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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

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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

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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

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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

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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

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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

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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

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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

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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

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