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Zinc in PDB 4gng: Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide

Enzymatic activity of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide

All present enzymatic activity of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide:
2.1.1.43;

Protein crystallography data

The structure of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide, PDB code: 4gng 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) 28.10 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.200, 59.960, 95.230, 90.00, 90.00, 90.00
R / Rfree (%) 18.1 / 21.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide (pdb code 4gng). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide, PDB code: 4gng:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4gng

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Zinc binding site 1 out of 8 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide


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 H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:20.5
occ:1.00
 ND1 A:HIS1346 2.0 19.8 1.0
SG A:CYS1349 2.2 23.4 1.0
SG A:CYS1327 2.3 21.5 1.0
SG A:CYS1324 2.3 17.7 1.0
CE1 A:HIS1346 3.0 20.0 1.0
CB A:CYS1324 3.0 19.0 1.0
CG A:HIS1346 3.1 19.0 1.0
CB A:CYS1327 3.3 22.9 1.0
CB A:CYS1349 3.3 21.8 1.0
CB A:HIS1346 3.5 17.8 1.0
N A:CYS1327 3.8 20.2 1.0
O2 B:GOL101 3.9 43.6 1.0
N A:HIS1346 4.0 16.1 1.0
CA A:CYS1327 4.1 22.9 1.0
NE2 A:HIS1346 4.1 20.8 1.0
CD2 A:HIS1346 4.2 19.9 1.0
C1 B:GOL101 4.3 45.6 1.0
O1 B:GOL101 4.3 49.1 1.0
CA A:HIS1346 4.4 17.0 1.0
CA A:CYS1324 4.5 19.5 1.0
CB A:GLN1326 4.5 22.0 1.0
CA A:CYS1349 4.7 22.1 1.0
C2 B:GOL101 4.7 45.0 1.0
C A:GLN1326 4.8 21.4 1.0
C A:CYS1327 4.8 23.8 1.0
N A:GLY1328 4.9 23.9 1.0
N A:CYS1349 4.9 21.9 1.0
C A:CYS1324 5.0 19.7 1.0

Zinc binding site 2 out of 8 in 4gng

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Zinc binding site 2 out of 8 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide


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 H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:15.4
occ:1.00
 NE2 A:HIS1365 2.1 16.9 1.0
SG A:CYS1336 2.3 16.1 1.0
SG A:CYS1341 2.3 16.6 1.0
SG A:CYS1362 2.4 15.5 1.0
CD2 A:HIS1365 3.0 16.4 1.0
CE1 A:HIS1365 3.1 18.6 1.0
CB A:CYS1336 3.1 16.8 1.0
CB A:CYS1341 3.2 18.6 1.0
CB A:CYS1362 3.4 14.9 1.0
N A:CYS1362 4.0 14.7 1.0
CA A:CYS1362 4.2 13.9 1.0
CG A:HIS1365 4.2 16.1 1.0
ND1 A:HIS1365 4.2 17.4 1.0
CB A:LYS1338 4.5 23.8 1.0
CA A:CYS1336 4.6 18.0 1.0
CB A:LYS1343 4.6 16.0 1.0
CA A:CYS1341 4.6 19.3 1.0
C A:CYS1362 4.7 14.5 1.0
O A:CYS1362 4.7 14.4 1.0
CB A:TRP1364 4.8 15.9 1.0
O A:HOH1661 4.8 29.3 1.0
CG A:LYS1343 4.9 16.6 1.0
CE3 A:TRP1364 4.9 15.4 1.0

Zinc binding site 3 out of 8 in 4gng

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Zinc binding site 3 out of 8 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide


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 H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1503

b:18.6
occ:1.00
 NE2 A:HIS1408 2.1 19.5 1.0
SG A:CYS1378 2.3 15.9 1.0
SG A:CYS1381 2.3 18.8 1.0
SG A:CYS1405 2.3 20.0 1.0
CD2 A:HIS1408 2.8 19.1 1.0
CE1 A:HIS1408 3.3 19.7 1.0
CB A:CYS1381 3.3 17.2 1.0
CB A:CYS1378 3.3 16.5 1.0
CB A:CYS1405 3.5 19.1 1.0
N A:CYS1381 3.6 16.9 1.0
N A:CYS1405 3.9 18.5 1.0
CA A:CYS1381 3.9 17.7 1.0
CG A:HIS1408 4.1 19.9 1.0
CA A:CYS1405 4.2 18.9 1.0
C A:PHE1380 4.2 17.4 1.0
CB A:HIS1383 4.3 19.0 1.0
ND1 A:HIS1408 4.3 19.6 1.0
O A:CYS1381 4.3 17.3 1.0
C A:CYS1381 4.3 16.6 1.0
CD2 A:HIS1383 4.4 20.9 1.0
CG A:HIS1383 4.5 20.8 1.0
CB A:GLU1407 4.6 30.7 1.0
CB A:PHE1380 4.7 17.5 1.0
C A:CYS1405 4.7 20.1 1.0
CA A:CYS1378 4.7 16.1 1.0
CA A:PHE1380 4.8 17.4 1.0
N A:PHE1380 4.8 16.2 1.0
CG A:GLU1407 4.8 35.5 1.0
N A:HIS1383 4.9 15.9 1.0
O A:CYS1405 4.9 19.0 1.0
O A:PHE1380 4.9 19.6 1.0

Zinc binding site 4 out of 8 in 4gng

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Zinc binding site 4 out of 8 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide


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 H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1504

b:26.5
occ:1.00
 SG A:CYS1386 2.1 28.3 1.0
ND1 A:HIS1389 2.2 33.9 1.0
SG A:CYS1370 2.3 27.3 1.0
SG A:CYS1367 2.3 22.3 1.0
CE1 A:HIS1389 3.0 35.4 1.0
CB A:CYS1367 3.2 21.5 1.0
CG A:HIS1389 3.2 32.9 1.0
CB A:CYS1370 3.4 28.2 1.0
CB A:CYS1386 3.4 24.8 1.0
CB A:HIS1389 3.6 31.1 1.0
N A:CYS1370 3.7 27.8 1.0
N A:CYS1386 4.0 22.9 1.0
CA A:CYS1370 4.1 29.9 1.0
NE2 A:HIS1389 4.2 34.6 1.0
C A:GLU1369 4.3 32.4 1.0
CA A:CYS1386 4.3 24.4 1.0
CD2 A:HIS1389 4.3 34.0 1.0
O A:HOH1629 4.4 39.2 1.0
N A:HIS1389 4.5 29.2 1.0
CB A:GLU1369 4.6 34.4 1.0
CA A:CYS1367 4.6 20.9 1.0
CB A:SER1372 4.7 28.5 1.0
C A:CYS1370 4.7 30.6 1.0
N A:GLU1369 4.7 27.9 1.0
CA A:GLU1369 4.7 30.3 1.0
CA A:HIS1389 4.7 29.4 1.0
CB A:ASP1388 4.9 37.2 1.0
O A:CYS1370 4.9 29.4 1.0
C A:CYS1386 4.9 26.5 1.0
O A:GLU1369 4.9 31.0 1.0
O A:CYS1386 5.0 25.7 1.0

Zinc binding site 5 out of 8 in 4gng

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Zinc binding site 5 out of 8 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1501

b:15.7
occ:1.00
 ND1 D:HIS1346 2.1 14.0 1.0
SG D:CYS1327 2.3 16.4 1.0
SG D:CYS1349 2.3 18.7 1.0
SG D:CYS1324 2.3 13.6 1.0
CB D:CYS1324 3.0 13.1 1.0
CE1 D:HIS1346 3.0 13.3 1.0
CG D:HIS1346 3.1 12.8 1.0
CB D:CYS1327 3.3 17.3 1.0
CB D:CYS1349 3.3 17.7 1.0
CB D:HIS1346 3.5 12.6 1.0
N D:CYS1327 3.7 17.3 1.0
O D:HOH1703 3.9 34.7 1.0
N D:HIS1346 4.0 12.2 1.0
CA D:CYS1327 4.1 17.4 1.0
NE2 D:HIS1346 4.2 14.2 1.0
O D:HOH1740 4.2 41.5 1.0
CD2 D:HIS1346 4.3 13.6 1.0
CA D:HIS1346 4.4 12.7 1.0
CB D:GLN1326 4.5 17.9 1.0
CA D:CYS1324 4.5 13.4 1.0
CA D:CYS1349 4.7 18.4 1.0
C D:GLN1326 4.8 17.4 1.0
O D:HOH1709 4.8 30.4 1.0
C D:CYS1327 4.8 17.9 1.0
N D:GLY1328 4.9 17.4 1.0
N D:CYS1349 5.0 18.3 1.0

Zinc binding site 6 out of 8 in 4gng

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Zinc binding site 6 out of 8 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1502

b:12.8
occ:1.00
 NE2 D:HIS1365 2.0 13.5 1.0
SG D:CYS1341 2.3 12.7 1.0
SG D:CYS1362 2.3 13.0 1.0
SG D:CYS1336 2.3 12.8 1.0
CD2 D:HIS1365 2.9 13.6 1.0
CE1 D:HIS1365 3.1 14.5 1.0
CB D:CYS1336 3.1 11.9 1.0
CB D:CYS1341 3.1 13.1 1.0
CB D:CYS1362 3.4 12.9 1.0
N D:CYS1362 3.9 13.8 1.0
CG D:HIS1365 4.1 14.1 1.0
ND1 D:HIS1365 4.2 14.0 1.0
CA D:CYS1362 4.2 13.0 1.0
CB D:LYS1338 4.5 17.6 1.0
CA D:CYS1336 4.5 11.7 1.0
CA D:CYS1341 4.6 14.2 1.0
CB D:LYS1343 4.6 12.1 1.0
O D:HOH1654 4.6 18.8 1.0
CB D:TRP1364 4.7 12.8 1.0
O D:CYS1362 4.7 11.8 1.0
C D:CYS1362 4.7 12.6 1.0
CG D:LYS1343 5.0 12.2 1.0
CE3 D:TRP1364 5.0 14.0 1.0

Zinc binding site 7 out of 8 in 4gng

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Zinc binding site 7 out of 8 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1503

b:15.2
occ:1.00
 NE2 D:HIS1408 2.1 14.2 1.0
SG D:CYS1381 2.3 15.9 1.0
SG D:CYS1378 2.3 14.5 1.0
SG D:CYS1405 2.4 14.8 1.0
CD2 D:HIS1408 2.8 14.9 1.0
CE1 D:HIS1408 3.2 16.4 1.0
CB D:CYS1378 3.3 13.6 1.0
CB D:CYS1381 3.3 15.2 1.0
CB D:CYS1405 3.5 14.6 1.0
N D:CYS1381 3.8 15.1 1.0
N D:CYS1405 3.9 14.2 1.0
CA D:CYS1381 4.0 14.4 1.0
CG D:HIS1408 4.1 16.1 1.0
ND1 D:HIS1408 4.3 16.1 1.0
CA D:CYS1405 4.3 14.5 1.0
CD2 D:HIS1383 4.3 18.2 1.0
C D:PHE1380 4.3 15.2 1.0
CB D:HIS1383 4.4 15.1 1.0
C D:CYS1381 4.4 13.7 1.0
O D:CYS1381 4.4 13.2 1.0
O D:HOH1624 4.4 26.8 1.0
CG D:HIS1383 4.5 17.6 1.0
CB D:GLU1407 4.6 19.9 1.0
CB D:PHE1380 4.7 16.3 1.0
CA D:CYS1378 4.7 13.6 1.0
C D:CYS1405 4.8 15.1 1.0
CA D:PHE1380 4.8 15.8 1.0
N D:PHE1380 4.9 15.9 1.0
N D:HIS1383 4.9 13.4 1.0
O D:PHE1380 4.9 16.7 1.0
O D:CYS1405 4.9 15.2 1.0

Zinc binding site 8 out of 8 in 4gng

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Zinc binding site 8 out of 8 in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains Complexed with H3K9ME3 Peptide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn1504

b:18.6
occ:1.00
 ND1 D:HIS1389 2.1 18.5 1.0
SG D:CYS1370 2.3 21.0 1.0
SG D:CYS1367 2.3 15.3 1.0
SG D:CYS1386 2.3 21.1 1.0
CE1 D:HIS1389 3.0 21.7 1.0
CG D:HIS1389 3.1 18.9 1.0
CB D:CYS1367 3.2 16.0 1.0
CB D:CYS1370 3.4 21.7 1.0
CB D:CYS1386 3.4 17.7 1.0
CB D:HIS1389 3.5 18.5 1.0
N D:CYS1370 3.8 20.5 1.0
N D:CYS1386 4.1 15.6 1.0
CA D:CYS1370 4.1 22.7 1.0
NE2 D:HIS1389 4.2 20.8 1.0
CB D:GLU1369 4.2 20.5 1.0
CD2 D:HIS1389 4.3 19.9 1.0
CA D:CYS1386 4.3 16.9 1.0
O D:HOH1693 4.5 37.2 1.0
N D:HIS1389 4.5 18.4 1.0
C D:GLU1369 4.5 21.8 1.0
CA D:CYS1367 4.6 16.7 1.0
CA D:HIS1389 4.6 17.9 1.0
C D:CYS1370 4.7 24.5 1.0
CB D:SER1372 4.7 28.7 1.0
CA D:GLU1369 4.8 20.4 1.0
N D:GLU1369 4.8 20.3 1.0
C D:CYS1386 4.9 18.6 1.0
O D:CYS1370 4.9 22.6 1.0
CB D:ASP1388 4.9 23.2 1.0
O D:CYS1386 5.0 17.1 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: Sat Oct 26 23:23:06 2024

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