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Zinc in PDB 5jj0: Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah

Enzymatic activity of Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah

All present enzymatic activity of Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah:
2.1.1.43;

Protein crystallography data

The structure of Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah, PDB code: 5jj0 was solved by H.Jayaram, S.F.Bellon, F.Poy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.91 / 1.72
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.667, 78.311, 73.056, 90.00, 90.20, 90.00
R / Rfree (%) 21.8 / 25.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah (pdb code 5jj0). 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 Histone H3K9M Peptide and Excess Sah, PDB code: 5jj0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5jj0

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Zinc binding site 1 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah


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 Histone H3K9M Peptide and Excess Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:27.4
occ:1.00
 SG A:CYS1021 2.3 23.9 1.0
SG A:CYS987 2.3 29.9 1.0
SG A:CYS1017 2.3 26.2 1.0
SG A:CYS974 2.4 26.1 1.0
CB A:CYS1017 3.1 26.0 1.0
CB A:CYS974 3.3 31.1 1.0
CB A:CYS1021 3.4 26.6 1.0
CB A:CYS987 3.4 27.8 1.0
N A:CYS974 3.6 29.9 1.0
CA A:CYS1017 3.6 24.9 1.0
ZN A:ZN1202 3.8 31.4 1.0
ZN A:ZN1203 3.8 27.9 1.0
CA A:CYS974 4.0 31.2 1.0
SG A:CYS1023 4.2 26.3 1.0
SG A:CYS985 4.3 30.9 1.0
N A:CYS1017 4.5 26.1 1.0
CA A:CYS1021 4.6 28.1 1.0
C A:HIS973 4.6 30.9 1.0
N A:ASN1018 4.6 23.1 1.0
SG A:CYS980 4.7 26.6 1.0
C A:CYS1017 4.7 23.9 1.0
CA A:CYS987 4.7 28.4 1.0
N A:CYS987 4.7 32.2 1.0
CA A:HIS973 4.8 29.2 1.0
C A:CYS974 4.9 32.3 1.0
O A:HOH1350 4.9 22.8 1.0

Zinc binding site 2 out of 8 in 5jj0

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Zinc binding site 2 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah


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 Histone H3K9M Peptide and Excess Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:31.4
occ:1.00
 SG A:CYS980 2.3 26.6 1.0
SG A:CYS985 2.3 30.9 1.0
SG A:CYS974 2.3 26.1 1.0
SG A:CYS976 2.4 31.7 1.0
CB A:CYS974 3.1 31.1 1.0
CB A:CYS976 3.2 35.5 1.0
CB A:CYS980 3.3 28.8 1.0
CB A:CYS985 3.4 35.8 1.0
ZN A:ZN1203 3.8 27.9 1.0
ZN A:ZN1201 3.8 27.4 1.0
CA A:CYS985 3.9 31.8 1.0
CA A:CYS980 4.0 32.6 1.0
SG A:CYS1017 4.1 26.2 1.0
CA A:CYS976 4.4 35.6 1.0
N A:CYS976 4.4 34.4 1.0
CA A:CYS974 4.6 31.2 1.0
C A:CYS985 4.7 29.8 1.0
CB A:CYS1023 4.8 25.4 1.0
N A:CYS980 4.8 31.0 1.0
N A:LEU986 4.9 30.5 1.0
SG A:CYS1023 4.9 26.3 1.0
O A:HOH1359 4.9 26.0 1.0
SG A:CYS987 4.9 29.9 1.0
C A:CYS980 5.0 35.3 1.0

Zinc binding site 3 out of 8 in 5jj0

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Zinc binding site 3 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah


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 Histone H3K9M Peptide and Excess Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1203

b:27.9
occ:1.00
 SG A:CYS1023 2.3 26.3 1.0
SG A:CYS1027 2.3 28.5 1.0
SG A:CYS1017 2.4 26.2 1.0
SG A:CYS980 2.4 26.6 1.0
CB A:CYS1017 3.2 26.0 1.0
CB A:CYS1023 3.2 25.4 1.0
CB A:CYS1027 3.3 30.9 1.0
CB A:CYS980 3.4 28.8 1.0
ZN A:ZN1202 3.8 31.4 1.0
ZN A:ZN1201 3.8 27.4 1.0
SG A:CYS974 4.0 26.1 1.0
NE A:ARG1030 4.3 32.6 1.0
NH2 A:ARG1030 4.5 29.1 1.0
CB A:ASN1029 4.6 25.2 1.0
CA A:CYS1017 4.6 24.9 1.0
CA A:CYS1023 4.7 28.1 1.0
CA A:CYS1027 4.7 29.3 1.0
CA A:CYS980 4.8 32.6 1.0
CZ A:ARG1030 4.8 34.6 1.0
O A:TRP1024 4.8 27.5 1.0
CB A:CYS1021 4.9 26.6 1.0

Zinc binding site 4 out of 8 in 5jj0

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Zinc binding site 4 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah


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 Histone H3K9M Peptide and Excess Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1204

b:29.8
occ:1.00
 SG A:CYS1115 2.3 31.1 1.0
SG A:CYS1168 2.3 26.8 1.0
SG A:CYS1175 2.3 28.1 1.0
SG A:CYS1170 2.3 31.1 1.0
CB A:CYS1175 3.2 33.7 1.0
CB A:CYS1168 3.3 27.1 1.0
CB A:CYS1115 3.4 29.0 1.0
CB A:CYS1170 3.4 29.9 1.0
CA A:CYS1175 3.8 37.0 1.0
O A:HOH1340 3.9 36.0 1.0
N A:CYS1115 4.0 29.6 1.0
N A:CYS1170 4.1 28.9 1.0
CA A:CYS1170 4.3 30.7 1.0
CA A:CYS1115 4.3 33.1 1.0
N A:LYS1176 4.4 39.3 1.0
C A:CYS1175 4.5 39.7 1.0
CD2 A:HIS1113 4.5 26.1 1.0
CA A:CYS1168 4.6 26.8 1.0
NE2 A:HIS1113 4.6 27.7 1.0
N A:HIS1177 4.6 30.2 1.0
C A:CYS1168 4.7 29.8 1.0
N A:GLY1171 4.8 36.3 1.0
CB A:HIS1177 4.9 27.4 1.0
N A:CYS1175 4.9 39.2 1.0
N A:SER1178 4.9 32.2 1.0
C A:CYS1170 5.0 32.9 1.0
N A:GLN1169 5.0 26.4 1.0

Zinc binding site 5 out of 8 in 5jj0

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Zinc binding site 5 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah


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 Histone H3K9M Peptide and Excess Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:20.5
occ:1.00
 SG B:CYS987 2.3 21.5 1.0
SG B:CYS1021 2.3 19.1 1.0
SG B:CYS1017 2.4 20.7 1.0
SG B:CYS974 2.4 22.7 1.0
CB B:CYS1017 3.2 21.8 1.0
CB B:CYS974 3.3 21.7 1.0
CB B:CYS987 3.3 19.6 1.0
CB B:CYS1021 3.4 19.3 1.0
N B:CYS974 3.5 22.2 1.0
CA B:CYS1017 3.6 20.2 1.0
ZN B:ZN1203 3.8 21.4 1.0
ZN B:ZN1202 3.8 20.4 1.0
CA B:CYS974 4.0 20.8 1.0
SG B:CYS1023 4.2 18.6 1.0
SG B:CYS985 4.3 24.3 1.0
C B:HIS973 4.5 23.9 1.0
N B:CYS1017 4.5 21.5 1.0
N B:ASN1018 4.6 19.5 1.0
CA B:CYS1021 4.6 20.5 1.0
CA B:CYS987 4.6 20.0 1.0
N B:CYS987 4.7 22.2 1.0
SG B:CYS980 4.7 21.5 1.0
C B:CYS1017 4.7 20.1 1.0
CA B:HIS973 4.7 24.4 1.0
C B:CYS974 4.8 22.5 1.0
O B:HOH1347 4.9 21.5 1.0
O B:CYS974 4.9 18.5 1.0

Zinc binding site 6 out of 8 in 5jj0

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Zinc binding site 6 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah


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 Histone H3K9M Peptide and Excess Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1202

b:20.4
occ:1.00
 SG B:CYS1023 2.2 18.6 1.0
SG B:CYS980 2.3 21.5 1.0
SG B:CYS1027 2.3 20.6 1.0
SG B:CYS1017 2.4 20.7 1.0
CB B:CYS1017 3.2 21.8 1.0
CB B:CYS1023 3.2 19.4 1.0
CB B:CYS1027 3.3 20.5 1.0
CB B:CYS980 3.3 24.0 1.0
ZN B:ZN1203 3.7 21.4 1.0
ZN B:ZN1201 3.8 20.5 1.0
SG B:CYS974 4.0 22.7 1.0
NE B:ARG1030 4.4 25.1 1.0
NH2 B:ARG1030 4.5 25.2 1.0
CA B:CYS1017 4.6 20.2 1.0
CA B:CYS1023 4.6 19.8 1.0
CB B:ASN1029 4.7 22.9 1.0
CA B:CYS980 4.7 24.1 1.0
CA B:CYS1027 4.8 20.5 1.0
O B:TRP1024 4.8 21.9 1.0
CZ B:ARG1030 4.9 24.8 1.0
CB B:CYS1021 4.9 19.3 1.0
N B:CYS980 5.0 24.7 1.0

Zinc binding site 7 out of 8 in 5jj0

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Zinc binding site 7 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah


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 Histone H3K9M Peptide and Excess Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1203

b:21.4
occ:1.00
 SG B:CYS980 2.3 21.5 1.0
SG B:CYS985 2.3 24.3 1.0
SG B:CYS974 2.3 22.7 1.0
SG B:CYS976 2.4 23.3 1.0
CB B:CYS974 3.2 21.7 1.0
CB B:CYS980 3.2 24.0 1.0
CB B:CYS976 3.3 24.5 1.0
CB B:CYS985 3.3 22.5 1.0
ZN B:ZN1202 3.7 20.4 1.0
ZN B:ZN1201 3.8 20.5 1.0
CA B:CYS980 3.9 24.1 1.0
CA B:CYS985 3.9 22.9 1.0
SG B:CYS1017 4.1 20.7 1.0
N B:CYS976 4.4 23.1 1.0
CA B:CYS976 4.5 24.9 1.0
O B:HOH1311 4.5 28.4 1.0
CA B:CYS974 4.6 20.8 1.0
C B:CYS985 4.7 23.5 1.0
N B:CYS980 4.8 24.7 1.0
N B:LEU986 4.8 20.5 1.0
CB B:CYS1023 4.8 19.4 1.0
SG B:CYS1023 4.8 18.6 1.0
O B:HOH1354 4.9 23.2 1.0
O B:HOH1355 4.9 22.0 1.0
SG B:CYS987 5.0 21.5 1.0

Zinc binding site 8 out of 8 in 5jj0

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Zinc binding site 8 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Peptide and Excess Sah


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 Histone H3K9M Peptide and Excess Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1204

b:31.0
occ:1.00
 SG B:CYS1115 2.3 31.7 1.0
SG B:CYS1170 2.3 32.7 1.0
SG B:CYS1175 2.3 31.9 1.0
SG B:CYS1168 2.3 27.2 1.0
CB B:CYS1175 3.2 35.6 1.0
CB B:CYS1168 3.3 30.8 1.0
CB B:CYS1170 3.4 35.4 1.0
CB B:CYS1115 3.4 31.9 1.0
CA B:CYS1175 3.8 35.8 1.0
N B:CYS1115 4.0 28.8 1.0
N B:CYS1170 4.0 33.0 1.0
CA B:CYS1170 4.2 33.0 1.0
CA B:CYS1115 4.3 31.6 1.0
N B:LYS1176 4.4 40.2 1.0
CD2 B:HIS1113 4.5 25.9 1.0
C B:CYS1175 4.5 39.5 1.0
NE2 B:HIS1113 4.5 31.2 1.0
N B:HIS1177 4.6 28.3 1.0
CA B:CYS1168 4.6 27.8 1.0
N B:GLY1171 4.7 40.4 1.0
C B:CYS1168 4.7 32.2 1.0
C B:CYS1170 4.9 35.1 1.0
O B:CYS1168 4.9 33.3 1.0
CB B:HIS1177 4.9 30.8 1.0
N B:CYS1175 5.0 40.8 1.0

Reference:

H.Jayaram, D.Hoelper, S.U.Jain, N.Cantone, S.M.Lundgren, F.Poy, C.D.Allis, R.Cummings, S.Bellon, P.W.Lewis. S-Adenosyl Methionine Is Necessary For Inhibition of the Methyltransferase G9A By the Lysine 9 to Methionine Mutation on Histone H3. Proc.Natl.Acad.Sci.Usa V. 113 6182 2016.
ISSN: ESSN 1091-6490
PubMed: 27185940
DOI: 10.1073/PNAS.1605523113
Page generated: Sun Oct 27 18:59:05 2024

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