Atomistry » Zinc » PDB 5jez-5jmx » 5jj0
Atomistry »
  Zinc »
    PDB 5jez-5jmx »
      5jj0 »

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

Go back to Zinc Binding Sites List in 5jj0
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

Go back to Zinc Binding Sites List in 5jj0
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

Go back to Zinc Binding Sites List in 5jj0
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

Go back to Zinc Binding Sites List in 5jj0
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

Go back to Zinc Binding Sites List in 5jj0
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

Go back to Zinc Binding Sites List in 5jj0
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

Go back to Zinc Binding Sites List in 5jj0
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

Go back to Zinc Binding Sites List in 5jj0
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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy