Atomistry » Zinc » PDB 5jf2-5jmz » 5jiy
Atomistry »
  Zinc »
    PDB 5jf2-5jmz »
      5jiy »

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

Go back to Zinc Binding Sites List in 5jiy
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

Go back to Zinc Binding Sites List in 5jiy
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

Go back to Zinc Binding Sites List in 5jiy
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

Go back to Zinc Binding Sites List in 5jiy
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

Go back to Zinc Binding Sites List in 5jiy
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

Go back to Zinc Binding Sites List in 5jiy
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

Go back to Zinc Binding Sites List in 5jiy
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

Go back to Zinc Binding Sites List in 5jiy
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: Sun Oct 27 18:59:05 2024

Last articles

Ag in 7SLM
Ag in 7SLK
Ag in 7SLL
Ag in 7SLJ
Ag in 7SLF
Ag in 7SLE
Ag in 7SLG
Ag in 7SLD
Ag in 7SDV
Ag in 7SLB
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy