Atomistry » Zinc » PDB 4ggk-4gsz » 4gnd
Atomistry »
  Zinc »
    PDB 4ggk-4gsz »
      4gnd »

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

Go back to Zinc Binding Sites List in 4gnd
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

Go back to Zinc Binding Sites List in 4gnd
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

Go back to Zinc Binding Sites List in 4gnd
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

Go back to Zinc Binding Sites List in 4gnd
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

Go back to Zinc Binding Sites List in 4gnd
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

Go back to Zinc Binding Sites List in 4gnd
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

Go back to Zinc Binding Sites List in 4gnd
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

Go back to Zinc Binding Sites List in 4gnd
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: Sat Oct 26 23:22:26 2024

Last articles

Mg in 7DR0
Mg in 7DR1
Mg in 7DU2
Mg in 7DSP
Mg in 7DSJ
Mg in 7DSI
Mg in 7DRP
Mg in 7DSH
Mg in 7DSA
Mg in 7DRX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy