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Zinc in PDB 5t0k: Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam

Enzymatic activity of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam

All present enzymatic activity of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam:
2.1.1.43;

Protein crystallography data

The structure of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam, PDB code: 5t0k was solved by K.Xu, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.101, 92.307, 93.143, 90.00, 90.00, 90.00
R / Rfree (%) 16.5 / 19.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam (pdb code 5t0k). 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 G9A Set-Domain with H3K9M Mutant Peptide and Sam, PDB code: 5t0k:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5t0k

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Zinc binding site 1 out of 8 in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1300

b:14.5
occ:1.00
 SG A:CYS987 2.3 13.9 1.0
SG A:CYS1021 2.3 13.8 1.0
SG A:CYS1017 2.4 14.8 1.0
SG A:CYS974 2.4 14.1 1.0
CB A:CYS1017 3.2 13.8 1.0
CB A:CYS974 3.3 13.5 1.0
CB A:CYS1021 3.3 12.5 1.0
CB A:CYS987 3.4 14.3 1.0
CA A:CYS1017 3.6 13.4 1.0
N A:CYS974 3.6 13.4 1.0
ZN A:ZN1302 3.8 15.4 1.0
ZN A:ZN1301 3.8 14.7 1.0
CA A:CYS974 4.0 15.6 1.0
SG A:CYS1023 4.2 14.7 1.0
SG A:CYS985 4.2 15.6 1.0
N A:CYS1017 4.5 11.5 1.0
CA A:CYS1021 4.5 17.1 1.0
N A:ASN1018 4.6 13.2 1.0
C A:HIS973 4.6 15.5 1.0
C A:CYS1017 4.7 14.5 1.0
CA A:CYS987 4.7 15.4 1.0
SG A:CYS980 4.7 15.1 1.0
N A:CYS987 4.7 14.6 1.0
CA A:HIS973 4.8 14.1 1.0
C A:CYS974 4.8 19.9 1.0
O A:HOH1554 4.9 13.3 1.0
O A:CYS974 4.9 15.6 1.0

Zinc binding site 2 out of 8 in 5t0k

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Zinc binding site 2 out of 8 in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1301

b:14.7
occ:1.00
 SG A:CYS1027 2.3 16.1 1.0
SG A:CYS1023 2.3 14.7 1.0
SG A:CYS980 2.3 15.1 1.0
SG A:CYS1017 2.4 14.8 1.0
CB A:CYS1023 3.2 15.6 1.0
CB A:CYS1017 3.2 13.8 1.0
CB A:CYS1027 3.2 16.9 1.0
CB A:CYS980 3.4 14.9 1.0
ZN A:ZN1302 3.8 15.4 1.0
ZN A:ZN1300 3.8 14.5 1.0
SG A:CYS974 4.1 14.1 1.0
NE A:ARG1030 4.2 18.5 1.0
NH2 A:ARG1030 4.3 18.6 1.0
CB A:ASN1029 4.6 14.9 1.0
CA A:CYS1023 4.6 15.3 1.0
CA A:CYS1017 4.6 13.4 1.0
CA A:CYS1027 4.7 17.3 1.0
CZ A:ARG1030 4.7 17.9 1.0
CA A:CYS980 4.7 16.4 1.0
O A:TRP1024 4.8 21.9 1.0
CB A:CYS1021 4.9 12.5 1.0
SG A:CYS985 5.0 15.6 1.0

Zinc binding site 3 out of 8 in 5t0k

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Zinc binding site 3 out of 8 in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1302

b:15.4
occ:1.00
 SG A:CYS985 2.3 15.6 1.0
SG A:CYS974 2.3 14.1 1.0
SG A:CYS976 2.4 17.1 1.0
SG A:CYS980 2.4 15.1 1.0
CB A:CYS974 3.1 13.5 1.0
CB A:CYS976 3.2 16.2 1.0
CB A:CYS985 3.2 18.2 1.0
CB A:CYS980 3.3 14.9 1.0
ZN A:ZN1300 3.8 14.5 1.0
ZN A:ZN1301 3.8 14.7 1.0
CA A:CYS985 3.8 18.2 1.0
CA A:CYS980 3.9 16.4 1.0
SG A:CYS1017 4.1 14.8 1.0
N A:CYS976 4.4 18.1 1.0
CA A:CYS976 4.4 18.5 1.0
O A:HOH1430 4.5 23.6 1.0
CA A:CYS974 4.6 15.6 1.0
C A:CYS985 4.7 18.3 1.0
SG A:CYS1023 4.7 14.7 1.0
CB A:CYS1023 4.8 15.6 1.0
N A:CYS980 4.9 20.0 1.0
N A:CYS985 4.9 20.6 1.0
N A:LEU986 4.9 14.8 1.0
O A:HOH1531 4.9 20.0 1.0
SG A:CYS987 5.0 13.9 1.0

Zinc binding site 4 out of 8 in 5t0k

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Zinc binding site 4 out of 8 in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1303

b:20.5
occ:1.00
 SG A:CYS1168 2.3 17.4 1.0
SG A:CYS1175 2.3 18.9 1.0
SG A:CYS1170 2.4 23.9 1.0
SG A:CYS1115 2.4 19.6 1.0
CB A:CYS1175 3.2 22.6 1.0
CB A:CYS1168 3.3 19.3 1.0
CB A:CYS1170 3.4 20.2 1.0
CB A:CYS1115 3.4 21.1 1.0
CA A:CYS1175 3.7 25.3 1.0
N A:CYS1115 4.1 15.8 1.0
O A:HOH1548 4.1 22.3 1.0
N A:CYS1170 4.1 20.3 1.0
N A:LYS1176 4.3 24.7 1.0
CA A:CYS1170 4.3 19.5 1.0
CA A:CYS1115 4.4 19.4 1.0
NE2 A:HIS1113 4.4 18.8 1.0
C A:CYS1175 4.4 28.8 1.0
CD2 A:HIS1113 4.5 18.9 1.0
N A:HIS1177 4.6 22.2 1.0
CA A:CYS1168 4.6 21.0 1.0
C A:CYS1168 4.7 20.3 1.0
N A:GLY1171 4.7 22.8 1.0
C A:CYS1170 4.9 23.6 1.0
O A:CYS1168 4.9 23.0 1.0
N A:CYS1175 4.9 30.7 1.0

Zinc binding site 5 out of 8 in 5t0k

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Zinc binding site 5 out of 8 in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1300

b:20.2
occ:1.00
 SG B:CYS985 2.3 23.3 1.0
SG B:CYS974 2.4 17.3 1.0
SG B:CYS976 2.4 22.7 1.0
SG B:CYS980 2.4 19.1 1.0
CB B:CYS976 3.2 21.5 1.0
CB B:CYS974 3.2 17.8 1.0
CB B:CYS985 3.2 25.8 1.0
CB B:CYS980 3.3 20.9 1.0
ZN B:ZN1302 3.8 16.9 1.0
ZN B:ZN1301 3.8 16.4 1.0
CA B:CYS985 3.9 30.5 1.0
CA B:CYS980 4.0 21.4 1.0
SG B:CYS1017 4.1 14.4 1.0
N B:CYS976 4.3 21.3 1.0
CA B:CYS976 4.4 22.5 1.0
CA B:CYS974 4.6 18.4 1.0
C B:CYS985 4.7 26.0 1.0
CB B:CYS1023 4.7 18.9 1.0
SG B:CYS1023 4.8 15.9 1.0
N B:LEU986 4.9 25.9 1.0
N B:CYS980 4.9 23.0 1.0

Zinc binding site 6 out of 8 in 5t0k

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Zinc binding site 6 out of 8 in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1301

b:16.4
occ:1.00
 SG B:CYS987 2.3 17.3 1.0
SG B:CYS1017 2.4 14.4 1.0
SG B:CYS1021 2.4 13.7 1.0
SG B:CYS974 2.4 17.3 1.0
CB B:CYS1017 3.2 13.5 1.0
CB B:CYS1021 3.3 13.9 1.0
CB B:CYS974 3.3 17.8 1.0
CB B:CYS987 3.4 18.9 1.0
CA B:CYS1017 3.6 13.4 1.0
N B:CYS974 3.6 16.9 1.0
ZN B:ZN1300 3.8 20.2 1.0
ZN B:ZN1302 3.9 16.9 1.0
CA B:CYS974 4.0 18.4 1.0
SG B:CYS1023 4.2 15.9 1.0
SG B:CYS985 4.4 23.3 1.0
N B:CYS1017 4.5 13.0 1.0
C B:HIS973 4.6 21.1 1.0
CA B:CYS1021 4.6 15.8 1.0
N B:ASN1018 4.6 13.4 1.0
CA B:CYS987 4.6 24.2 1.0
C B:CYS1017 4.7 14.6 1.0
N B:CYS987 4.7 22.6 1.0
SG B:CYS980 4.7 19.1 1.0
CA B:HIS973 4.7 17.4 1.0
O B:HOH1601 4.8 16.4 1.0
C B:CYS974 4.8 20.5 1.0
ND2 B:ASN1029 4.9 17.6 1.0
O B:CYS974 5.0 18.7 1.0

Zinc binding site 7 out of 8 in 5t0k

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Zinc binding site 7 out of 8 in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1302

b:16.9
occ:1.00
 SG B:CYS1027 2.3 16.4 1.0
SG B:CYS1023 2.3 15.9 1.0
SG B:CYS980 2.3 19.1 1.0
SG B:CYS1017 2.4 14.4 1.0
CB B:CYS1027 3.2 19.3 1.0
CB B:CYS1017 3.2 13.5 1.0
CB B:CYS1023 3.2 18.9 1.0
CB B:CYS980 3.5 20.9 1.0
ZN B:ZN1300 3.8 20.2 1.0
ZN B:ZN1301 3.9 16.4 1.0
SG B:CYS974 4.1 17.3 1.0
NE B:ARG1030 4.2 25.4 1.0
NH2 B:ARG1030 4.4 19.2 1.0
CB B:ASN1029 4.5 13.4 1.0
O B:TRP1024 4.6 21.0 1.0
CA B:CYS1027 4.6 16.4 1.0
CA B:CYS1017 4.6 13.4 1.0
CA B:CYS1023 4.6 16.7 1.0
CZ B:ARG1030 4.7 21.5 1.0
CA B:CYS980 4.8 21.4 1.0
N B:CYS980 4.9 23.0 1.0
N B:ASN1029 4.9 16.7 1.0
CB B:CYS1021 5.0 13.9 1.0

Zinc binding site 8 out of 8 in 5t0k

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Zinc binding site 8 out of 8 in the Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of G9A Set-Domain with H3K9M Mutant Peptide and Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1303

b:18.5
occ:1.00
 SG B:CYS1168 2.3 18.2 1.0
SG B:CYS1175 2.3 16.5 1.0
SG B:CYS1170 2.3 20.1 1.0
SG B:CYS1115 2.4 17.7 1.0
CB B:CYS1175 3.2 19.2 1.0
CB B:CYS1168 3.3 20.6 1.0
CB B:CYS1115 3.4 13.9 1.0
CB B:CYS1170 3.4 20.6 1.0
CA B:CYS1175 3.7 20.6 1.0
O B:HOH1559 4.0 24.4 1.0
N B:CYS1170 4.1 18.6 1.0
N B:CYS1115 4.1 16.8 1.0
N B:LYS1176 4.2 20.1 1.0
CA B:CYS1170 4.3 21.8 1.0
CA B:CYS1115 4.4 19.7 1.0
NE2 B:HIS1113 4.4 14.6 1.0
C B:CYS1175 4.4 22.4 1.0
CD2 B:HIS1113 4.5 15.4 1.0
N B:HIS1177 4.5 18.6 1.0
CA B:CYS1168 4.6 17.9 1.0
C B:CYS1168 4.6 22.3 1.0
N B:GLY1171 4.8 26.2 1.0
O B:CYS1168 4.8 21.6 1.0
N B:CYS1175 4.9 23.8 1.0
C B:CYS1170 4.9 28.1 1.0

Reference:

C.M.Shan, J.Wang, K.Xu, H.Chen, J.X.Yue, S.Andrews, J.J.Moresco, J.R.Yates, P.L.Nagy, L.Tong, S.Jia. A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27648579
DOI: 10.7554/ELIFE.17903
Page generated: Mon Oct 28 08:13:13 2024

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