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Zinc in PDB 4gnd: Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains

Enzymatic activity of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains

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

Protein crystallography data

The structure of Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains, PDB code: 4gnd 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) 50.67 / 2.27
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 58.510, 58.510, 108.581, 90.00, 90.00, 120.00
R / Rfree (%) 17.2 / 21.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of NSD3 Tandem PHD5-C5HCH Domains (pdb code 4gnd). 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, PDB code: 4gnd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4gnd

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


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

b:14.4
occ:1.00
 SG A:CYS1349 2.1 17.9 1.0
ND1 A:HIS1346 2.2 16.7 1.0
SG A:CYS1327 2.3 17.3 1.0
SG A:CYS1324 2.4 18.4 1.0
CB A:CYS1324 3.0 18.6 1.0
CG A:HIS1346 3.1 16.4 1.0
CE1 A:HIS1346 3.2 16.7 1.0
CB A:CYS1349 3.3 17.7 1.0
CB A:CYS1327 3.4 19.1 1.0
CB A:HIS1346 3.4 16.1 1.0
N A:CYS1327 3.8 19.8 1.0
N A:HIS1346 4.1 15.0 1.0
CA A:CYS1327 4.2 19.9 1.0
CD2 A:HIS1346 4.3 16.3 1.0
NE2 A:HIS1346 4.3 16.9 1.0
CA A:HIS1346 4.3 15.4 1.0
CB A:GLN1326 4.5 21.4 1.0
CA A:CYS1324 4.5 19.4 1.0
CA A:CYS1349 4.7 17.4 1.0
C A:GLN1326 4.7 20.2 1.0
C A:CYS1327 4.9 19.9 1.0
CA A:GLN1326 5.0 20.4 1.0
O A:ASP1329 5.0 20.6 1.0

Zinc binding site 2 out of 8 in 4gnd

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


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

b:17.8
occ:1.00
 NE2 A:HIS1365 2.0 22.7 1.0
SG A:CYS1336 2.2 19.1 1.0
SG A:CYS1341 2.2 18.8 1.0
SG A:CYS1362 2.3 18.5 1.0
CB A:CYS1336 3.0 18.6 1.0
CE1 A:HIS1365 3.0 22.9 1.0
CD2 A:HIS1365 3.0 23.1 1.0
CB A:CYS1341 3.1 19.4 1.0
CB A:CYS1362 3.4 18.2 1.0
N A:CYS1362 3.9 19.6 1.0
ND1 A:HIS1365 4.1 23.3 1.0
CG A:HIS1365 4.1 23.4 1.0
CA A:CYS1362 4.2 19.0 1.0
CB A:LYS1338 4.3 26.0 1.0
CA A:CYS1336 4.4 18.8 1.0
CB A:TRP1364 4.5 19.4 1.0
CA A:CYS1341 4.5 19.6 1.0
CB A:LYS1343 4.5 14.6 1.0
O A:CYS1362 4.6 18.9 1.0
C A:CYS1362 4.7 19.5 1.0
CE3 A:TRP1364 4.9 18.6 1.0
CG A:LYS1343 5.0 14.2 1.0

Zinc binding site 3 out of 8 in 4gnd

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


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

b:20.9
occ:1.00
 NE2 A:HIS1408 2.0 23.7 1.0
SG A:CYS1378 2.2 24.2 1.0
SG A:CYS1381 2.2 23.6 1.0
SG A:CYS1405 2.3 28.7 1.0
CD2 A:HIS1408 2.7 24.8 1.0
CE1 A:HIS1408 3.2 24.2 1.0
CB A:CYS1378 3.3 22.4 1.0
CB A:CYS1381 3.4 23.4 1.0
CB A:CYS1405 3.4 27.4 1.0
N A:CYS1381 3.7 23.4 1.0
N A:CYS1405 3.9 29.1 1.0
CA A:CYS1381 4.0 23.1 1.0
CG A:HIS1408 4.0 24.5 1.0
ND1 A:HIS1408 4.2 24.2 1.0
CA A:CYS1405 4.2 27.8 1.0
O A:CYS1381 4.2 22.7 1.0
C A:CYS1381 4.3 22.0 1.0
CB A:HIS1383 4.4 20.4 1.0
CD2 A:HIS1383 4.5 20.1 1.0
C A:PHE1380 4.5 23.5 1.0
CB A:GLU1407 4.5 30.4 1.0
CB A:PHE1380 4.6 23.6 1.0
CG A:HIS1383 4.6 20.2 1.0
CA A:CYS1378 4.7 22.7 1.0
C A:CYS1405 4.7 27.7 1.0
O A:CYS1405 4.8 26.7 1.0
N A:HIS1383 4.9 20.9 1.0
CA A:PHE1380 4.9 23.6 1.0
N A:PHE1380 4.9 23.1 1.0

Zinc binding site 4 out of 8 in 4gnd

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


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

b:31.7
occ:1.00
 ND1 A:HIS1389 2.3 39.2 1.0
SG A:CYS1370 2.3 38.5 1.0
SG A:CYS1386 2.3 30.1 1.0
SG A:CYS1367 2.5 30.5 1.0
CE1 A:HIS1389 2.8 40.5 1.0
CB A:CYS1367 3.3 32.8 1.0
CB A:CYS1386 3.4 32.3 1.0
CG A:HIS1389 3.5 39.6 1.0
N A:CYS1370 3.6 40.7 1.0
CB A:CYS1370 3.6 41.2 1.0
N A:CYS1386 4.0 30.1 1.0
CA A:CYS1370 4.1 42.9 1.0
NE2 A:HIS1389 4.1 40.7 1.0
CB A:HIS1389 4.2 40.7 1.0
CA A:CYS1386 4.3 32.6 1.0
CB A:GLU1369 4.4 42.3 1.0
OG A:SER1372 4.5 37.5 1.0
CD2 A:HIS1389 4.5 39.1 1.0
C A:GLU1369 4.6 42.9 1.0
CB A:SER1372 4.7 37.8 1.0
C A:CYS1370 4.7 44.5 1.0
CA A:CYS1367 4.8 33.7 1.0
CG A:GLU1369 4.8 43.6 1.0
N A:HIS1389 4.8 43.5 1.0
C A:CYS1386 4.9 35.7 1.0
CA A:GLU1369 4.9 43.1 1.0
N A:SER1371 4.9 46.3 1.0

Zinc binding site 5 out of 8 in 4gnd

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1501

b:20.0
occ:1.00
 SG C:CYS1349 2.1 21.9 1.0
ND1 C:HIS1346 2.2 21.1 1.0
SG C:CYS1324 2.3 21.8 1.0
SG C:CYS1327 2.5 17.6 1.0
CE1 C:HIS1346 3.0 21.5 1.0
CB C:CYS1324 3.0 21.4 1.0
CG C:HIS1346 3.2 21.7 1.0
CB C:CYS1349 3.3 21.0 1.0
CB C:CYS1327 3.5 18.6 1.0
CB C:HIS1346 3.7 21.2 1.0
N C:HIS1346 3.9 20.6 1.0
N C:CYS1327 3.9 18.4 1.0
NE2 C:HIS1346 4.2 21.6 1.0
CA C:CYS1327 4.3 19.4 1.0
CD2 C:HIS1346 4.3 22.1 1.0
CA C:HIS1346 4.4 21.4 1.0
CA C:CYS1324 4.5 21.5 1.0
CB C:GLN1326 4.6 18.0 1.0
CA C:CYS1349 4.7 20.7 1.0
C C:GLN1326 4.9 18.7 1.0
O C:HIS1346 4.9 22.1 1.0
N C:GLY1328 4.9 20.8 1.0
N C:CYS1349 5.0 21.4 1.0

Zinc binding site 6 out of 8 in 4gnd

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1502

b:17.7
occ:1.00
 NE2 C:HIS1365 1.9 16.4 1.0
SG C:CYS1362 2.3 17.9 1.0
SG C:CYS1341 2.3 23.1 1.0
SG C:CYS1336 2.3 21.3 1.0
CD2 C:HIS1365 2.7 16.9 1.0
CE1 C:HIS1365 3.1 16.2 1.0
CB C:CYS1336 3.2 21.2 1.0
CB C:CYS1341 3.2 23.0 1.0
CB C:CYS1362 3.3 17.3 1.0
N C:CYS1362 3.8 18.4 1.0
CG C:HIS1365 3.9 17.2 1.0
CA C:CYS1362 4.1 17.3 1.0
ND1 C:HIS1365 4.1 16.5 1.0
CB C:LYS1343 4.3 20.0 1.0
CB C:TRP1364 4.5 18.7 1.0
CA C:CYS1341 4.6 23.8 1.0
CA C:CYS1336 4.6 21.5 1.0
CB C:LYS1338 4.7 25.6 1.0
C C:CYS1362 4.7 16.8 1.0
CG C:LYS1343 4.7 19.6 1.0
O C:CYS1362 4.7 15.6 1.0
CE3 C:TRP1364 4.8 19.0 1.0
C C:CYS1341 5.0 22.1 1.0
N C:LYS1343 5.0 19.5 1.0
OH C:TYR1345 5.0 20.4 1.0

Zinc binding site 7 out of 8 in 4gnd

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1503

b:17.6
occ:1.00
 NE2 C:HIS1408 2.0 22.6 1.0
SG C:CYS1381 2.2 17.2 1.0
SG C:CYS1405 2.3 17.2 1.0
SG C:CYS1378 2.3 14.4 1.0
CD2 C:HIS1408 2.9 23.4 1.0
CE1 C:HIS1408 3.0 22.9 1.0
CB C:CYS1378 3.3 15.4 1.0
CB C:CYS1381 3.4 17.8 1.0
CB C:CYS1405 3.4 18.1 1.0
N C:CYS1381 3.6 18.4 1.0
N C:CYS1405 3.8 18.2 1.0
CA C:CYS1381 3.9 18.0 1.0
ND1 C:HIS1408 4.1 22.8 1.0
CG C:HIS1408 4.1 23.9 1.0
CB C:HIS1383 4.1 18.9 1.0
CA C:CYS1405 4.1 18.3 1.0
O C:CYS1381 4.3 18.3 1.0
C C:PHE1380 4.3 19.0 1.0
C C:CYS1381 4.3 17.9 1.0
CB C:PHE1380 4.5 19.8 1.0
CG C:HIS1383 4.6 20.4 1.0
CA C:CYS1378 4.7 16.5 1.0
N C:PHE1380 4.7 19.1 1.0
CA C:PHE1380 4.7 19.6 1.0
C C:CYS1405 4.7 18.8 1.0
N C:HIS1383 4.8 17.3 1.0
CB C:GLU1407 4.9 30.9 1.0
O C:CYS1405 4.9 18.2 1.0
C C:CYS1404 5.0 18.4 1.0
O C:PHE1380 5.0 20.2 1.0

Zinc binding site 8 out of 8 in 4gnd

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


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1504

b:21.4
occ:1.00
 SG C:CYS1367 2.2 13.6 1.0
SG C:CYS1370 2.3 18.0 1.0
ND1 C:HIS1389 2.4 18.0 1.0
SG C:CYS1386 2.4 17.3 1.0
CB C:CYS1367 3.2 15.3 1.0
CE1 C:HIS1389 3.3 17.7 1.0
CG C:HIS1389 3.4 18.1 1.0
CB C:CYS1386 3.4 17.0 1.0
CB C:CYS1370 3.6 18.0 1.0
CB C:HIS1389 3.7 18.4 1.0
N C:CYS1370 3.8 17.3 1.0
N C:CYS1386 3.9 16.4 1.0
CA C:CYS1370 4.2 18.0 1.0
CA C:CYS1386 4.2 17.7 1.0
CB C:GLU1369 4.3 17.2 1.0
NE2 C:HIS1389 4.4 17.9 1.0
CD2 C:HIS1389 4.5 17.9 1.0
C C:GLU1369 4.5 17.4 1.0
CB C:SER1372 4.6 16.6 1.0
CA C:CYS1367 4.6 15.6 1.0
N C:HIS1389 4.7 19.1 1.0
CG C:GLU1369 4.7 17.7 1.0
CA C:GLU1369 4.8 17.7 1.0
N C:SER1372 4.8 16.4 1.0
C C:CYS1370 4.8 18.4 1.0
CA C:HIS1389 4.8 19.1 1.0
N C:SER1371 4.9 18.3 1.0
C C:CYS1386 4.9 18.3 1.0
N C:GLU1369 4.9 17.2 1.0
CB C:ASP1388 4.9 19.1 1.0
C C:CYS1367 4.9 16.0 1.0
OG C:SER1372 5.0 17.2 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 05:20:09 2020

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