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Zinc in PDB 5jin: Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine

Enzymatic activity of Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine

All present enzymatic activity of Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine:
2.1.1.43;

Protein crystallography data

The structure of Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine, PDB code: 5jin 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) 72.76 / 1.85
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.434, 78.684, 72.769, 90.00, 90.69, 90.00
R / Rfree (%) 19.7 / 24

Zinc Binding Sites:

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

Zinc binding site 1 out of 8 in 5jin

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Zinc binding site 1 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine


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 Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:41.1
occ:1.00
 SG A:CYS987 2.2 41.2 1.0
SG A:CYS1017 2.3 37.7 1.0
SG A:CYS1021 2.4 37.8 1.0
SG A:CYS974 2.4 37.5 1.0
CB A:CYS1017 3.2 35.1 1.0
CB A:CYS974 3.2 42.7 1.0
CB A:CYS1021 3.3 47.2 1.0
CB A:CYS987 3.4 42.3 1.0
N A:CYS974 3.5 43.9 1.0
CA A:CYS1017 3.6 34.7 1.0
ZN A:ZN1202 3.7 43.7 1.0
ZN A:ZN1203 3.8 40.4 1.0
CA A:CYS974 4.0 44.6 1.0
SG A:CYS1023 4.2 40.2 1.0
SG A:CYS985 4.3 50.6 1.0
N A:CYS1017 4.5 34.7 1.0
C A:HIS973 4.5 43.0 1.0
CA A:CYS1021 4.5 42.9 1.0
SG A:CYS980 4.5 36.6 1.0
N A:ASN1018 4.7 35.3 1.0
CA A:CYS987 4.7 45.8 1.0
C A:CYS1017 4.7 35.9 1.0
N A:CYS987 4.7 49.7 1.0
CA A:HIS973 4.8 38.9 1.0
C A:CYS974 4.9 42.1 1.0
O A:HOH1350 4.9 32.0 1.0

Zinc binding site 2 out of 8 in 5jin

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Zinc binding site 2 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine


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 Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:43.7
occ:1.00
 SG A:CYS980 2.1 36.6 1.0
SG A:CYS985 2.3 50.6 1.0
SG A:CYS974 2.3 37.5 1.0
SG A:CYS976 2.5 45.6 1.0
CB A:CYS974 3.1 42.7 1.0
CB A:CYS976 3.2 49.0 1.0
CB A:CYS980 3.3 48.6 1.0
CB A:CYS985 3.3 52.1 1.0
ZN A:ZN1201 3.7 41.1 1.0
ZN A:ZN1203 3.8 40.4 1.0
CA A:CYS985 3.9 50.4 1.0
CA A:CYS980 3.9 47.7 1.0
SG A:CYS1017 4.0 37.7 1.0
N A:CYS976 4.4 48.6 1.0
CA A:CYS976 4.4 55.0 1.0
CA A:CYS974 4.5 44.6 1.0
C A:CYS985 4.7 46.8 1.0
N A:CYS980 4.8 39.6 1.0
SG A:CYS1023 4.8 40.2 1.0
SG A:CYS987 4.8 41.2 1.0
N A:LEU986 4.8 46.5 1.0
CB A:CYS1023 4.9 42.2 1.0
C A:CYS980 5.0 52.1 1.0

Zinc binding site 3 out of 8 in 5jin

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Zinc binding site 3 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine


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 Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1203

b:40.4
occ:1.00
 SG A:CYS1027 2.2 39.9 1.0
SG A:CYS1023 2.3 40.2 1.0
SG A:CYS1017 2.3 37.7 1.0
SG A:CYS980 2.5 36.6 1.0
CB A:CYS1027 3.1 42.5 1.0
CB A:CYS1017 3.1 35.1 1.0
CB A:CYS1023 3.2 42.2 1.0
CB A:CYS980 3.3 48.6 1.0
ZN A:ZN1202 3.8 43.7 1.0
ZN A:ZN1201 3.8 41.1 1.0
SG A:CYS974 4.1 37.5 1.0
NE A:ARG1030 4.3 48.1 1.0
NH2 A:ARG1030 4.5 54.4 1.0
CB A:ASN1029 4.5 35.0 1.0
CA A:CYS1027 4.6 43.8 1.0
CA A:CYS1017 4.6 34.7 1.0
CA A:CYS980 4.7 47.7 1.0
CA A:CYS1023 4.7 38.5 1.0
O A:TRP1024 4.8 41.7 1.0
CZ A:ARG1030 4.8 49.6 1.0
N A:ASN1029 4.9 40.3 1.0
CB A:CYS1021 4.9 47.2 1.0
N A:CYS980 5.0 39.6 1.0

Zinc binding site 4 out of 8 in 5jin

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Zinc binding site 4 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine


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 Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1204

b:42.4
occ:1.00
 SG A:CYS1170 2.2 41.6 1.0
SG A:CYS1168 2.3 39.8 1.0
SG A:CYS1115 2.4 46.2 1.0
SG A:CYS1175 2.4 45.5 1.0
CB A:CYS1175 3.1 50.0 1.0
CB A:CYS1170 3.3 46.4 1.0
CB A:CYS1115 3.3 41.6 1.0
CB A:CYS1168 3.4 36.1 1.0
CA A:CYS1175 3.7 49.0 1.0
O A:HOH1362 4.0 51.2 1.0
N A:CYS1115 4.0 41.1 1.0
N A:CYS1170 4.0 38.9 1.0
CA A:CYS1170 4.2 45.0 1.0
CA A:CYS1115 4.3 46.1 1.0
N A:LYS1176 4.3 50.6 1.0
CD2 A:HIS1113 4.4 37.6 1.0
C A:CYS1175 4.4 55.5 1.0
NE2 A:HIS1113 4.4 37.4 1.0
N A:HIS1177 4.6 38.5 1.0
CA A:CYS1168 4.6 40.3 1.0
C A:CYS1168 4.7 44.2 1.0
N A:GLY1171 4.7 55.8 1.0
C A:CYS1170 4.9 52.5 1.0
N A:CYS1175 4.9 47.8 1.0
O A:CYS1168 4.9 44.8 1.0
N A:SER1178 5.0 43.6 1.0

Zinc binding site 5 out of 8 in 5jin

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Zinc binding site 5 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine


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 Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:32.9
occ:1.00
 SG B:CYS987 2.2 38.6 1.0
SG B:CYS1021 2.3 32.0 1.0
SG B:CYS974 2.4 33.7 1.0
SG B:CYS1017 2.4 33.2 1.0
CB B:CYS1017 3.2 31.3 1.0
CB B:CYS1021 3.2 31.3 1.0
CB B:CYS974 3.2 36.8 1.0
CB B:CYS987 3.5 56.0 1.0
N B:CYS974 3.5 36.9 1.0
CA B:CYS1017 3.6 32.7 1.0
ZN B:ZN1203 3.7 35.7 1.0
ZN B:ZN1202 3.8 31.8 1.0
CA B:CYS974 3.9 35.1 1.0
SG B:CYS1023 4.1 34.5 1.0
SG B:CYS985 4.3 45.8 1.0
CA B:CYS1021 4.5 29.5 1.0
C B:HIS973 4.5 41.0 1.0
N B:CYS1017 4.5 27.2 1.0
SG B:CYS980 4.6 34.9 1.0
N B:ASN1018 4.7 31.8 1.0
CA B:HIS973 4.7 35.1 1.0
C B:CYS1017 4.7 35.0 1.0
CA B:CYS987 4.7 62.2 1.0
N B:CYS987 4.8 60.9 1.0
O B:HOH1378 4.8 46.3 1.0
C B:CYS974 4.8 34.5 1.0

Zinc binding site 6 out of 8 in 5jin

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Zinc binding site 6 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine


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 Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1202

b:31.8
occ:1.00
 SG B:CYS1017 2.3 33.2 1.0
SG B:CYS1027 2.3 33.8 1.0
SG B:CYS1023 2.3 34.5 1.0
SG B:CYS980 2.4 34.9 1.0
CB B:CYS1017 3.1 31.3 1.0
CB B:CYS1023 3.2 33.6 1.0
CB B:CYS1027 3.2 34.7 1.0
CB B:CYS980 3.2 36.7 1.0
ZN B:ZN1203 3.7 35.7 1.0
ZN B:ZN1201 3.8 32.9 1.0
SG B:CYS974 4.1 33.7 1.0
NE B:ARG1030 4.3 35.2 1.0
NH2 B:ARG1030 4.5 38.0 1.0
CB B:ASN1029 4.6 33.2 1.0
CA B:CYS1017 4.6 32.7 1.0
CA B:CYS980 4.6 37.5 1.0
CA B:CYS1023 4.6 32.9 1.0
CA B:CYS1027 4.6 34.5 1.0
CZ B:ARG1030 4.8 36.5 1.0
O B:TRP1024 4.8 32.5 1.0
N B:ASN1029 4.9 33.4 1.0
CB B:CYS1021 4.9 31.3 1.0
N B:CYS980 4.9 35.5 1.0
SG B:CYS985 5.0 45.8 1.0

Zinc binding site 7 out of 8 in 5jin

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Zinc binding site 7 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine


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 Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1203

b:35.7
occ:1.00
 SG B:CYS980 2.2 34.9 1.0
SG B:CYS985 2.3 45.8 1.0
SG B:CYS974 2.4 33.7 1.0
SG B:CYS976 2.5 38.3 1.0
CB B:CYS974 3.1 36.8 1.0
CB B:CYS976 3.2 33.6 1.0
CB B:CYS985 3.3 49.2 1.0
CB B:CYS980 3.3 36.7 1.0
ZN B:ZN1202 3.7 31.8 1.0
ZN B:ZN1201 3.7 32.9 1.0
CA B:CYS985 3.9 49.5 1.0
CA B:CYS980 3.9 37.5 1.0
SG B:CYS1017 4.0 33.2 1.0
N B:CYS976 4.4 37.0 1.0
CA B:CYS976 4.4 39.7 1.0
CA B:CYS974 4.6 35.1 1.0
O B:HOH1307 4.6 42.4 1.0
C B:CYS985 4.7 51.1 1.0
N B:CYS980 4.8 35.5 1.0
SG B:CYS1023 4.8 34.5 1.0
SG B:CYS987 4.8 38.6 1.0
N B:LEU986 4.8 51.9 1.0
CB B:CYS1023 4.9 33.6 1.0
C B:CYS980 5.0 43.3 1.0

Zinc binding site 8 out of 8 in 5jin

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Zinc binding site 8 out of 8 in the Structure of G9A Set-Domain with Histone H3K9M Mutant Peptide and Bound S-Adenosylmethionine


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 Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1204

b:46.4
occ:1.00
 SG B:CYS1170 2.1 47.4 1.0
SG B:CYS1168 2.3 43.8 1.0
SG B:CYS1175 2.4 56.5 1.0
SG B:CYS1115 2.5 51.5 1.0
CB B:CYS1175 3.1 55.1 1.0
CB B:CYS1170 3.2 55.4 1.0
CB B:CYS1115 3.4 49.4 1.0
CB B:CYS1168 3.4 47.5 1.0
CA B:CYS1175 3.7 56.7 1.0
N B:CYS1170 3.9 43.3 1.0
N B:CYS1115 4.0 45.1 1.0
CA B:CYS1170 4.1 52.6 1.0
CA B:CYS1115 4.3 42.9 1.0
N B:LYS1176 4.4 50.9 1.0
CD2 B:HIS1113 4.5 42.4 1.0
NE2 B:HIS1113 4.5 41.2 1.0
C B:CYS1175 4.5 56.8 1.0
N B:GLY1171 4.6 57.2 1.0
CA B:CYS1168 4.6 42.1 1.0
C B:CYS1168 4.7 47.8 1.0
N B:HIS1177 4.7 44.7 1.0
C B:CYS1170 4.7 56.6 1.0
O B:CYS1168 4.9 51.4 1.0
N B:CYS1175 4.9 56.2 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 18:58:10 2024

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