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Zinc in PDB 5jhn: Structure of G9A Set-Domain with Histone H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine

Enzymatic activity of Structure of G9A Set-Domain with Histone H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine

All present enzymatic activity of Structure of G9A Set-Domain with Histone H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine:
2.1.1.43;

Protein crystallography data

The structure of Structure of G9A Set-Domain with Histone H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine, PDB code: 5jhn 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) 34.50 / 1.67
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.782, 78.270, 73.121, 90.00, 90.34, 90.00
R / Rfree (%) 20.9 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of G9A Set-Domain with Histone H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine (pdb code 5jhn). 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine, PDB code: 5jhn:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5jhn

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Zinc binding site 1 out of 8 in the Structure of G9A Set-Domain with Histone H3K9ALA 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:34.1
occ:1.00
 SG A:CYS1027 2.3 37.2 1.0
SG A:CYS1023 2.3 33.3 1.0
SG A:CYS1017 2.3 33.2 1.0
SG A:CYS980 2.4 36.5 1.0
CB A:CYS1017 3.1 30.3 1.0
CB A:CYS1027 3.2 38.9 1.0
CB A:CYS1023 3.3 36.8 1.0
CB A:CYS980 3.4 40.7 1.0
ZN A:ZN1202 3.7 36.0 1.0
ZN A:ZN1203 3.8 33.0 1.0
SG A:CYS974 4.0 32.9 1.0
NE A:ARG1030 4.3 37.3 1.0
NH2 A:ARG1030 4.4 34.8 1.0
CA A:CYS1017 4.6 26.7 1.0
CB A:ASN1029 4.6 28.9 1.0
CA A:CYS1027 4.6 36.4 1.0
CA A:CYS1023 4.7 33.7 1.0
CZ A:ARG1030 4.7 39.0 1.0
CA A:CYS980 4.8 42.4 1.0
O A:TRP1024 4.8 33.2 1.0
CB A:CYS1021 4.9 34.6 1.0
N A:ASN1029 5.0 34.4 1.0

Zinc binding site 2 out of 8 in 5jhn

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Zinc binding site 2 out of 8 in the Structure of G9A Set-Domain with Histone H3K9ALA 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:36.0
occ:1.00
 SG A:CYS980 2.2 36.5 1.0
SG A:CYS985 2.3 37.2 1.0
SG A:CYS974 2.4 32.9 1.0
SG A:CYS976 2.4 37.8 1.0
CB A:CYS974 3.2 32.4 1.0
CB A:CYS976 3.3 36.6 1.0
CB A:CYS985 3.3 44.5 1.0
CB A:CYS980 3.3 40.7 1.0
ZN A:ZN1201 3.7 34.1 1.0
ZN A:ZN1203 3.8 33.0 1.0
CA A:CYS980 3.9 42.4 1.0
CA A:CYS985 3.9 42.3 1.0
SG A:CYS1017 4.0 33.2 1.0
N A:CYS976 4.4 41.5 1.0
CA A:CYS976 4.5 38.3 1.0
CA A:CYS974 4.6 36.8 1.0
SG A:CYS1023 4.7 33.3 1.0
C A:CYS985 4.8 38.1 1.0
N A:CYS980 4.8 42.0 1.0
CB A:CYS1023 4.9 36.8 1.0
N A:LEU986 4.9 34.5 1.0
SG A:CYS987 4.9 34.3 1.0
C A:CYS980 5.0 42.2 1.0

Zinc binding site 3 out of 8 in 5jhn

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Zinc binding site 3 out of 8 in the Structure of G9A Set-Domain with Histone H3K9ALA 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1203

b:33.0
occ:1.00
 SG A:CYS987 2.3 34.3 1.0
SG A:CYS1021 2.3 29.5 1.0
SG A:CYS1017 2.3 33.2 1.0
SG A:CYS974 2.4 32.9 1.0
CB A:CYS1017 3.1 30.3 1.0
CB A:CYS974 3.2 32.4 1.0
CB A:CYS1021 3.3 34.6 1.0
CB A:CYS987 3.4 30.8 1.0
CA A:CYS1017 3.5 26.7 1.0
N A:CYS974 3.6 34.2 1.0
ZN A:ZN1202 3.8 36.0 1.0
ZN A:ZN1201 3.8 34.1 1.0
CA A:CYS974 4.0 36.8 1.0
SG A:CYS1023 4.1 33.3 1.0
SG A:CYS985 4.3 37.2 1.0
N A:CYS1017 4.5 28.9 1.0
N A:ASN1018 4.6 28.4 1.0
CA A:CYS1021 4.6 31.9 1.0
C A:HIS973 4.6 36.4 1.0
C A:CYS1017 4.6 27.2 1.0
SG A:CYS980 4.7 36.5 1.0
CA A:CYS987 4.7 34.1 1.0
N A:CYS987 4.8 36.6 1.0
CA A:HIS973 4.8 35.5 1.0
O A:HOH1363 4.9 28.5 1.0
C A:CYS974 4.9 37.9 1.0
ND2 A:ASN1029 5.0 31.4 1.0

Zinc binding site 4 out of 8 in 5jhn

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Zinc binding site 4 out of 8 in the Structure of G9A Set-Domain with Histone H3K9ALA 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1204

b:33.8
occ:1.00
 SG A:CYS1168 2.3 29.2 1.0
SG A:CYS1115 2.3 33.6 1.0
SG A:CYS1175 2.3 31.7 1.0
SG A:CYS1170 2.4 34.2 1.0
CB A:CYS1175 3.3 37.8 1.0
CB A:CYS1115 3.3 31.5 1.0
CB A:CYS1168 3.3 29.6 1.0
CB A:CYS1170 3.5 33.4 1.0
CA A:CYS1175 3.7 37.5 1.0
N A:CYS1115 4.0 34.0 1.0
N A:CYS1170 4.1 33.4 1.0
O A:HOH1361 4.2 36.4 1.0
CA A:CYS1115 4.3 38.2 1.0
CA A:CYS1170 4.3 35.2 1.0
N A:LYS1176 4.3 38.7 1.0
NE2 A:HIS1113 4.5 31.3 1.0
N A:HIS1177 4.5 33.1 1.0
C A:CYS1175 4.5 40.3 1.0
CD2 A:HIS1113 4.5 31.6 1.0
CA A:CYS1168 4.6 31.2 1.0
C A:CYS1168 4.7 33.1 1.0
CB A:HIS1177 4.8 34.0 1.0
N A:SER1178 4.9 33.3 1.0
N A:CYS1175 4.9 43.7 1.0
N A:GLY1171 4.9 38.6 1.0
C A:CYS1170 5.0 41.8 1.0

Zinc binding site 5 out of 8 in 5jhn

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Zinc binding site 5 out of 8 in the Structure of G9A Set-Domain with Histone H3K9ALA 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:23.7
occ:1.00
 SG B:CYS987 2.3 24.8 1.0
SG B:CYS1021 2.3 22.9 1.0
SG B:CYS1017 2.3 24.3 1.0
SG B:CYS974 2.4 25.9 1.0
CB B:CYS1017 3.2 22.9 1.0
CB B:CYS974 3.2 24.9 1.0
CB B:CYS1021 3.3 24.5 1.0
CB B:CYS987 3.4 25.8 1.0
N B:CYS974 3.5 25.2 1.0
CA B:CYS1017 3.6 22.7 1.0
ZN B:ZN1203 3.8 25.4 1.0
ZN B:ZN1202 3.8 24.0 1.0
CA B:CYS974 4.0 26.8 1.0
SG B:CYS1023 4.2 23.5 1.0
SG B:CYS985 4.3 26.2 1.0
N B:CYS1017 4.5 23.5 1.0
C B:HIS973 4.5 25.5 1.0
CA B:CYS1021 4.6 24.9 1.0
N B:ASN1018 4.6 23.1 1.0
CA B:CYS987 4.7 26.6 1.0
SG B:CYS980 4.7 24.9 1.0
C B:CYS1017 4.7 23.3 1.0
CA B:HIS973 4.7 25.4 1.0
N B:CYS987 4.7 26.6 1.0
C B:CYS974 4.9 25.6 1.0
O B:HOH1363 5.0 24.9 1.0
ND2 B:ASN1029 5.0 25.5 1.0

Zinc binding site 6 out of 8 in 5jhn

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Zinc binding site 6 out of 8 in the Structure of G9A Set-Domain with Histone H3K9ALA 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1202

b:24.0
occ:1.00
 SG B:CYS1023 2.3 23.5 1.0
SG B:CYS1027 2.3 24.0 1.0
SG B:CYS980 2.3 24.9 1.0
SG B:CYS1017 2.3 24.3 1.0
CB B:CYS1017 3.1 22.9 1.0
CB B:CYS1023 3.2 23.9 1.0
CB B:CYS1027 3.2 23.5 1.0
CB B:CYS980 3.3 26.4 1.0
ZN B:ZN1203 3.8 25.4 1.0
ZN B:ZN1201 3.8 23.7 1.0
SG B:CYS974 4.0 25.9 1.0
NE B:ARG1030 4.3 25.8 1.0
NH2 B:ARG1030 4.5 30.4 1.0
CA B:CYS1017 4.6 22.7 1.0
CB B:ASN1029 4.7 24.2 1.0
CA B:CYS1023 4.7 23.4 1.0
CA B:CYS980 4.7 25.3 1.0
CA B:CYS1027 4.7 24.5 1.0
CZ B:ARG1030 4.8 27.5 1.0
O B:TRP1024 4.9 25.2 1.0
CB B:CYS1021 4.9 24.5 1.0

Zinc binding site 7 out of 8 in 5jhn

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Zinc binding site 7 out of 8 in the Structure of G9A Set-Domain with Histone H3K9ALA 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1203

b:25.4
occ:1.00
 SG B:CYS985 2.3 26.2 1.0
SG B:CYS974 2.3 25.9 1.0
SG B:CYS980 2.3 24.9 1.0
SG B:CYS976 2.4 25.1 1.0
CB B:CYS974 3.2 24.9 1.0
CB B:CYS976 3.2 24.7 1.0
CB B:CYS985 3.3 27.9 1.0
CB B:CYS980 3.4 26.4 1.0
ZN B:ZN1201 3.8 23.7 1.0
ZN B:ZN1202 3.8 24.0 1.0
CA B:CYS985 3.9 28.7 1.0
CA B:CYS980 3.9 25.3 1.0
SG B:CYS1017 4.0 24.3 1.0
N B:CYS976 4.4 23.5 1.0
O B:HOH1325 4.4 28.7 1.0
CA B:CYS976 4.4 25.3 1.0
CA B:CYS974 4.6 26.8 1.0
C B:CYS985 4.7 27.1 1.0
N B:CYS980 4.8 24.2 1.0
SG B:CYS1023 4.8 23.5 1.0
N B:LEU986 4.8 25.4 1.0
O B:HOH1368 4.8 27.1 1.0
CB B:CYS1023 4.9 23.9 1.0
O B:HOH1362 4.9 27.8 1.0
SG B:CYS987 5.0 24.8 1.0

Zinc binding site 8 out of 8 in 5jhn

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Zinc binding site 8 out of 8 in the Structure of G9A Set-Domain with Histone H3K9ALA 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 H3K9ALA Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1204

b:34.3
occ:1.00
 SG B:CYS1170 2.3 39.6 1.0
SG B:CYS1175 2.3 34.2 1.0
SG B:CYS1168 2.3 30.5 1.0
SG B:CYS1115 2.4 34.9 1.0
CB B:CYS1175 3.3 40.6 1.0
CB B:CYS1115 3.3 36.9 1.0
CB B:CYS1168 3.3 34.3 1.0
O B:CYS1170 3.4 73.7 1.0
CB B:CYS1170 3.6 44.9 1.0
CA B:CYS1175 3.8 41.7 1.0
N B:CYS1115 4.0 32.4 1.0
C B:CYS1170 4.0 53.1 1.0
N B:CYS1170 4.1 41.3 1.0
CA B:CYS1170 4.2 51.2 1.0
CA B:CYS1115 4.3 33.7 1.0
N B:LYS1176 4.4 41.7 1.0
NE2 B:HIS1113 4.5 32.7 1.0
C B:CYS1175 4.5 41.0 1.0
CD2 B:HIS1113 4.5 29.9 1.0
N B:HIS1177 4.6 32.2 1.0
CA B:CYS1168 4.6 29.9 1.0
C B:CYS1168 4.7 34.0 1.0
N B:CYS1175 4.9 42.7 1.0
O B:CYS1168 4.9 39.5 1.0
CB B:HIS1177 5.0 32.3 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 18:57:10 2024

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