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Zinc in PDB 5tuy: Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124

Enzymatic activity of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124

All present enzymatic activity of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124:
2.1.1.43;

Protein crystallography data

The structure of Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124, PDB code: 5tuy 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) 56.97 / 2.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.970, 82.300, 73.740, 90.00, 89.97, 90.00
R / Rfree (%) 17.1 / 23.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Human G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 (pdb code 5tuy). 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 MS0124, PDB code: 5tuy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5tuy

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Zinc binding site 1 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1501

b:45.8
occ:1.00
 SG A:CYS1027 2.0 38.4 1.0
SG A:CYS1017 2.2 33.1 1.0
SG A:CYS1023 2.3 40.4 1.0
SG A:CYS980 2.3 43.4 1.0
CB A:CYS1017 3.1 25.8 1.0
CB A:CYS1027 3.2 37.2 1.0
CB A:CYS1023 3.2 32.8 1.0
CB A:CYS980 3.5 51.4 1.0
ZN A:ZN1503 3.7 36.2 1.0
ZN A:ZN1502 3.7 38.5 1.0
SG A:CYS974 4.2 35.4 1.0
NH2 A:ARG1030 4.4 29.9 1.0
NE A:ARG1030 4.4 30.5 1.0
CB A:ASN1029 4.5 31.4 1.0
CA A:CYS1027 4.5 37.4 1.0
CA A:CYS1017 4.6 30.1 1.0
CA A:CYS1023 4.6 36.7 1.0
CZ A:ARG1030 4.7 32.4 1.0
O A:TRP1024 4.8 41.4 1.0
CA A:CYS980 4.9 47.1 1.0
N A:ASN1029 5.0 40.4 1.0

Zinc binding site 2 out of 8 in 5tuy

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Zinc binding site 2 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1502

b:38.5
occ:1.00
 SG A:CYS1021 2.2 41.8 1.0
SG A:CYS1017 2.2 33.1 1.0
SG A:CYS987 2.2 26.7 1.0
SG A:CYS974 2.4 35.4 1.0
CB A:CYS1017 3.0 25.8 1.0
CB A:CYS1021 3.1 36.5 1.0
CA A:CYS1017 3.4 30.1 1.0
CB A:CYS987 3.5 50.4 1.0
CB A:CYS974 3.6 30.6 1.0
ZN A:ZN1501 3.7 45.8 1.0
N A:CYS974 3.8 35.8 1.0
SG A:CYS1023 3.9 40.4 1.0
ZN A:ZN1503 3.9 36.2 1.0
CA A:CYS974 4.3 41.9 1.0
N A:ASN1018 4.3 37.9 1.0
N A:CYS1017 4.4 36.3 1.0
SG A:CYS985 4.4 42.2 1.0
C A:CYS1017 4.4 30.6 1.0
CA A:CYS1021 4.5 42.0 1.0
SG A:CYS980 4.6 43.4 1.0
C A:HIS973 4.8 35.9 1.0
CA A:CYS987 4.8 44.3 1.0
ND2 A:ASN1029 4.9 33.1 1.0
CA A:HIS973 4.9 36.4 1.0
N A:CYS987 5.0 40.1 1.0

Zinc binding site 3 out of 8 in 5tuy

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Zinc binding site 3 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1503

b:36.2
occ:1.00
 SG A:CYS980 2.3 43.4 1.0
SG A:CYS985 2.3 42.2 1.0
SG A:CYS976 2.4 42.6 1.0
SG A:CYS974 2.4 35.4 1.0
CB A:CYS976 2.8 45.3 1.0
CB A:CYS980 3.2 51.4 1.0
CB A:CYS985 3.3 53.5 1.0
CB A:CYS974 3.4 30.6 1.0
ZN A:ZN1501 3.7 45.8 1.0
SG A:CYS1017 3.8 33.1 1.0
CA A:CYS980 3.9 47.1 1.0
ZN A:ZN1502 3.9 38.5 1.0
CA A:CYS976 4.1 40.5 1.0
CA A:CYS985 4.1 54.9 1.0
N A:CYS976 4.3 42.3 1.0
SG A:CYS1023 4.6 40.4 1.0
N A:CYS980 4.8 46.3 1.0
CA A:CYS974 4.8 41.9 1.0
CB A:CYS1023 4.9 32.8 1.0
SG A:CYS987 4.9 26.7 1.0
C A:CYS980 4.9 46.8 1.0
C A:CYS985 4.9 51.6 1.0
O A:CYS980 5.0 41.7 1.0

Zinc binding site 4 out of 8 in 5tuy

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Zinc binding site 4 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1504

b:27.3
occ:1.00
 SG A:CYS1170 2.3 22.3 1.0
SG A:CYS1168 2.3 22.1 1.0
SG A:CYS1115 2.3 29.3 1.0
SG A:CYS1175 2.4 30.2 1.0
CB A:CYS1115 3.1 20.4 1.0
CB A:CYS1175 3.2 24.3 1.0
CB A:CYS1170 3.2 19.2 1.0
CB A:CYS1168 3.5 36.5 1.0
CA A:CYS1175 3.6 21.8 1.0
O A:HOH1628 3.9 29.0 1.0
N A:CYS1170 4.0 31.9 1.0
N A:CYS1115 4.0 25.0 1.0
CA A:CYS1115 4.2 27.0 1.0
CA A:CYS1170 4.2 19.4 1.0
NE2 A:HIS1113 4.4 18.8 1.0
N A:LYS1176 4.4 21.9 1.0
CD2 A:HIS1113 4.5 18.4 1.0
C A:CYS1175 4.5 22.2 1.0
N A:HIS1177 4.7 21.2 1.0
N A:CYS1175 4.8 25.7 1.0
CA A:CYS1168 4.8 27.9 1.0
N A:GLY1171 4.8 29.7 1.0
C A:CYS1168 4.8 28.2 1.0
O A:HOH1626 4.9 34.2 1.0
C A:CYS1170 4.9 27.8 1.0
N A:GLN1169 5.0 23.6 1.0

Zinc binding site 5 out of 8 in 5tuy

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Zinc binding site 5 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1501

b:27.0
occ:1.00
 SG B:CYS1017 2.2 31.1 1.0
SG B:CYS980 2.3 32.1 1.0
SG B:CYS1027 2.3 29.6 1.0
SG B:CYS1023 2.3 27.6 1.0
CB B:CYS1027 3.2 21.2 1.0
CB B:CYS1017 3.2 19.1 1.0
CB B:CYS1023 3.2 21.4 1.0
CB B:CYS980 3.3 24.5 1.0
ZN B:ZN1503 3.7 30.4 1.0
ZN B:ZN1502 3.9 25.6 1.0
SG B:CYS974 4.0 31.2 1.0
NE B:ARG1030 4.3 31.0 1.0
CB B:ASN1029 4.4 25.5 1.0
NH2 B:ARG1030 4.4 24.5 1.0
CA B:CYS1017 4.6 29.8 1.0
CA B:CYS1027 4.6 22.8 1.0
CA B:CYS1023 4.7 24.0 1.0
CA B:CYS980 4.7 26.2 1.0
CZ B:ARG1030 4.8 25.5 1.0
O B:TRP1024 4.8 30.8 1.0
N B:ASN1029 4.9 25.2 1.0

Zinc binding site 6 out of 8 in 5tuy

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Zinc binding site 6 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1502

b:25.6
occ:1.00
 SG B:CYS987 2.3 31.4 1.0
SG B:CYS1021 2.3 27.1 1.0
SG B:CYS1017 2.3 31.1 1.0
SG B:CYS974 2.5 31.2 1.0
CB B:CYS1017 3.3 19.1 1.0
CB B:CYS974 3.3 24.8 1.0
CB B:CYS987 3.5 26.6 1.0
CB B:CYS1021 3.5 32.9 1.0
N B:CYS974 3.5 23.3 1.0
CA B:CYS1017 3.6 29.8 1.0
ZN B:ZN1503 3.8 30.4 1.0
ZN B:ZN1501 3.9 27.0 1.0
CA B:CYS974 4.0 24.7 1.0
SG B:CYS1023 4.2 27.6 1.0
SG B:CYS985 4.3 27.7 1.0
C B:HIS973 4.4 23.6 1.0
N B:CYS1017 4.5 25.9 1.0
N B:ASN1018 4.6 29.7 1.0
CA B:HIS973 4.7 29.1 1.0
C B:CYS1017 4.7 34.3 1.0
SG B:CYS980 4.7 32.1 1.0
ND2 B:ASN1029 4.7 21.4 1.0
CA B:CYS1021 4.7 22.3 1.0
CA B:CYS987 4.8 30.1 1.0
N B:CYS987 4.9 29.0 1.0
C B:CYS974 5.0 37.1 1.0

Zinc binding site 7 out of 8 in 5tuy

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Zinc binding site 7 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1503

b:30.4
occ:1.00
 SG B:CYS976 2.3 29.8 1.0
SG B:CYS985 2.3 27.7 1.0
SG B:CYS974 2.3 31.2 1.0
SG B:CYS980 2.4 32.1 1.0
CB B:CYS974 3.1 24.8 1.0
CB B:CYS976 3.2 26.5 1.0
CB B:CYS980 3.3 24.5 1.0
CB B:CYS985 3.3 52.9 1.0
ZN B:ZN1501 3.7 27.0 1.0
ZN B:ZN1502 3.8 25.6 1.0
CA B:CYS980 4.0 26.2 1.0
SG B:CYS1017 4.0 31.1 1.0
CA B:CYS985 4.1 47.0 1.0
N B:CYS976 4.4 26.5 1.0
CA B:CYS976 4.4 27.0 1.0
CA B:CYS974 4.6 24.7 1.0
O B:HOH1608 4.7 29.9 1.0
SG B:CYS1023 4.7 27.6 1.0
N B:CYS980 4.8 26.3 1.0
C B:CYS985 4.9 47.7 1.0
SG B:CYS987 4.9 31.4 1.0
CB B:CYS1023 4.9 21.4 1.0

Zinc binding site 8 out of 8 in 5tuy

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Zinc binding site 8 out of 8 in the Structure of Human G9A Set-Domain (EHMT2) 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 G9A Set-Domain (EHMT2) in Complex with Inhibitor MS0124 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1504

b:36.6
occ:1.00
 SG B:CYS1170 2.1 36.2 1.0
SG B:CYS1115 2.3 30.2 1.0
SG B:CYS1168 2.4 28.4 1.0
SG B:CYS1175 2.4 33.5 1.0
CB B:CYS1115 3.0 37.0 1.0
CB B:CYS1170 3.2 24.9 1.0
CB B:CYS1175 3.3 29.3 1.0
CB B:CYS1168 3.5 28.6 1.0
CA B:CYS1175 3.7 27.6 1.0
O B:HOH1641 3.8 31.0 1.0
N B:CYS1170 4.0 38.8 1.0
N B:CYS1115 4.1 34.7 1.0
CA B:CYS1170 4.2 36.3 1.0
CA B:CYS1115 4.2 33.1 1.0
N B:LYS1176 4.2 36.6 1.0
C B:CYS1175 4.4 38.2 1.0
N B:HIS1177 4.5 27.9 1.0
NE2 B:HIS1113 4.6 24.0 1.0
N B:GLY1171 4.6 31.7 1.0
CD2 B:HIS1113 4.7 23.7 1.0
C B:CYS1170 4.8 37.1 1.0
C B:CYS1168 4.8 34.3 1.0
CA B:CYS1168 4.8 27.2 1.0
N B:CYS1175 4.9 28.1 1.0
CB B:HIS1177 5.0 37.3 1.0
N B:GLN1169 5.0 34.3 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 08:48:19 2024

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