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Zinc in PDB 9isz: Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation

Enzymatic activity of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation

All present enzymatic activity of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation:
2.1.1.355; 2.1.1.366; 2.1.1.367;

Protein crystallography data

The structure of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation, PDB code: 9isz was solved by Y.X.Du, L.Liu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 37.53 / 2.60
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 53.175, 105.977, 131.906, 90, 90, 90
R / Rfree (%) 23.1 / 27.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation (pdb code 9isz). 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 CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation, PDB code: 9isz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 9isz

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Zinc binding site 1 out of 8 in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:105.2
occ:1.00
 SG A:CYS477 2.3 93.0 1.0
SG A:CYS479 2.3 98.9 1.0
SG A:CYS484 2.3 118.3 1.0
SG A:CYS412 2.3 108.1 1.0
CB A:CYS484 3.2 116.8 1.0
CB A:CYS477 3.5 106.8 1.0
CB A:CYS412 3.6 105.4 1.0
CB A:CYS479 3.6 94.8 1.0
CA A:CYS484 3.6 118.7 1.0
O A:ARG485 3.8 128.3 1.0
N A:CYS412 3.9 93.3 1.0
N A:CYS479 4.2 95.0 1.0
C A:CYS484 4.3 122.7 1.0
CA A:CYS412 4.4 98.3 1.0
CA A:CYS479 4.4 95.3 1.0
N A:ARG485 4.4 125.7 1.0
OG A:SER481 4.5 105.5 1.0
O A:CYS477 4.6 101.1 1.0
C A:CYS477 4.6 99.7 1.0
CA A:CYS477 4.6 105.8 1.0
CB A:SER481 4.7 110.3 1.0
N A:GLY480 4.7 103.1 1.0
NE2 A:HIS410 4.7 89.5 1.0
C A:ARG485 4.8 131.7 1.0
N A:SER481 4.8 108.7 1.0
C A:SER411 4.8 88.8 1.0
C A:CYS479 4.8 101.0 1.0
CD2 A:HIS410 4.9 85.5 1.0
N A:CYS484 4.9 120.2 1.0
CA A:SER411 5.0 88.5 1.0

Zinc binding site 2 out of 8 in 9isz

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Zinc binding site 2 out of 8 in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation


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Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:51.8
occ:1.00
 SG A:CYS311 2.3 54.3 1.0
SG A:CYS278 2.3 58.6 1.0
SG A:CYS307 2.3 53.6 1.0
SG A:CYS260 2.3 52.6 1.0
CB A:CYS307 3.1 49.3 1.0
CB A:CYS260 3.2 63.8 1.0
CB A:CYS311 3.4 54.2 1.0
CA A:CYS307 3.6 49.0 1.0
ZN A:ZN505 3.6 58.8 1.0
N A:CYS260 3.6 51.8 1.0
CB A:CYS278 3.7 69.9 1.0
ZN A:ZN504 3.8 49.0 1.0
O A:HOH617 3.9 43.9 1.0
CA A:CYS260 4.0 60.6 1.0
SG A:CYS276 4.2 61.1 1.0
SG A:CYS268 4.2 64.8 1.0
N A:CYS307 4.4 51.4 1.0
SG A:CYS313 4.5 51.8 1.0
CA A:CYS311 4.6 56.4 1.0
C A:CYS307 4.8 51.3 1.0
N A:ASN308 4.8 49.3 1.0
C A:GLY259 4.8 55.0 1.0
C A:CYS260 4.8 57.9 1.0
N A:CYS278 4.8 76.8 1.0
CA A:CYS278 4.9 75.9 1.0
CA A:GLY259 5.0 56.7 1.0

Zinc binding site 3 out of 8 in 9isz

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Zinc binding site 3 out of 8 in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:49.0
occ:1.00
 O A:HOH617 2.2 43.9 1.0
SG A:CYS307 2.3 53.6 1.0
SG A:CYS313 2.3 51.8 1.0
SG A:CYS268 2.3 64.8 1.0
SG A:CYS317 2.3 51.3 1.0
CB A:CYS317 3.4 49.5 1.0
CB A:CYS313 3.4 55.7 1.0
CB A:CYS307 3.4 49.3 1.0
CB A:CYS268 3.8 61.3 1.0
ZN A:ZN503 3.8 51.8 1.0
N A:CYS268 3.9 65.2 1.0
ZN A:ZN505 4.1 58.8 1.0
SG A:CYS260 4.2 52.6 1.0
NE A:ARG320 4.4 50.8 1.0
CA A:CYS268 4.5 64.2 1.0
CB A:ASN319 4.6 51.3 1.0
CA A:CYS317 4.8 52.5 1.0
CA A:CYS307 4.8 49.0 1.0
CA A:CYS313 4.8 56.0 1.0
C A:GLY267 4.8 66.0 1.0
CA A:GLY267 4.9 68.7 1.0
CG A:ARG320 4.9 47.2 1.0
CB A:CYS311 4.9 54.2 1.0

Zinc binding site 4 out of 8 in 9isz

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Zinc binding site 4 out of 8 in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:58.8
occ:1.00
 SG A:CYS260 2.3 52.6 1.0
SG A:CYS262 2.3 63.5 1.0
SG A:CYS276 2.3 61.1 1.0
SG A:CYS268 2.3 64.8 1.0
CB A:CYS260 3.1 63.8 1.0
CB A:CYS262 3.2 67.9 1.0
CB A:CYS268 3.3 61.3 1.0
CB A:CYS276 3.3 76.3 1.0
ZN A:ZN503 3.6 51.8 1.0
O A:HOH617 3.7 43.9 1.0
CA A:CYS276 3.7 76.9 1.0
ZN A:ZN504 4.1 49.0 1.0
N A:CYS262 4.2 63.4 1.0
CA A:CYS268 4.3 64.2 1.0
CA A:CYS262 4.3 69.2 1.0
SG A:CYS278 4.4 58.6 1.0
SG A:CYS307 4.4 53.6 1.0
CA A:CYS260 4.5 60.6 1.0
C A:CYS276 4.6 75.3 1.0
N A:GLU277 4.6 68.5 1.0
CZ A:PHE288 4.7 72.7 1.0
N A:CYS276 4.9 81.5 1.0
N A:ASN261 4.9 58.4 1.0
N A:CYS268 4.9 65.2 1.0
C A:CYS260 5.0 57.9 1.0

Zinc binding site 5 out of 8 in 9isz

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Zinc binding site 5 out of 8 in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:92.8
occ:1.00
 SG B:CYS477 2.3 82.4 1.0
SG B:CYS479 2.3 82.1 1.0
SG B:CYS484 2.3 93.0 1.0
SG B:CYS412 2.3 88.7 1.0
CB B:CYS484 3.3 100.1 1.0
CB B:CYS477 3.4 99.0 1.0
CB B:CYS412 3.6 85.5 1.0
CB B:CYS479 3.6 73.6 1.0
CA B:CYS484 3.6 102.8 1.0
N B:CYS412 3.8 68.8 1.0
N B:ARG485 4.0 106.6 1.0
N B:GLY486 4.1 121.6 1.0
C B:CYS484 4.1 106.2 1.0
N B:CYS479 4.2 76.9 1.0
CA B:CYS412 4.3 72.8 1.0
O B:CYS477 4.4 91.8 1.0
CA B:CYS479 4.5 74.4 1.0
C B:CYS477 4.5 89.2 1.0
CA B:CYS477 4.6 93.9 1.0
NE2 B:HIS410 4.7 68.9 1.0
CD2 B:HIS410 4.7 69.0 1.0
CA B:GLY486 4.7 120.0 1.0
C B:SER411 4.8 65.6 1.0
N B:CYS484 5.0 104.5 1.0
N B:GLY480 5.0 77.1 1.0
CA B:ARG485 5.0 116.1 1.0
CA B:SER411 5.0 65.9 1.0

Zinc binding site 6 out of 8 in 9isz

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Zinc binding site 6 out of 8 in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:50.5
occ:1.00
 SG B:CYS311 2.3 45.2 1.0
SG B:CYS278 2.3 47.0 1.0
SG B:CYS307 2.3 54.7 1.0
SG B:CYS260 2.3 49.9 1.0
CB B:CYS260 3.2 50.8 1.0
CB B:CYS307 3.2 44.0 1.0
CB B:CYS311 3.4 46.5 1.0
CA B:CYS307 3.6 41.9 1.0
ZN B:ZN504 3.7 52.6 1.0
N B:CYS260 3.8 50.4 1.0
ZN B:ZN505 3.8 52.5 1.0
CB B:CYS278 3.9 51.0 1.0
CA B:CYS260 4.1 53.0 1.0
SG B:CYS276 4.2 50.6 1.0
O B:HOH617 4.2 36.2 1.0
SG B:CYS268 4.3 52.3 1.0
N B:CYS307 4.5 45.0 1.0
SG B:CYS313 4.6 45.0 1.0
CA B:CYS311 4.6 50.7 1.0
N B:ASN308 4.7 41.8 1.0
C B:GLY259 4.7 50.2 1.0
C B:CYS307 4.7 44.4 1.0
C B:CYS260 4.8 55.9 1.0
N B:CYS278 4.9 59.3 1.0
O B:CYS260 4.9 53.6 1.0
CA B:CYS278 5.0 48.9 1.0

Zinc binding site 7 out of 8 in 9isz

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Zinc binding site 7 out of 8 in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:52.6
occ:1.00
 SG B:CYS260 2.3 49.9 1.0
SG B:CYS276 2.3 50.6 1.0
SG B:CYS262 2.3 56.5 1.0
SG B:CYS268 2.3 52.3 1.0
CB B:CYS262 3.1 54.4 1.0
CB B:CYS260 3.3 50.8 1.0
CB B:CYS276 3.6 59.6 1.0
ZN B:ZN503 3.7 50.5 1.0
CB B:CYS268 3.7 52.7 1.0
O B:HOH617 3.9 36.2 1.0
CA B:CYS276 4.0 63.3 1.0
ZN B:ZN505 4.1 52.5 1.0
CA B:CYS268 4.2 64.3 1.0
N B:CYS262 4.2 57.9 1.0
SG B:CYS307 4.3 54.7 1.0
CA B:CYS262 4.3 60.6 1.0
CA B:CYS260 4.7 53.0 1.0
CZ B:PHE288 4.7 51.4 1.0
SG B:CYS278 4.8 47.0 1.0
N B:GLU277 4.9 59.4 1.0
N B:CYS268 4.9 65.9 1.0
C B:CYS260 4.9 55.9 1.0
C B:CYS276 4.9 62.2 1.0
N B:ASN261 5.0 54.5 1.0

Zinc binding site 8 out of 8 in 9isz

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Zinc binding site 8 out of 8 in the Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of CLR4 Catalyzing K14-Ubiquitinated Histone H3 K9 Methylation within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn505

b:52.5
occ:1.00
 O B:HOH617 2.1 36.2 1.0
SG B:CYS307 2.3 54.7 1.0
SG B:CYS313 2.3 45.0 1.0
SG B:CYS317 2.3 56.1 1.0
SG B:CYS268 2.3 52.3 1.0
CB B:CYS313 3.3 60.4 1.0
CB B:CYS317 3.3 52.0 1.0
CB B:CYS268 3.4 52.7 1.0
CB B:CYS307 3.4 44.0 1.0
ZN B:ZN503 3.8 50.5 1.0
ZN B:ZN504 4.1 52.6 1.0
SG B:CYS260 4.2 49.9 1.0
NE B:ARG320 4.5 49.7 1.0
CB B:ASN319 4.6 50.5 1.0
CA B:CYS317 4.7 55.0 1.0
CA B:CYS313 4.7 63.9 1.0
CA B:CYS268 4.8 64.3 1.0
CA B:CYS307 4.8 41.9 1.0
CB B:CYS311 4.8 46.5 1.0
CG B:ARG320 4.9 51.2 1.0

Reference:

Y.X.Du, L.Liu. Mechanism of Histone H3K9 Methyltransferase CLR4 Regulation By Proximal H3K14 Ubiquitination in-Cis To Be Published.
Page generated: Fri Aug 22 18:15:03 2025

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