Atomistry » Zinc » PDB 5vmz-5vuq » 5vsc
Atomistry »
  Zinc »
    PDB 5vmz-5vuq »
      5vsc »

Zinc in PDB 5vsc: Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13

Enzymatic activity of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13

All present enzymatic activity of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13, PDB code: 5vsc 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) 39.05 / 1.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.440, 78.430, 73.060, 90.00, 90.96, 90.00
R / Rfree (%) 16.5 / 18.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 (pdb code 5vsc). 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13, PDB code: 5vsc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5vsc

Go back to Zinc Binding Sites List in 5vsc
Zinc binding site 1 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:17.1
occ:1.00
 SG A:CYS1027 2.3 17.6 1.0
SG A:CYS1023 2.3 17.8 1.0
SG A:CYS980 2.3 19.6 1.0
SG A:CYS1017 2.4 18.5 1.0
CB A:CYS1017 3.1 19.9 1.0
CB A:CYS1023 3.2 19.1 1.0
CB A:CYS1027 3.3 22.0 1.0
CB A:CYS980 3.3 21.0 1.0
ZN A:ZN1503 3.8 18.3 1.0
ZN A:ZN1502 3.8 17.7 1.0
SG A:CYS974 4.0 18.3 1.0
NE A:ARG1030 4.3 21.4 1.0
NH2 A:ARG1030 4.4 22.9 1.0
CB A:ASN1029 4.6 19.7 1.0
CA A:CYS1017 4.6 14.7 1.0
CA A:CYS1023 4.6 20.9 1.0
CA A:CYS980 4.7 22.1 1.0
CA A:CYS1027 4.7 18.4 1.0
CZ A:ARG1030 4.8 20.3 1.0
O A:TRP1024 4.8 20.5 1.0
CB A:CYS1021 5.0 17.9 1.0
N A:ASN1029 5.0 18.9 1.0

Zinc binding site 2 out of 8 in 5vsc

Go back to Zinc Binding Sites List in 5vsc
Zinc binding site 2 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:17.7
occ:1.00
 SG A:CYS1017 2.3 18.5 1.0
SG A:CYS1021 2.3 17.4 1.0
SG A:CYS974 2.3 18.3 1.0
SG A:CYS987 2.4 20.2 1.0
CB A:CYS1017 3.2 19.9 1.0
CB A:CYS974 3.2 19.0 1.0
CB A:CYS1021 3.3 17.9 1.0
CB A:CYS987 3.5 26.8 1.0
N A:CYS974 3.5 18.8 1.0
CA A:CYS1017 3.6 14.7 1.0
ZN A:ZN1503 3.8 18.3 1.0
ZN A:ZN1501 3.8 17.1 1.0
CA A:CYS974 4.0 20.0 1.0
SG A:CYS1023 4.2 17.8 1.0
SG A:CYS985 4.3 22.5 1.0
N A:CYS1017 4.5 16.7 1.0
C A:HIS973 4.5 20.6 1.0
CA A:CYS1021 4.6 18.1 1.0
N A:ASN1018 4.6 17.6 1.0
C A:CYS1017 4.7 16.9 1.0
SG A:CYS980 4.7 19.6 1.0
CA A:CYS987 4.7 24.4 1.0
N A:CYS987 4.7 22.8 1.0
CA A:HIS973 4.7 19.5 1.0
C A:CYS974 4.8 18.9 1.0
O A:CYS974 4.9 18.9 1.0
O A:HOH1719 5.0 23.0 1.0
ND2 A:ASN1029 5.0 19.0 1.0

Zinc binding site 3 out of 8 in 5vsc

Go back to Zinc Binding Sites List in 5vsc
Zinc binding site 3 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1503

b:18.3
occ:1.00
 SG A:CYS976 2.3 21.3 1.0
SG A:CYS985 2.3 22.5 1.0
SG A:CYS974 2.4 18.3 1.0
SG A:CYS980 2.5 19.6 1.0
CB A:CYS976 3.1 22.5 1.0
CB A:CYS974 3.2 19.0 1.0
CB A:CYS985 3.3 23.5 1.0
CB A:CYS980 3.3 21.0 1.0
ZN A:ZN1502 3.8 17.7 1.0
ZN A:ZN1501 3.8 17.1 1.0
CA A:CYS985 3.9 24.6 1.0
CA A:CYS980 3.9 22.1 1.0
SG A:CYS1017 4.1 18.5 1.0
N A:CYS976 4.4 20.2 1.0
CA A:CYS976 4.4 23.4 1.0
O A:HOH1626 4.6 22.4 1.0
CA A:CYS974 4.6 20.0 1.0
C A:CYS985 4.7 29.4 1.0
SG A:CYS1023 4.8 17.8 1.0
N A:CYS980 4.8 22.1 1.0
O A:HOH1742 4.8 25.6 1.0
N A:LEU986 4.9 24.3 1.0
O A:HOH1691 4.9 32.6 1.0
CB A:CYS1023 4.9 19.1 1.0
C A:CYS980 5.0 23.4 1.0

Zinc binding site 4 out of 8 in 5vsc

Go back to Zinc Binding Sites List in 5vsc
Zinc binding site 4 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1504

b:25.9
occ:1.00
 SG A:CYS1175 2.2 30.0 1.0
SG A:CYS1168 2.3 27.9 1.0
SG A:CYS1170 2.4 32.1 1.0
SG A:CYS1115 2.4 29.4 1.0
CB A:CYS1175 3.2 32.1 1.0
CB A:CYS1115 3.3 35.1 1.0
CB A:CYS1168 3.3 27.6 1.0
CB A:CYS1170 3.4 30.1 1.0
CA A:CYS1175 3.7 33.5 1.0
O A:HOH1720 4.0 31.5 1.0
N A:CYS1115 4.0 27.9 1.0
N A:CYS1170 4.1 28.8 1.0
CA A:CYS1170 4.3 32.3 1.0
CA A:CYS1115 4.3 35.6 1.0
N A:LYS1176 4.4 33.2 1.0
C A:CYS1175 4.5 34.6 1.0
NE2 A:HIS1113 4.5 26.5 1.0
CD2 A:HIS1113 4.5 25.8 1.0
N A:HIS1177 4.6 30.7 1.0
CA A:CYS1168 4.6 30.4 1.0
C A:CYS1168 4.7 27.4 1.0
N A:GLY1171 4.8 31.9 1.0
N A:CYS1175 4.8 37.2 1.0
C A:CYS1170 4.9 33.3 1.0
CB A:HIS1177 4.9 29.5 1.0
N A:SER1178 5.0 29.0 1.0
O A:CYS1168 5.0 30.5 1.0

Zinc binding site 5 out of 8 in 5vsc

Go back to Zinc Binding Sites List in 5vsc
Zinc binding site 5 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1501

b:18.9
occ:1.00
 SG B:CYS980 2.3 20.6 1.0
SG B:CYS1023 2.3 20.0 1.0
SG B:CYS1017 2.3 19.2 1.0
SG B:CYS1027 2.4 20.2 1.0
CB B:CYS1017 3.2 20.4 1.0
CB B:CYS1027 3.2 22.5 1.0
CB B:CYS1023 3.2 18.9 1.0
CB B:CYS980 3.3 22.2 1.0
ZN B:ZN1503 3.8 20.1 1.0
ZN B:ZN1502 3.8 18.9 1.0
SG B:CYS974 4.0 20.8 1.0
NE B:ARG1030 4.4 22.3 1.0
NH2 B:ARG1030 4.4 24.7 1.0
CB B:ASN1029 4.6 20.2 1.0
CA B:CYS1017 4.6 14.7 1.0
CA B:CYS1023 4.7 21.7 1.0
CA B:CYS1027 4.7 21.6 1.0
CA B:CYS980 4.7 22.7 1.0
O B:TRP1024 4.8 22.4 1.0
CZ B:ARG1030 4.8 22.8 1.0
CB B:CYS1021 5.0 20.1 1.0

Zinc binding site 6 out of 8 in 5vsc

Go back to Zinc Binding Sites List in 5vsc
Zinc binding site 6 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1502

b:18.9
occ:1.00
 SG B:CYS1021 2.3 17.9 1.0
SG B:CYS974 2.3 20.8 1.0
SG B:CYS987 2.3 19.1 1.0
SG B:CYS1017 2.4 19.2 1.0
CB B:CYS1017 3.2 20.4 1.0
CB B:CYS974 3.3 21.6 1.0
CB B:CYS1021 3.3 20.1 1.0
CB B:CYS987 3.5 21.7 1.0
N B:CYS974 3.6 19.2 1.0
CA B:CYS1017 3.6 14.7 1.0
ZN B:ZN1503 3.8 20.1 1.0
ZN B:ZN1501 3.8 18.9 1.0
CA B:CYS974 4.0 20.3 1.0
SG B:CYS1023 4.2 20.0 1.0
SG B:CYS985 4.3 22.1 1.0
N B:CYS1017 4.5 17.2 1.0
C B:HIS973 4.6 23.1 1.0
CA B:CYS1021 4.6 20.1 1.0
N B:ASN1018 4.6 17.0 1.0
SG B:CYS980 4.7 20.6 1.0
C B:CYS1017 4.7 17.0 1.0
CA B:CYS987 4.7 18.6 1.0
CA B:HIS973 4.7 20.1 1.0
N B:CYS987 4.7 19.0 1.0
C B:CYS974 4.9 22.6 1.0
O B:HOH1753 4.9 20.2 1.0

Zinc binding site 7 out of 8 in 5vsc

Go back to Zinc Binding Sites List in 5vsc
Zinc binding site 7 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1503

b:20.1
occ:1.00
 SG B:CYS976 2.2 24.6 1.0
SG B:CYS985 2.3 22.1 1.0
SG B:CYS974 2.4 20.8 1.0
SG B:CYS980 2.4 20.6 1.0
CB B:CYS974 3.1 21.6 1.0
CB B:CYS976 3.2 22.2 1.0
CB B:CYS985 3.2 25.0 1.0
CB B:CYS980 3.3 22.2 1.0
ZN B:ZN1502 3.8 18.9 1.0
ZN B:ZN1501 3.8 18.9 1.0
CA B:CYS985 3.8 26.2 1.0
CA B:CYS980 3.9 22.7 1.0
SG B:CYS1017 4.0 19.2 1.0
N B:CYS976 4.4 24.7 1.0
CA B:CYS976 4.4 25.7 1.0
O B:HOH1612 4.5 25.8 1.0
CA B:CYS974 4.5 20.3 1.0
C B:CYS985 4.7 24.3 1.0
SG B:CYS1023 4.8 20.0 1.0
N B:CYS980 4.8 23.2 1.0
N B:LEU986 4.8 22.6 1.0
O B:HOH1694 4.9 27.8 1.0
CB B:CYS1023 4.9 18.9 1.0
SG B:CYS987 5.0 19.1 1.0
C B:CYS980 5.0 24.7 1.0

Zinc binding site 8 out of 8 in 5vsc

Go back to Zinc Binding Sites List in 5vsc
Zinc binding site 8 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor 13


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 G9A Set-Domain (EHMT2) in Complex with Inhibitor 13 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1504

b:24.7
occ:1.00
 SG B:CYS1175 2.2 26.5 1.0
SG B:CYS1168 2.3 22.0 1.0
SG B:CYS1170 2.4 25.7 1.0
SG B:CYS1115 2.4 25.1 1.0
CB B:CYS1175 3.3 28.9 1.0
CB B:CYS1168 3.3 22.2 1.0
CB B:CYS1115 3.4 28.4 1.0
CB B:CYS1170 3.4 24.5 1.0
CA B:CYS1175 3.7 28.6 1.0
N B:CYS1115 4.1 23.7 1.0
N B:CYS1170 4.1 26.4 1.0
O B:HOH1749 4.2 29.4 1.0
CA B:CYS1170 4.3 27.8 1.0
CA B:CYS1115 4.3 26.4 1.0
N B:LYS1176 4.4 27.9 1.0
C B:CYS1175 4.5 34.0 1.0
CD2 B:HIS1113 4.5 20.1 1.0
NE2 B:HIS1113 4.5 21.9 1.0
N B:HIS1177 4.6 25.1 1.0
CA B:CYS1168 4.6 23.0 1.0
C B:CYS1168 4.7 24.6 1.0
N B:GLY1171 4.8 32.4 1.0
CB B:HIS1177 4.9 24.8 1.0
N B:CYS1175 4.9 34.0 1.0
C B:CYS1170 4.9 33.1 1.0
N B:SER1178 4.9 24.9 1.0
O B:CYS1168 4.9 26.1 1.0

Reference:

Y.Xiong, F.Li, N.Babault, H.Wu, A.Dong, H.Zeng, X.Chen, C.H.Arrowsmith, P.J.Brown, J.Liu, M.Vedadi, J.Jin. Structure-Activity Relationship Studies of G9A-Like Protein (Glp) Inhibitors. Bioorg. Med. Chem. V. 25 4414 2017.
ISSN: ESSN 1464-3391
PubMed: 28662962
DOI: 10.1016/J.BMC.2017.06.021
Page generated: Mon Oct 28 13:20:03 2024

Last articles

Zn in 9J0N
Zn in 9J0O
Zn in 9J0P
Zn in 9FJX
Zn in 9EKB
Zn in 9C0F
Zn in 9CAH
Zn in 9CH0
Zn in 9CH3
Zn in 9CH1
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy