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Zinc in PDB 5jiy: Structure of G9A Set-Domain with Histone H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine

Enzymatic activity of Structure of G9A Set-Domain with Histone H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine

All present enzymatic activity of Structure of G9A Set-Domain with Histone H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine:
2.1.1.43;

Protein crystallography data

The structure of Structure of G9A Set-Domain with Histone H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine, PDB code: 5jiy 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) 38.95 / 1.48
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.611, 78.463, 73.084, 90.00, 90.28, 90.00
R / Rfree (%) 20.9 / 23.3

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine (pdb code 5jiy). 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine, PDB code: 5jiy:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5jiy

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Zinc binding site 1 out of 8 in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:24.2
occ:1.00
SG A:CYS1021 2.3 21.8 1.0
SG A:CYS987 2.4 24.3 1.0
SG A:CYS974 2.4 23.8 1.0
SG A:CYS1017 2.4 21.6 1.0
CB A:CYS1017 3.2 20.8 1.0
CB A:CYS1021 3.2 23.0 1.0
CB A:CYS974 3.3 27.5 1.0
CB A:CYS987 3.5 24.0 1.0
CA A:CYS1017 3.6 19.4 1.0
N A:CYS974 3.7 23.8 1.0
ZN A:ZN1202 3.8 25.8 1.0
ZN A:ZN1203 3.8 24.0 1.0
CA A:CYS974 4.1 24.0 1.0
SG A:CYS1023 4.2 24.0 1.0
SG A:CYS985 4.3 25.6 1.0
N A:CYS1017 4.5 20.7 1.0
CA A:CYS1021 4.5 21.6 1.0
N A:ASN1018 4.6 21.0 1.0
C A:HIS973 4.6 26.1 1.0
SG A:CYS980 4.7 26.7 1.0
C A:CYS1017 4.7 19.8 1.0
CA A:CYS987 4.7 23.8 1.0
N A:CYS987 4.8 26.4 1.0
CA A:HIS973 4.8 24.8 1.0
O A:HOH1346 4.9 23.0 1.0
C A:CYS974 5.0 26.2 1.0

Zinc binding site 2 out of 8 in 5jiy

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Zinc binding site 2 out of 8 in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:25.8
occ:1.00
SG A:CYS985 2.3 25.6 1.0
SG A:CYS976 2.3 27.3 1.0
SG A:CYS980 2.4 26.7 1.0
SG A:CYS974 2.4 23.8 1.0
CB A:CYS974 3.1 27.5 1.0
CB A:CYS976 3.2 29.9 1.0
CB A:CYS985 3.2 26.5 1.0
CB A:CYS980 3.4 24.8 1.0
ZN A:ZN1201 3.8 24.2 1.0
ZN A:ZN1203 3.8 24.0 1.0
CA A:CYS985 3.9 28.9 1.0
CA A:CYS980 3.9 27.3 1.0
SG A:CYS1017 4.1 21.6 1.0
N A:CYS976 4.4 30.5 1.0
CA A:CYS976 4.4 31.1 1.0
CA A:CYS974 4.6 24.0 1.0
C A:CYS985 4.7 26.7 1.0
N A:CYS980 4.8 25.4 1.0
SG A:CYS1023 4.8 24.0 1.0
N A:LEU986 4.9 24.9 1.0
O A:HOH1364 4.9 28.6 1.0
CB A:CYS1023 5.0 23.1 1.0
N A:CYS985 5.0 28.1 1.0

Zinc binding site 3 out of 8 in 5jiy

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Zinc binding site 3 out of 8 in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1203

b:24.0
occ:1.00
SG A:CYS1023 2.3 24.0 1.0
SG A:CYS980 2.3 26.7 1.0
SG A:CYS1027 2.4 24.7 1.0
SG A:CYS1017 2.4 21.6 1.0
CB A:CYS1017 3.1 20.8 1.0
CB A:CYS1027 3.2 25.4 1.0
CB A:CYS1023 3.3 23.1 1.0
CB A:CYS980 3.4 24.8 1.0
ZN A:ZN1201 3.8 24.2 1.0
ZN A:ZN1202 3.8 25.8 1.0
SG A:CYS974 4.1 23.8 1.0
NE A:ARG1030 4.3 29.3 1.0
NH2 A:ARG1030 4.5 32.3 1.0
CB A:ASN1029 4.6 23.7 1.0
CA A:CYS1017 4.7 19.4 1.0
CA A:CYS1027 4.7 23.9 1.0
CA A:CYS980 4.7 27.3 1.0
CA A:CYS1023 4.8 24.6 1.0
O A:TRP1024 4.8 25.6 1.0
CZ A:ARG1030 4.8 28.3 1.0
CB A:CYS1021 4.9 23.0 1.0
N A:ASN1029 5.0 25.0 1.0

Zinc binding site 4 out of 8 in 5jiy

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Zinc binding site 4 out of 8 in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1204

b:24.6
occ:1.00
SG A:CYS1175 2.3 24.8 1.0
SG A:CYS1168 2.3 22.6 1.0
SG A:CYS1170 2.4 27.3 1.0
SG A:CYS1115 2.4 26.1 1.0
CB A:CYS1175 3.2 29.0 1.0
CB A:CYS1115 3.3 24.6 1.0
CB A:CYS1168 3.3 23.4 1.0
CB A:CYS1170 3.4 25.3 1.0
CA A:CYS1175 3.8 26.3 1.0
N A:CYS1115 4.1 25.8 1.0
N A:CYS1170 4.1 25.7 1.0
CA A:CYS1170 4.3 26.8 1.0
CA A:CYS1115 4.3 27.2 1.0
N A:LYS1176 4.3 32.2 1.0
NE2 A:HIS1113 4.5 21.4 1.0
C A:CYS1175 4.5 33.6 1.0
CD2 A:HIS1113 4.5 21.2 1.0
N A:HIS1177 4.5 25.2 1.0
CA A:CYS1168 4.6 23.5 1.0
C A:CYS1168 4.7 24.1 1.0
CB A:HIS1177 4.7 23.1 1.0
N A:GLY1171 4.8 29.1 1.0
O A:CYS1168 4.9 23.9 1.0
N A:SER1178 4.9 26.2 1.0
C A:CYS1170 4.9 27.6 1.0
N A:CYS1175 5.0 31.5 1.0

Zinc binding site 5 out of 8 in 5jiy

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Zinc binding site 5 out of 8 in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:19.2
occ:1.00
SG B:CYS1021 2.3 18.6 1.0
SG B:CYS987 2.4 19.7 1.0
SG B:CYS1017 2.4 18.0 1.0
SG B:CYS974 2.4 20.0 1.0
CB B:CYS1017 3.3 16.6 1.0
CB B:CYS1021 3.3 16.9 1.0
CB B:CYS974 3.3 18.6 1.0
CB B:CYS987 3.4 20.3 1.0
N B:CYS974 3.6 19.2 1.0
CA B:CYS1017 3.6 16.1 1.0
ZN B:ZN1203 3.8 19.7 1.0
ZN B:ZN1202 3.8 18.4 1.0
CA B:CYS974 4.0 19.0 1.0
SG B:CYS1023 4.2 19.1 1.0
SG B:CYS985 4.3 21.8 1.0
N B:CYS1017 4.5 17.6 1.0
CA B:CYS1021 4.6 17.5 1.0
C B:HIS973 4.6 20.5 1.0
CA B:CYS987 4.6 21.2 1.0
N B:ASN1018 4.7 16.9 1.0
SG B:CYS980 4.7 18.9 1.0
N B:CYS987 4.7 21.1 1.0
C B:CYS1017 4.7 17.9 1.0
CA B:HIS973 4.7 20.4 1.0
C B:CYS974 4.9 20.5 1.0
O B:HOH1347 4.9 19.7 1.0
O B:CYS974 5.0 20.2 1.0

Zinc binding site 6 out of 8 in 5jiy

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Zinc binding site 6 out of 8 in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1202

b:18.4
occ:1.00
SG B:CYS980 2.3 18.9 1.0
SG B:CYS1023 2.3 19.1 1.0
SG B:CYS1027 2.3 19.0 1.0
SG B:CYS1017 2.4 18.0 1.0
CB B:CYS1017 3.2 16.6 1.0
CB B:CYS1023 3.2 18.5 1.0
CB B:CYS1027 3.2 20.6 1.0
CB B:CYS980 3.3 19.6 1.0
ZN B:ZN1203 3.8 19.7 1.0
ZN B:ZN1201 3.8 19.2 1.0
SG B:CYS974 4.0 20.0 1.0
NE B:ARG1030 4.3 21.2 1.0
NH2 B:ARG1030 4.4 23.5 1.0
CA B:CYS1017 4.6 16.1 1.0
CA B:CYS1023 4.6 18.0 1.0
CB B:ASN1029 4.7 19.2 1.0
CA B:CYS1027 4.7 19.6 1.0
CA B:CYS980 4.7 20.2 1.0
CZ B:ARG1030 4.8 21.1 1.0
O B:TRP1024 4.9 19.5 1.0
CB B:CYS1021 4.9 16.9 1.0

Zinc binding site 7 out of 8 in 5jiy

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Zinc binding site 7 out of 8 in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1203

b:19.7
occ:1.00
SG B:CYS976 2.3 19.8 1.0
SG B:CYS985 2.3 21.8 1.0
SG B:CYS974 2.4 20.0 1.0
SG B:CYS980 2.4 18.9 1.0
CB B:CYS974 3.1 18.6 1.0
CB B:CYS976 3.2 20.5 1.0
CB B:CYS980 3.3 19.6 1.0
CB B:CYS985 3.3 19.7 1.0
ZN B:ZN1202 3.8 18.4 1.0
ZN B:ZN1201 3.8 19.2 1.0
CA B:CYS985 3.9 23.0 1.0
CA B:CYS980 4.0 20.2 1.0
SG B:CYS1017 4.1 18.0 1.0
N B:CYS976 4.4 19.7 1.0
CA B:CYS976 4.4 19.7 1.0
CA B:CYS974 4.6 19.0 1.0
O B:HOH1308 4.6 23.3 1.0
C B:CYS985 4.7 22.2 1.0
N B:LEU986 4.8 21.0 1.0
N B:CYS980 4.8 20.0 1.0
SG B:CYS1023 4.8 19.1 1.0
CB B:CYS1023 4.9 18.5 1.0
O B:HOH1355 5.0 22.5 1.0
O B:HOH1346 5.0 24.4 1.0

Zinc binding site 8 out of 8 in 5jiy

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Zinc binding site 8 out of 8 in the Structure of G9A Set-Domain with Histone H3K9NORLEUCINE 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 H3K9NORLEUCINE Mutant Peptide and Bound S-Adenosylmethionine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1204

b:26.9
occ:1.00
SG B:CYS1175 2.3 26.0 1.0
SG B:CYS1168 2.3 23.7 1.0
SG B:CYS1170 2.3 28.0 1.0
SG B:CYS1115 2.5 26.8 1.0
CB B:CYS1168 3.3 26.7 1.0
CB B:CYS1175 3.3 28.2 1.0
CB B:CYS1115 3.3 28.1 1.0
CB B:CYS1170 3.4 28.6 1.0
CA B:CYS1175 3.8 29.4 1.0
N B:CYS1115 4.0 25.2 1.0
N B:CYS1170 4.1 25.9 1.0
CA B:CYS1170 4.3 27.9 1.0
CA B:CYS1115 4.3 25.6 1.0
N B:LYS1176 4.4 31.0 1.0
NE2 B:HIS1113 4.5 25.3 1.0
CD2 B:HIS1113 4.5 22.6 1.0
C B:CYS1175 4.5 32.1 1.0
N B:HIS1177 4.5 25.2 1.0
CA B:CYS1168 4.6 24.5 1.0
N B:GLY1171 4.7 32.0 1.0
C B:CYS1168 4.7 25.9 1.0
C B:CYS1170 4.9 28.6 1.0
O B:CYS1168 5.0 27.8 1.0
N B:CYS1175 5.0 35.1 1.0
CB B:HIS1177 5.0 26.0 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: Wed Dec 16 06:25:18 2020

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