 2.0 21.3 1.0 SG A:CYS1336 2.3 21.3 1.0 SG A:CYS1341 2.3 19.8 1.0 SG A:CYS1362 2.4 21.9 1.0 CD2 A:HIS1365 3.0 21.7 1.0 CE1 A:HIS1365 3.0 20.4 1.0 CB A:CYS1336 3.1 19.1 1.0 CB A:CYS1341 3.1 18.7 1.0 CB A:CYS1362 3.4 22.1 1.0 N A:CYS1362 3.9 21.8 1.0 ND1 A:HIS1365 4.1 21.6 1.0 CG A:HIS1365 4.1 20.3 1.0 CA A:CYS1362 4.2 22.5 1.0 CB A:LYS1338 4.3 21.4 1.0 CA A:CYS1336 4.5 19.1 1.0 CA A:CYS1341 4.5 16.9 1.0 CB A:LYS1343 4.5 17.3 1.0 CB A:TRP1364 4.6 20.5 1.0 C A:CYS1362 4.7 21.3 1.0 O A:CYS1362 4.7 22.8 1.0 CE3 A:TRP1364 4.8 18.2 1.0 O A:HOH1661 4.8 34.2 1.0 CG A:LYS1343 4.9 17.9 1.0 CG A:LYS1338 5.0 24.7 1.0 C A:CYS1341 5.0 18.2 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15


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 NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1503 b:23.4 occ:1.00 NE2 A:HIS1408 2.0 24.2 1.0 SG A:CYS1381 2.3 24.4 1.0 SG A:CYS1378 2.3 20.8 1.0 SG A:CYS1405 2.4 24.2 1.0 CD2 A:HIS1408 2.9 23.3 1.0 CE1 A:HIS1408 3.1 22.7 1.0 CB A:CYS1378 3.3 20.8 1.0 CB A:CYS1381 3.3 22.1 1.0 CB A:CYS1405 3.5 24.2 1.0 N A:CYS1381 3.7 21.2 1.0 N A:CYS1405 3.9 22.3 1.0 CA A:CYS1381 4.0 21.5 1.0 CG A:HIS1408 4.1 22.9 1.0 ND1 A:HIS1408 4.2 23.8 1.0 CD2 A:HIS1383 4.2 31.5 1.0 CB A:HIS1383 4.2 23.4 1.0 CA A:CYS1405 4.2 21.1 1.0 O A:CYS1381 4.3 20.1 1.0 C A:CYS1381 4.3 20.7 1.0 C A:PHE1380 4.3 20.5 1.0 CG A:HIS1383 4.5 29.2 1.0 CA A:CYS1378 4.7 19.8 1.0 CB A:PHE1380 4.7 21.1 1.0 N A:HIS1383 4.8 24.7 1.0 CB A:GLU1407 4.8 26.5 1.0 C A:CYS1405 4.8 24.3 1.0 CA A:PHE1380 4.8 19.3 1.0 N A:PHE1380 4.9 18.5 1.0 O A:CYS1405 5.0 22.7 1.0 O A:PHE1380 5.0 24.4 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-15 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1504 b:37.3 occ:1.00 ND1 A:HIS1389 2.1 39.5 1.0 SG A:CYS1370 2.2 39.0 1.0 SG A:CYS1367 2.3 34.9 1.0 SG A:CYS1386 2.4 34.4 1.0 CE1 A:HIS1389 3.0 43.2 1.0 CG A:HIS1389 3.2 40.8 1.0 CB A:CYS1367 3.2 29.3 1.0 CB A:CYS1386 3.4 28.0 1.0 CB A:CYS1370 3.4 37.4 1.0 N A:CYS1370 3.6 35.8 1.0 CB A:HIS1389 3.7 35.1 1.0 N A:CYS1386 3.9 29.6 1.0 CA A:CYS1370 4.0 36.4 1.0 NE2 A:HIS1389 4.2 48.1 1.0 CA A:CYS1386 4.2 29.4 1.0 CD2 A:HIS1389 4.3 40.9 1.0 C A:GLU1369 4.4 39.0 1.0 CB A:GLU1369 4.4 37.1 1.0 C A:CYS1370 4.5 39.3 1.0 N A:HIS1389 4.5 34.5 1.0 O A:CYS1370 4.6 36.4 1.0 CB A:SER1372 4.7 35.8 1.0 N A:GLU1369 4.7 34.7 1.0 CA A:GLU1369 4.7 34.9 1.0 CA A:CYS1367 4.7 26.8 1.0 CA A:HIS1389 4.8 36.6 1.0 C A:CYS1386 4.9 32.4 1.0 OG A:SER1372 5.0 46.3 1.0

C.He, F.Li, J.Zhang, J.Wu, Y.Shi. The Methyltransferase NSD3 Has Chromatin-Binding Motifs, PHD5-C5HCH, That Are Distinct From Other Nsd (Nuclear Receptor Set Domain) Family Members in Their Histone H3 Recognition. J.Biol.Chem. V. 288 4692 2013.
ISSN: ISSN 0021-9258
PubMed: 23269674
DOI: 10.1074/JBC.M112.426148