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Zinc in PDB 6z2a: Structure of CLR4 Mutant - F256A/F310A/F427A Bound to Sah

Enzymatic activity of Structure of CLR4 Mutant - F256A/F310A/F427A Bound to Sah

All present enzymatic activity of Structure of CLR4 Mutant - F256A/F310A/F427A Bound to Sah:
2.1.1.355;

Protein crystallography data

The structure of Structure of CLR4 Mutant - F256A/F310A/F427A Bound to Sah, PDB code: 6z2a was solved by A.Stirpe, T.Schalch, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 70.68 / 2.46
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 92.444, 110.288, 70.684, 90, 90, 90
R / Rfree (%) 23.9 / 25

Other elements in 6z2a:

The structure of Structure of CLR4 Mutant - F256A/F310A/F427A Bound to Sah also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to Sah (pdb code 6z2a). 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 Mutant - F256A/F310A/F427A Bound to Sah, PDB code: 6z2a:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6z2a

Go back to Zinc Binding Sites List in 6z2a
Zinc binding site 1 out of 8 in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to 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 CLR4 Mutant - F256A/F310A/F427A Bound to Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:22.8
occ:1.00
 SG A:CYS268 2.3 37.0 1.0
SG A:CYS276 2.3 34.6 1.0
SG A:CYS260 2.3 37.6 1.0
SG A:CYS262 2.4 42.1 1.0
CB A:CYS260 3.3 39.1 1.0
CB A:CYS276 3.3 36.4 1.0
CB A:CYS262 3.3 45.5 1.0
CB A:CYS268 3.4 38.5 1.0
ZN A:ZN502 3.8 21.8 1.0
CA A:CYS276 3.9 38.0 1.0
ZN A:ZN503 3.9 21.9 1.0
SG A:CYS307 4.3 31.1 1.0
N A:CYS262 4.4 48.6 1.0
CA A:CYS262 4.5 49.3 1.0
CA A:CYS268 4.5 41.5 1.0
CA A:CYS260 4.7 40.4 1.0
C A:CYS276 4.7 37.8 1.0
CZ A:PHE288 4.8 26.4 1.0
CE1 A:PHE288 5.0 24.9 1.0
N A:GLU277 5.0 39.0 1.0
N A:ASN261 5.0 45.1 1.0
N A:CYS276 5.0 39.5 1.0
C A:CYS260 5.0 42.8 1.0

Zinc binding site 2 out of 8 in 6z2a

Go back to Zinc Binding Sites List in 6z2a
Zinc binding site 2 out of 8 in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to 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 CLR4 Mutant - F256A/F310A/F427A Bound to Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:21.8
occ:1.00
 SG A:CYS311 2.3 33.3 1.0
SG A:CYS260 2.3 37.6 1.0
SG A:CYS307 2.3 31.1 1.0
SG A:CYS278 2.4 32.3 1.0
CB A:CYS311 3.3 34.9 1.0
CB A:CYS307 3.3 29.7 1.0
CB A:CYS260 3.4 39.1 1.0
CB A:CYS278 3.5 31.8 1.0
CA A:CYS307 3.6 27.7 1.0
ZN A:ZN501 3.8 22.8 1.0
ZN A:ZN503 3.8 21.9 1.0
N A:CYS260 3.9 38.6 1.0
SG A:CYS276 4.2 34.6 1.0
CA A:CYS260 4.3 40.4 1.0
SG A:CYS313 4.4 35.8 1.0
SG A:CYS268 4.5 37.0 1.0
N A:ASN308 4.5 28.9 1.0
CA A:CYS311 4.5 36.4 1.0
C A:GLY259 4.6 37.9 1.0
C A:CYS307 4.6 27.5 1.0
N A:CYS307 4.6 25.9 1.0
CA A:CYS278 4.7 33.0 1.0
CA A:GLY259 4.8 36.2 1.0
N A:CYS278 4.9 35.0 1.0

Zinc binding site 3 out of 8 in 6z2a

Go back to Zinc Binding Sites List in 6z2a
Zinc binding site 3 out of 8 in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to 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 CLR4 Mutant - F256A/F310A/F427A Bound to Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:21.9
occ:1.00
 SG A:CYS268 2.3 37.0 1.0
SG A:CYS313 2.3 35.8 1.0
SG A:CYS307 2.3 31.1 1.0
SG A:CYS317 2.4 33.4 1.0
CB A:CYS313 3.3 38.5 1.0
CB A:CYS307 3.4 29.7 1.0
CB A:CYS268 3.4 38.5 1.0
CB A:CYS317 3.5 34.2 1.0
ZN A:ZN502 3.8 21.8 1.0
ZN A:ZN501 3.9 22.8 1.0
N A:CYS268 4.2 44.4 1.0
SG A:CYS260 4.2 37.6 1.0
CB A:ASN319 4.3 24.9 1.0
CA A:CYS268 4.4 41.5 1.0
CA A:CYS313 4.7 40.6 1.0
CA A:CYS307 4.8 27.7 1.0
CA A:CYS317 4.8 34.8 1.0
CB A:CYS311 4.9 34.9 1.0
NE A:ARG320 4.9 29.6 1.0

Zinc binding site 4 out of 8 in 6z2a

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Zinc binding site 4 out of 8 in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to 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 CLR4 Mutant - F256A/F310A/F427A Bound to Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:22.8
occ:1.00
 SG A:CYS477 2.3 30.3 1.0
SG A:CYS479 2.3 30.4 1.0
SG A:CYS484 2.3 31.0 1.0
SG A:CYS412 2.4 37.1 1.0
CB A:CYS477 3.3 32.5 1.0
CB A:CYS479 3.4 31.5 1.0
CB A:CYS484 3.4 31.7 1.0
CB A:CYS412 3.5 34.9 1.0
CA A:CYS484 3.8 32.1 1.0
N A:CYS412 3.9 29.1 1.0
N A:CYS479 4.1 32.0 1.0
N A:ARG485 4.2 34.1 1.0
CA A:CYS479 4.3 32.0 1.0
NE2 A:HIS410 4.3 26.2 1.0
CA A:CYS412 4.3 31.1 1.0
C A:CYS484 4.5 33.3 1.0
CA A:CYS477 4.5 33.7 1.0
C A:CYS477 4.6 33.0 1.0
CD2 A:HIS410 4.6 25.2 1.0
N A:GLY480 4.7 32.1 1.0
N A:GLY486 4.8 34.1 1.0
O A:CYS477 4.9 33.1 1.0
C A:CYS479 4.9 32.3 1.0
N A:LYS478 4.9 32.5 1.0
C A:SER411 5.0 26.3 1.0

Zinc binding site 5 out of 8 in 6z2a

Go back to Zinc Binding Sites List in 6z2a
Zinc binding site 5 out of 8 in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to 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 CLR4 Mutant - F256A/F310A/F427A Bound to Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:24.4
occ:1.00
 SG B:CYS276 2.3 35.9 1.0
SG B:CYS268 2.3 38.3 1.0
SG B:CYS260 2.3 39.5 1.0
SG B:CYS262 2.5 44.6 1.0
CB B:CYS276 3.3 37.6 1.0
CB B:CYS262 3.3 48.0 1.0
CB B:CYS260 3.4 42.1 1.0
CB B:CYS268 3.4 40.3 1.0
CA B:CYS276 3.8 39.3 1.0
ZN B:ZN503 3.9 23.0 1.0
ZN B:ZN502 4.0 23.3 1.0
SG B:CYS307 4.3 32.5 1.0
CA B:CYS268 4.5 43.5 1.0
CA B:CYS262 4.5 52.3 1.0
N B:CYS262 4.6 51.8 1.0
C B:CYS276 4.7 39.1 1.0
CA B:CYS260 4.7 43.2 1.0
CZ B:PHE288 4.7 25.8 1.0
CE1 B:PHE288 4.9 24.2 1.0
N B:ASN261 4.9 48.6 1.0
N B:CYS276 4.9 40.9 1.0
C B:CYS260 4.9 46.5 1.0
N B:GLU277 5.0 40.5 1.0
C B:ASN261 5.0 53.3 1.0

Zinc binding site 6 out of 8 in 6z2a

Go back to Zinc Binding Sites List in 6z2a
Zinc binding site 6 out of 8 in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to 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 CLR4 Mutant - F256A/F310A/F427A Bound to Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:23.3
occ:1.00
 SG B:CYS268 2.3 38.3 1.0
SG B:CYS313 2.3 35.5 1.0
SG B:CYS307 2.3 32.5 1.0
SG B:CYS317 2.3 32.8 1.0
CB B:CYS313 3.3 38.5 1.0
CB B:CYS307 3.3 30.6 1.0
CB B:CYS317 3.4 33.7 1.0
CB B:CYS268 3.5 40.3 1.0
ZN B:ZN503 3.9 23.0 1.0
N B:CYS268 4.0 46.3 1.0
ZN B:ZN501 4.0 24.4 1.0
SG B:CYS260 4.2 39.5 1.0
CB B:ASN319 4.3 25.2 1.0
CA B:CYS268 4.4 43.5 1.0
CA B:CYS313 4.7 40.5 1.0
CA B:CYS307 4.7 28.6 1.0
CA B:CYS317 4.8 34.1 1.0
CB B:CYS311 4.9 36.4 1.0
NE B:ARG320 4.9 28.6 1.0

Zinc binding site 7 out of 8 in 6z2a

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Zinc binding site 7 out of 8 in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to 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 CLR4 Mutant - F256A/F310A/F427A Bound to Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:23.0
occ:1.00
 SG B:CYS260 2.3 39.5 1.0
SG B:CYS307 2.3 32.5 1.0
SG B:CYS311 2.3 35.1 1.0
SG B:CYS278 2.4 33.9 1.0
CB B:CYS307 3.3 30.6 1.0
CB B:CYS260 3.3 42.1 1.0
CB B:CYS311 3.4 36.4 1.0
CB B:CYS278 3.4 33.4 1.0
CA B:CYS307 3.6 28.6 1.0
N B:CYS260 3.8 41.6 1.0
ZN B:ZN501 3.9 24.4 1.0
ZN B:ZN502 3.9 23.3 1.0
CA B:CYS260 4.1 43.2 1.0
SG B:CYS276 4.2 35.9 1.0
N B:ASN308 4.5 30.1 1.0
SG B:CYS268 4.5 38.3 1.0
SG B:CYS313 4.5 35.5 1.0
C B:GLY259 4.5 41.0 1.0
N B:CYS307 4.6 26.5 1.0
C B:CYS307 4.6 28.5 1.0
CA B:CYS311 4.6 37.7 1.0
CA B:CYS278 4.6 34.6 1.0
N B:CYS278 4.8 37.0 1.0
CA B:GLY259 4.9 39.4 1.0

Zinc binding site 8 out of 8 in 6z2a

Go back to Zinc Binding Sites List in 6z2a
Zinc binding site 8 out of 8 in the Structure of CLR4 Mutant - F256A/F310A/F427A Bound to 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 CLR4 Mutant - F256A/F310A/F427A Bound to Sah within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:20.7
occ:1.00
 SG B:CYS477 2.3 28.5 1.0
SG B:CYS479 2.3 29.1 1.0
SG B:CYS484 2.3 30.6 1.0
SG B:CYS412 2.3 33.2 1.0
CB B:CYS477 3.3 29.9 1.0
CB B:CYS484 3.3 32.7 1.0
CB B:CYS412 3.4 31.4 1.0
CB B:CYS479 3.4 28.9 1.0
CA B:CYS484 3.7 33.6 1.0
N B:CYS412 3.9 26.3 1.0
N B:ARG485 4.1 36.9 1.0
N B:CYS479 4.1 28.1 1.0
CA B:CYS412 4.3 28.2 1.0
CA B:CYS479 4.3 28.8 1.0
NE2 B:HIS410 4.3 24.0 1.0
C B:CYS484 4.4 35.6 1.0
CA B:CYS477 4.5 30.2 1.0
C B:CYS477 4.6 29.3 1.0
N B:GLY486 4.6 38.6 1.0
CD2 B:HIS410 4.6 23.1 1.0
N B:GLY480 4.7 29.8 1.0
O B:CYS477 4.9 29.9 1.0
C B:CYS479 4.9 29.6 1.0
N B:CYS484 4.9 34.2 1.0
N B:LYS478 5.0 28.2 1.0
C B:SER411 5.0 23.7 1.0

Reference:

A.Stirpe, N.Guidotti, S.Northall, S.Kilic, A.Hainard, O.Vadas, B.Fierz, T.Schalch. Heterochromatin Depends on Sensing of Histone H3K14 Ubiquitination By the Set Domain of CLR4SUV39 To Be Published.
Page generated: Tue Oct 29 15:22:38 2024

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