Atomistry » Zinc » PDB 5tte-5u0e » 5tuz
Atomistry »
  Zinc »
    PDB 5tte-5u0e »
      5tuz »

Zinc in PDB 5tuz: Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124

Enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124

All present enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124, PDB code: 5tuz was solved by N.Babault, Y.Xiong, J.Liu, J.Jin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.02 / 1.95
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.940, 95.780, 102.360, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 (pdb code 5tuz). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124, PDB code: 5tuz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5tuz

Go back to Zinc Binding Sites List in 5tuz
Zinc binding site 1 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3002

b:16.1
occ:1.00
 SG A:CYS1105 2.3 15.1 1.0
SG A:CYS1109 2.3 15.5 1.0
SG A:CYS1075 2.3 15.8 1.0
SG A:CYS1062 2.4 13.4 1.0
CB A:CYS1105 3.2 14.2 1.0
CB A:CYS1062 3.2 18.4 1.0
CB A:CYS1109 3.3 11.8 1.0
CB A:CYS1075 3.4 15.2 1.0
CA A:CYS1105 3.6 12.1 1.0
N A:CYS1062 3.6 13.5 1.0
ZN A:ZN3003 3.8 14.6 1.0
ZN A:ZN3004 3.8 15.2 1.0
CA A:CYS1062 4.0 17.0 1.0
SG A:CYS1111 4.2 13.6 1.0
SG A:CYS1073 4.3 14.2 1.0
N A:CYS1105 4.5 11.7 1.0
C A:TYR1061 4.5 18.0 1.0
N A:ASN1106 4.6 11.1 1.0
CA A:CYS1109 4.6 17.1 1.0
C A:CYS1105 4.6 14.1 1.0
CA A:CYS1075 4.7 14.9 1.0
N A:CYS1075 4.7 16.2 1.0
SG A:CYS1068 4.7 14.1 1.0
CA A:TYR1061 4.8 16.1 1.0
C A:CYS1062 4.8 18.1 1.0
O A:CYS1062 4.9 13.6 1.0
O A:HOH3222 4.9 18.1 1.0
ND2 A:ASN1117 5.0 13.6 1.0

Zinc binding site 2 out of 8 in 5tuz

Go back to Zinc Binding Sites List in 5tuz
Zinc binding site 2 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3003

b:14.6
occ:1.00
 SG A:CYS1111 2.3 13.6 1.0
SG A:CYS1115 2.3 14.9 1.0
SG A:CYS1105 2.3 15.1 1.0
SG A:CYS1068 2.4 14.1 1.0
CB A:CYS1105 3.1 14.2 1.0
CB A:CYS1111 3.2 11.4 1.0
CB A:CYS1115 3.2 14.2 1.0
CB A:CYS1068 3.3 15.6 1.0
ZN A:ZN3004 3.7 15.2 1.0
ZN A:ZN3002 3.8 16.1 1.0
SG A:CYS1062 4.0 13.4 1.0
NH2 A:ARG1118 4.4 18.4 1.0
NE A:ARG1118 4.4 15.8 1.0
CB A:ASN1117 4.5 15.0 1.0
CA A:CYS1105 4.6 12.1 1.0
CA A:CYS1111 4.6 15.1 1.0
CA A:CYS1115 4.7 16.4 1.0
CA A:CYS1068 4.7 15.3 1.0
CZ A:ARG1118 4.8 15.1 1.0
O A:TRP1112 4.8 11.4 1.0
N A:ASN1117 4.9 14.4 1.0
CB A:CYS1109 5.0 11.8 1.0

Zinc binding site 3 out of 8 in 5tuz

Go back to Zinc Binding Sites List in 5tuz
Zinc binding site 3 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3004

b:15.2
occ:1.00
 SG A:CYS1068 2.3 14.1 1.0
SG A:CYS1073 2.3 14.2 1.0
SG A:CYS1062 2.3 13.4 1.0
SG A:CYS1064 2.4 16.3 1.0
CB A:CYS1062 3.2 18.4 1.0
CB A:CYS1064 3.2 15.7 1.0
CB A:CYS1068 3.3 15.6 1.0
CB A:CYS1073 3.3 21.2 1.0
ZN A:ZN3003 3.7 14.6 1.0
ZN A:ZN3002 3.8 16.1 1.0
CA A:CYS1073 3.9 15.3 1.0
CA A:CYS1068 3.9 15.3 1.0
SG A:CYS1105 4.0 15.1 1.0
N A:CYS1064 4.4 15.5 1.0
CA A:CYS1064 4.4 17.7 1.0
O A:HOH3131 4.6 23.2 1.0
CA A:CYS1062 4.6 17.0 1.0
C A:CYS1073 4.7 17.1 1.0
N A:MET1074 4.8 17.9 1.0
SG A:CYS1111 4.8 13.6 1.0
N A:CYS1068 4.8 15.7 1.0
O A:HOH3217 4.8 20.0 1.0
O A:HOH3170 4.8 35.8 1.0
CB A:CYS1111 4.8 11.4 1.0

Zinc binding site 4 out of 8 in 5tuz

Go back to Zinc Binding Sites List in 5tuz
Zinc binding site 4 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn3005

b:20.2
occ:1.00
 SG A:CYS1256 2.3 19.8 1.0
SG A:CYS1258 2.3 18.9 1.0
SG A:CYS1203 2.3 21.0 1.0
SG A:CYS1263 2.4 20.4 1.0
CB A:CYS1263 3.3 19.7 1.0
CB A:CYS1256 3.3 21.7 1.0
CB A:CYS1258 3.3 17.7 1.0
CB A:CYS1203 3.4 23.4 1.0
CA A:CYS1263 3.8 25.4 1.0
O A:HOH3188 3.9 21.2 1.0
N A:CYS1203 4.1 18.1 1.0
N A:CYS1258 4.1 20.9 1.0
N A:ARG1264 4.2 22.0 1.0
NE2 A:HIS1201 4.2 21.5 1.0
CA A:CYS1258 4.2 20.1 1.0
CD2 A:HIS1201 4.3 18.7 1.0
CA A:CYS1203 4.3 19.6 1.0
C A:CYS1263 4.5 20.1 1.0
N A:HIS1265 4.6 21.9 1.0
CA A:CYS1256 4.6 25.2 1.0
N A:GLY1259 4.7 22.9 1.0
C A:CYS1256 4.7 28.5 1.0
C A:CYS1258 4.8 22.2 1.0
CB A:HIS1265 5.0 26.0 1.0
O A:CYS1256 5.0 26.6 1.0

Zinc binding site 5 out of 8 in 5tuz

Go back to Zinc Binding Sites List in 5tuz
Zinc binding site 5 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3002

b:17.1
occ:1.00
 SG B:CYS1075 2.3 15.7 1.0
SG B:CYS1109 2.3 16.2 1.0
SG B:CYS1105 2.4 15.4 1.0
SG B:CYS1062 2.4 15.3 1.0
CB B:CYS1105 3.2 14.8 1.0
CB B:CYS1062 3.2 18.4 1.0
CB B:CYS1109 3.3 16.9 1.0
CB B:CYS1075 3.4 12.9 1.0
CA B:CYS1105 3.6 13.3 1.0
N B:CYS1062 3.6 17.2 1.0
ZN B:ZN3004 3.8 17.6 1.0
ZN B:ZN3003 3.8 15.7 1.0
CA B:CYS1062 4.0 18.1 1.0
SG B:CYS1111 4.1 16.4 1.0
SG B:CYS1073 4.3 16.9 1.0
N B:ASN1106 4.5 12.1 1.0
N B:CYS1105 4.5 10.5 1.0
CA B:CYS1109 4.6 16.0 1.0
C B:TYR1061 4.6 20.4 1.0
C B:CYS1105 4.6 14.5 1.0
SG B:CYS1068 4.7 16.8 1.0
CA B:CYS1075 4.7 14.6 1.0
N B:CYS1075 4.7 15.4 1.0
C B:CYS1062 4.8 19.0 1.0
CA B:TYR1061 4.9 17.7 1.0
O B:CYS1062 4.9 18.5 1.0

Zinc binding site 6 out of 8 in 5tuz

Go back to Zinc Binding Sites List in 5tuz
Zinc binding site 6 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3003

b:15.7
occ:1.00
 SG B:CYS1068 2.3 16.8 1.0
SG B:CYS1115 2.3 15.0 1.0
SG B:CYS1111 2.3 16.4 1.0
SG B:CYS1105 2.4 15.4 1.0
CB B:CYS1111 3.2 14.7 1.0
CB B:CYS1105 3.2 14.8 1.0
CB B:CYS1115 3.2 13.3 1.0
CB B:CYS1068 3.3 13.4 1.0
ZN B:ZN3004 3.7 17.6 1.0
ZN B:ZN3002 3.8 17.1 1.0
SG B:CYS1062 4.0 15.3 1.0
NE B:ARG1118 4.3 13.4 1.0
NH2 B:ARG1118 4.4 17.4 1.0
CB B:ASN1117 4.6 13.6 1.0
CA B:CYS1111 4.6 15.7 1.0
CA B:CYS1105 4.7 13.3 1.0
CA B:CYS1068 4.7 15.8 1.0
CA B:CYS1115 4.7 15.0 1.0
CZ B:ARG1118 4.8 17.6 1.0
O B:TRP1112 4.8 15.4 1.0
N B:ASN1117 4.9 11.8 1.0
SG B:CYS1073 5.0 16.9 1.0

Zinc binding site 7 out of 8 in 5tuz

Go back to Zinc Binding Sites List in 5tuz
Zinc binding site 7 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3004

b:17.6
occ:1.00
 SG B:CYS1068 2.3 16.8 1.0
SG B:CYS1073 2.4 16.9 1.0
SG B:CYS1062 2.4 15.3 1.0
SG B:CYS1064 2.4 17.6 1.0
CB B:CYS1062 3.1 18.4 1.0
CB B:CYS1064 3.2 22.8 1.0
CB B:CYS1073 3.2 15.5 1.0
CB B:CYS1068 3.3 13.4 1.0
ZN B:ZN3003 3.7 15.7 1.0
ZN B:ZN3002 3.8 17.1 1.0
CA B:CYS1068 3.9 15.8 1.0
CA B:CYS1073 3.9 20.0 1.0
SG B:CYS1105 4.0 15.4 1.0
N B:CYS1064 4.4 20.5 1.0
CA B:CYS1064 4.4 25.5 1.0
CA B:CYS1062 4.6 18.1 1.0
O B:HOH3141 4.6 22.2 1.0
C B:CYS1073 4.7 22.1 1.0
SG B:CYS1111 4.7 16.4 1.0
N B:CYS1068 4.7 15.3 1.0
CB B:CYS1111 4.8 14.7 1.0
O B:HOH3134 4.8 20.5 1.0
N B:MET1074 4.8 19.0 1.0
C B:CYS1062 4.9 19.0 1.0

Zinc binding site 8 out of 8 in 5tuz

Go back to Zinc Binding Sites List in 5tuz
Zinc binding site 8 out of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn3005

b:25.2
occ:1.00
 SG B:CYS1256 2.3 23.8 1.0
SG B:CYS1258 2.3 23.8 1.0
SG B:CYS1203 2.4 23.9 1.0
SG B:CYS1263 2.4 27.8 1.0
CB B:CYS1263 3.3 33.7 1.0
CB B:CYS1258 3.3 21.6 1.0
CB B:CYS1256 3.3 27.7 1.0
CB B:CYS1203 3.6 22.2 1.0
CA B:CYS1263 3.7 33.4 1.0
O B:HOH3221 4.0 23.6 1.0
N B:CYS1258 4.0 24.9 1.0
N B:CYS1203 4.1 22.3 1.0
CA B:CYS1258 4.2 24.6 1.0
N B:ARG1264 4.2 33.8 1.0
NE2 B:HIS1201 4.3 20.5 1.0
CD2 B:HIS1201 4.4 20.7 1.0
C B:CYS1263 4.4 33.0 1.0
CA B:CYS1203 4.5 19.9 1.0
N B:HIS1265 4.6 32.8 1.0
CA B:CYS1256 4.6 32.9 1.0
C B:CYS1256 4.7 30.8 1.0
N B:GLY1259 4.8 26.6 1.0
O B:CYS1256 4.8 31.0 1.0
C B:CYS1258 4.9 30.3 1.0
N B:CYS1263 5.0 32.3 1.0
CB B:HIS1265 5.0 32.9 1.0

Reference:

Y.Xiong, F.Li, N.Babault, A.Dong, H.Zeng, H.Wu, X.Chen, C.H.Arrowsmith, P.J.Brown, J.Liu, M.Vedadi, J.Jin. Discovery of Potent and Selective Inhibitors For G9A-Like Protein (Glp) Lysine Methyltransferase. J. Med. Chem. V. 60 1876 2017.
ISSN: ISSN 1520-4804
PubMed: 28135087
DOI: 10.1021/ACS.JMEDCHEM.6B01645
Page generated: Mon Oct 28 08:48:18 2024

Last articles

Fe in 2AIU
Fe in 2AFI
Fe in 2AFH
Fe in 2AI5
Fe in 2AHJ
Fe in 2AH7
Fe in 2ACZ
Fe in 2A5H
Fe in 2ABK
Fe in 2ACP
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy