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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

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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

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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

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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

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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

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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

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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

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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

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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

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