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Zinc in PDB 4gne: Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7

Enzymatic activity of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7

All present enzymatic activity of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7, PDB code: 4gne 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) 36.42 / 1.47
Space group P 65 2 2
Cell size a, b, c (Å), α, β, γ (°) 57.200, 57.200, 107.440, 90.00, 90.00, 120.00
R / Rfree (%) 14.8 / 17.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7 (pdb code 4gne). 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 1-7, PDB code: 4gne:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in 4gne

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Zinc binding site 1 out of 4 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7


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 1-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:14.4
occ:1.00
ND1 A:HIS1346 2.1 13.8 1.0
SG A:CYS1349 2.3 16.5 1.0
SG A:CYS1324 2.3 13.7 1.0
SG A:CYS1327 2.3 15.9 1.0
CE1 A:HIS1346 3.0 13.7 1.0
CB A:CYS1324 3.1 13.2 1.0
CG A:HIS1346 3.1 12.8 1.0
CB A:CYS1327 3.3 17.9 1.0
CB A:CYS1349 3.3 16.7 1.0
CB A:HIS1346 3.5 14.3 1.0
N A:CYS1327 3.8 15.4 1.0
N A:HIS1346 4.0 13.1 1.0
CA A:CYS1327 4.1 15.9 1.0
NE2 A:HIS1346 4.2 13.9 1.0
CD2 A:HIS1346 4.3 13.9 1.0
CA A:HIS1346 4.4 13.9 1.0
CA A:CYS1324 4.6 11.7 1.0
CB A:GLN1326 4.6 18.9 1.0
CA A:CYS1349 4.7 19.1 1.0
C A:GLN1326 4.8 19.5 1.0
C A:CYS1327 4.9 16.7 1.0
N A:GLY1328 4.9 16.8 1.0

Zinc binding site 2 out of 4 in 4gne

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Zinc binding site 2 out of 4 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7


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 1-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:11.3
occ:1.00
NE2 A:HIS1365 2.1 11.6 1.0
SG A:CYS1341 2.3 12.4 1.0
SG A:CYS1336 2.3 11.7 1.0
SG A:CYS1362 2.3 11.4 1.0
CD2 A:HIS1365 3.0 12.0 1.0
CE1 A:HIS1365 3.1 13.1 1.0
CB A:CYS1336 3.1 11.0 1.0
CB A:CYS1341 3.1 13.1 1.0
CB A:CYS1362 3.4 11.4 1.0
N A:CYS1362 3.9 11.5 1.0
CA A:CYS1362 4.1 11.6 1.0
CG A:HIS1365 4.2 12.1 1.0
ND1 A:HIS1365 4.2 12.9 1.0
CB A:LYS1338 4.2 17.0 1.0
CA A:CYS1336 4.5 10.2 1.0
CA A:CYS1341 4.5 13.0 1.0
CB A:LYS1343 4.6 11.0 1.0
CB A:TRP1364 4.6 11.5 1.0
C A:CYS1362 4.6 11.5 1.0
O A:CYS1362 4.6 12.7 1.0
O A:HOH1669 4.8 24.1 1.0
CG A:LYS1343 4.9 12.1 1.0
CE3 A:TRP1364 5.0 12.6 1.0

Zinc binding site 3 out of 4 in 4gne

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Zinc binding site 3 out of 4 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7


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 1-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1503

b:11.2
occ:1.00
NE2 A:HIS1408 2.1 11.1 1.0
SG A:CYS1381 2.3 11.7 1.0
SG A:CYS1378 2.3 10.2 1.0
SG A:CYS1405 2.4 11.8 1.0
CD2 A:HIS1408 2.9 10.4 1.0
CE1 A:HIS1408 3.2 12.5 1.0
CB A:CYS1378 3.3 9.8 1.0
CB A:CYS1381 3.3 12.0 1.0
CB A:CYS1405 3.5 10.1 1.0
N A:CYS1381 3.7 11.0 1.0
N A:CYS1405 3.9 8.5 1.0
CA A:CYS1381 4.0 10.6 1.0
CG A:HIS1408 4.1 11.1 1.0
CA A:CYS1405 4.2 9.4 1.0
ND1 A:HIS1408 4.2 13.2 1.0
CB A:HIS1383 4.3 11.3 1.0
O A:CYS1381 4.3 9.9 1.0
C A:PHE1380 4.4 11.3 1.0
C A:CYS1381 4.4 9.7 1.0
CB A:GLU1407 4.5 21.0 1.0
CB A:PHE1380 4.6 11.5 1.0
ND1 A:HIS1383 4.7 22.1 1.0
CG A:HIS1383 4.7 15.9 1.0
CA A:CYS1378 4.7 8.9 1.0
C A:CYS1405 4.7 9.3 1.0
CG A:GLU1407 4.7 25.2 1.0
CA A:PHE1380 4.8 10.3 1.0
N A:PHE1380 4.8 10.5 1.0
N A:HIS1383 4.9 9.9 1.0
O A:CYS1405 4.9 10.3 1.0
O A:HOH1677 4.9 29.6 1.0

Zinc binding site 4 out of 4 in 4gne

Go back to Zinc Binding Sites List in 4gne
Zinc binding site 4 out of 4 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3 Peptide 1-7


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 1-7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1504

b:14.9
occ:1.00
ND1 A:HIS1389 2.1 15.0 1.0
SG A:CYS1367 2.3 13.1 1.0
SG A:CYS1386 2.3 16.3 1.0
SG A:CYS1370 2.3 16.4 1.0
CE1 A:HIS1389 3.0 17.5 1.0
CG A:HIS1389 3.2 15.3 1.0
CB A:CYS1367 3.2 12.5 1.0
CB A:CYS1386 3.4 15.6 1.0
CB A:CYS1370 3.5 15.2 1.0
CB A:HIS1389 3.6 15.3 1.0
N A:CYS1370 3.9 12.9 1.0
N A:CYS1386 4.0 12.3 1.0
NE2 A:HIS1389 4.1 18.1 1.0
CB A:GLU1369 4.2 12.8 1.0
CA A:CYS1370 4.3 15.1 1.0
CD2 A:HIS1389 4.3 17.8 1.0
CA A:CYS1386 4.3 14.1 1.0
N A:HIS1389 4.6 15.3 1.0
CB A:SER1372 4.6 18.6 1.0
CA A:CYS1367 4.6 11.5 1.0
CG A:GLU1369 4.6 13.1 1.0
C A:GLU1369 4.7 12.1 1.0
CA A:HIS1389 4.8 13.9 1.0
O A:HOH1689 4.8 35.2 1.0
CA A:GLU1369 4.8 11.4 1.0
C A:CYS1370 4.9 15.6 1.0
N A:SER1372 4.9 16.5 1.0
N A:GLU1369 4.9 11.8 1.0
C A:CYS1386 4.9 14.1 1.0
OG A:SER1372 5.0 24.5 1.0
CB A:ASP1388 5.0 20.7 1.0

Reference:

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
Page generated: Wed Dec 16 05:20:10 2020

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