Atomistry » Zinc » PDB 5sva-5t6b » 5t0m
Atomistry »
  Zinc »
    PDB 5sva-5t6b »
      5t0m »

Zinc in PDB 5t0m: A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading

Enzymatic activity of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading

All present enzymatic activity of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading:
2.1.1.43;

Protein crystallography data

The structure of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading, PDB code: 5t0m was solved by K.Xu, L.Tong, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.90 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 56.623, 78.284, 71.803, 90.00, 91.16, 90.00
R / Rfree (%) 18.5 / 22.4

Zinc Binding Sites:

The binding sites of Zinc atom in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading (pdb code 5t0m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading, PDB code: 5t0m:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 5t0m

Go back to Zinc Binding Sites List in 5t0m
Zinc binding site 1 out of 8 in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1201

b:27.4
occ:1.00
 SG A:CYS1021 2.2 25.2 1.0
SG A:CYS987 2.3 28.1 1.0
SG A:CYS1017 2.4 30.4 1.0
SG A:CYS974 2.4 23.9 1.0
CB A:CYS1017 3.2 34.5 1.0
CB A:CYS987 3.3 27.5 1.0
CB A:CYS974 3.3 28.0 1.0
CB A:CYS1021 3.4 27.4 1.0
CA A:CYS1017 3.6 29.9 1.0
N A:CYS974 3.6 34.5 1.0
ZN A:ZN1203 3.8 27.6 1.0
ZN A:ZN1202 3.8 28.7 1.0
CA A:CYS974 4.0 30.5 1.0
SG A:CYS1023 4.2 26.9 1.0
SG A:CYS985 4.3 30.4 1.0
N A:CYS1017 4.5 22.4 1.0
C A:HIS973 4.6 35.4 1.0
N A:ASN1018 4.6 28.4 1.0
CA A:CYS987 4.6 32.6 1.0
C A:CYS1017 4.7 26.6 1.0
CA A:CYS1021 4.7 30.1 1.0
N A:CYS987 4.7 30.3 1.0
SG A:CYS980 4.7 29.9 1.0
CA A:HIS973 4.7 28.2 1.0
C A:CYS974 4.8 28.0 1.0
O A:CYS974 4.9 26.0 1.0

Zinc binding site 2 out of 8 in 5t0m

Go back to Zinc Binding Sites List in 5t0m
Zinc binding site 2 out of 8 in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1202

b:28.7
occ:1.00
 SG A:CYS1023 2.2 26.9 1.0
SG A:CYS1017 2.4 30.4 1.0
SG A:CYS980 2.4 29.9 1.0
SG A:CYS1027 2.4 27.3 1.0
CB A:CYS1023 3.2 33.3 1.0
CB A:CYS1017 3.2 34.5 1.0
CB A:CYS1027 3.2 36.1 1.0
CB A:CYS980 3.4 28.5 1.0
ZN A:ZN1203 3.8 27.6 1.0
ZN A:ZN1201 3.8 27.4 1.0
SG A:CYS974 4.1 23.9 1.0
NE A:ARG1030 4.3 32.0 1.0
NH2 A:ARG1030 4.4 37.7 1.0
CB A:ASN1029 4.6 22.6 1.0
CA A:CYS1023 4.6 30.2 1.0
CA A:CYS1017 4.6 29.9 1.0
CA A:CYS1027 4.7 29.9 1.0
CZ A:ARG1030 4.8 34.4 1.0
CA A:CYS980 4.8 30.4 1.0
O A:TRP1024 4.8 31.5 1.0
CB A:CYS1021 5.0 27.4 1.0

Zinc binding site 3 out of 8 in 5t0m

Go back to Zinc Binding Sites List in 5t0m
Zinc binding site 3 out of 8 in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1203

b:27.6
occ:1.00
 SG A:CYS985 2.3 30.4 1.0
SG A:CYS980 2.3 29.9 1.0
SG A:CYS974 2.3 23.9 1.0
SG A:CYS976 2.4 28.4 1.0
CB A:CYS976 3.2 29.1 1.0
CB A:CYS974 3.2 28.0 1.0
CB A:CYS985 3.3 28.4 1.0
CB A:CYS980 3.3 28.5 1.0
ZN A:ZN1201 3.8 27.4 1.0
ZN A:ZN1202 3.8 28.7 1.0
CA A:CYS985 3.9 29.6 1.0
CA A:CYS980 4.0 30.4 1.0
SG A:CYS1017 4.1 30.4 1.0
N A:CYS976 4.4 24.8 1.0
CA A:CYS976 4.4 28.4 1.0
O A:HOH1354 4.6 28.4 1.0
CA A:CYS974 4.6 30.5 1.0
C A:CYS985 4.7 29.7 1.0
O A:HOH1387 4.7 34.1 1.0
SG A:CYS1023 4.7 26.9 1.0
N A:CYS980 4.9 31.4 1.0
N A:LEU986 4.9 24.8 1.0
CB A:CYS1023 4.9 33.3 1.0
SG A:CYS987 5.0 28.1 1.0

Zinc binding site 4 out of 8 in 5t0m

Go back to Zinc Binding Sites List in 5t0m
Zinc binding site 4 out of 8 in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1204

b:39.1
occ:1.00
 SG A:CYS1170 2.2 37.5 1.0
SG A:CYS1168 2.2 38.5 1.0
SG A:CYS1175 2.4 38.1 1.0
SG A:CYS1115 2.6 41.8 1.0
CB A:CYS1170 3.3 39.1 1.0
CB A:CYS1175 3.3 37.5 1.0
CB A:CYS1115 3.3 40.8 1.0
CB A:CYS1168 3.3 38.3 1.0
CA A:CYS1175 3.8 42.0 1.0
N A:CYS1170 4.0 39.4 1.0
N A:CYS1115 4.1 34.9 1.0
CA A:CYS1170 4.2 42.2 1.0
O A:HOH1359 4.2 41.6 1.0
N A:LYS1176 4.3 41.5 1.0
CA A:CYS1115 4.3 39.9 1.0
CD2 A:HIS1113 4.5 30.2 1.0
C A:CYS1175 4.5 47.7 1.0
NE2 A:HIS1113 4.5 32.6 1.0
CA A:CYS1168 4.6 38.1 1.0
C A:CYS1168 4.6 39.5 1.0
N A:HIS1177 4.7 37.7 1.0
N A:GLY1171 4.7 43.9 1.0
O A:CYS1168 4.8 40.8 1.0
C A:CYS1170 4.8 43.1 1.0

Zinc binding site 5 out of 8 in 5t0m

Go back to Zinc Binding Sites List in 5t0m
Zinc binding site 5 out of 8 in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1201

b:35.6
occ:1.00
 SG B:CYS1021 2.3 32.5 1.0
SG B:CYS987 2.3 38.2 1.0
SG B:CYS1017 2.3 41.0 1.0
SG B:CYS974 2.5 29.4 1.0
CB B:CYS1017 3.2 34.7 1.0
CB B:CYS974 3.3 31.8 1.0
CB B:CYS1021 3.3 33.2 1.0
CB B:CYS987 3.4 33.4 1.0
N B:CYS974 3.5 37.7 1.0
CA B:CYS1017 3.5 33.5 1.0
ZN B:ZN1203 3.7 36.9 1.0
ZN B:ZN1202 3.9 33.8 1.0
CA B:CYS974 4.0 39.2 1.0
SG B:CYS1023 4.1 34.5 1.0
SG B:CYS985 4.2 38.7 1.0
N B:CYS1017 4.4 33.3 1.0
C B:HIS973 4.5 40.5 1.0
N B:ASN1018 4.6 29.6 1.0
CA B:CYS1021 4.6 35.0 1.0
SG B:CYS980 4.6 33.0 1.0
C B:CYS1017 4.6 27.9 1.0
CA B:CYS987 4.7 36.5 1.0
CA B:HIS973 4.7 32.4 1.0
N B:CYS987 4.8 36.7 1.0
C B:CYS974 4.9 34.8 1.0
O B:HOH1412 4.9 32.6 1.0
O B:CYS974 5.0 30.5 1.0

Zinc binding site 6 out of 8 in 5t0m

Go back to Zinc Binding Sites List in 5t0m
Zinc binding site 6 out of 8 in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1202

b:33.8
occ:1.00
 SG B:CYS1027 2.2 39.0 1.0
SG B:CYS1023 2.2 34.5 1.0
SG B:CYS1017 2.3 41.0 1.0
SG B:CYS980 2.4 33.0 1.0
CB B:CYS1017 3.1 34.7 1.0
CB B:CYS1027 3.2 51.6 1.0
CB B:CYS1023 3.2 32.5 1.0
CB B:CYS980 3.4 38.6 1.0
ZN B:ZN1203 3.8 36.9 1.0
ZN B:ZN1201 3.9 35.6 1.0
SG B:CYS974 4.1 29.4 1.0
NE B:ARG1030 4.3 38.0 1.0
NH2 B:ARG1030 4.4 36.5 1.0
CA B:CYS1027 4.5 34.7 1.0
CB B:ASN1029 4.5 28.6 1.0
CA B:CYS1017 4.6 33.5 1.0
CA B:CYS1023 4.6 27.8 1.0
CZ B:ARG1030 4.7 40.4 1.0
O B:TRP1024 4.8 32.1 1.0
CA B:CYS980 4.8 39.1 1.0
N B:ASN1029 5.0 36.6 1.0
O B:ASP979 5.0 43.4 1.0
CB B:CYS1021 5.0 33.2 1.0

Zinc binding site 7 out of 8 in 5t0m

Go back to Zinc Binding Sites List in 5t0m
Zinc binding site 7 out of 8 in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1203

b:36.9
occ:1.00
 SG B:CYS980 2.2 33.0 1.0
SG B:CYS974 2.3 29.4 1.0
SG B:CYS985 2.3 38.7 1.0
SG B:CYS976 2.4 36.4 1.0
CB B:CYS974 3.0 31.8 1.0
CB B:CYS976 3.1 34.4 1.0
CB B:CYS980 3.2 38.6 1.0
CB B:CYS985 3.3 44.0 1.0
ZN B:ZN1201 3.7 35.6 1.0
ZN B:ZN1202 3.8 33.8 1.0
CA B:CYS980 3.9 39.1 1.0
CA B:CYS985 4.0 38.3 1.0
SG B:CYS1017 4.0 41.0 1.0
CA B:CYS976 4.4 40.5 1.0
N B:CYS976 4.5 39.6 1.0
CA B:CYS974 4.5 39.2 1.0
SG B:CYS1023 4.7 34.5 1.0
N B:CYS980 4.8 41.5 1.0
C B:CYS985 4.8 35.9 1.0
CB B:CYS1023 4.8 32.5 1.0
N B:LEU986 4.9 34.6 1.0
O B:HOH1379 4.9 45.3 1.0
SG B:CYS987 4.9 38.2 1.0
C B:CYS980 5.0 42.8 1.0

Zinc binding site 8 out of 8 in 5t0m

Go back to Zinc Binding Sites List in 5t0m
Zinc binding site 8 out of 8 in the A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1204

b:37.7
occ:1.00
 SG B:CYS1168 2.2 36.1 1.0
SG B:CYS1175 2.4 36.4 1.0
SG B:CYS1170 2.4 40.6 1.0
SG B:CYS1115 2.4 43.1 1.0
CB B:CYS1168 3.3 29.8 1.0
CB B:CYS1175 3.3 46.0 1.0
CB B:CYS1170 3.3 40.0 1.0
CB B:CYS1115 3.4 40.8 1.0
CA B:CYS1175 3.7 43.8 1.0
N B:CYS1170 4.1 39.5 1.0
N B:CYS1115 4.1 34.9 1.0
N B:LYS1176 4.2 43.6 1.0
O B:HOH1392 4.2 37.4 1.0
CA B:CYS1170 4.3 44.7 1.0
NE2 B:HIS1113 4.3 35.1 1.0
CA B:CYS1115 4.3 40.2 1.0
C B:CYS1175 4.4 47.0 1.0
CD2 B:HIS1113 4.4 34.7 1.0
N B:HIS1177 4.5 38.1 1.0
CA B:CYS1168 4.6 39.5 1.0
C B:CYS1168 4.7 40.4 1.0
N B:CYS1175 4.9 52.1 1.0
O B:CYS1168 4.9 38.8 1.0
C B:CYS1170 4.9 52.1 1.0
N B:GLY1171 5.0 49.3 1.0

Reference:

C.M.Shan, J.Wang, K.Xu, H.Chen, J.X.Yue, S.Andrews, J.J.Moresco, J.R.Yates, P.L.Nagy, L.Tong, S.Jia. A Histone H3K9M Mutation Traps Histone Methyltransferase CLR4 to Prevent Heterochromatin Spreading. Elife V. 5 2016.
ISSN: ESSN 2050-084X
PubMed: 27648579
DOI: 10.7554/ELIFE.17903
Page generated: Mon Oct 28 08:13:13 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