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Zinc in PDB 6bp4: Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam

Enzymatic activity of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam

All present enzymatic activity of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam:
2.1.1.43;

Protein crystallography data

The structure of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam, PDB code: 6bp4 was solved by M.A.Currie, D.Moazed, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 59.35 / 2.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 131.919, 71.040, 96.674, 90.00, 125.06, 90.00
R / Rfree (%) 22.3 / 26.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam (pdb code 6bp4). 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 the S. Pombe CLR4 Catalytic Domain Bound to Sam, PDB code: 6bp4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6bp4

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Zinc binding site 1 out of 8 in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:38.2
occ:1.00
SG B:CYS479 2.2 34.6 1.0
SG B:CYS477 2.3 31.3 1.0
SG B:CYS484 2.3 47.0 1.0
SG B:CYS412 2.3 58.1 1.0
HB2 B:CYS484 3.1 57.8 1.0
H B:CYS479 3.2 38.3 1.0
CB B:CYS484 3.2 48.2 1.0
H B:CYS412 3.2 52.8 1.0
HA B:CYS484 3.3 60.0 1.0
HB2 B:CYS412 3.5 54.3 1.0
HB3 B:CYS477 3.5 49.4 1.0
CB B:CYS412 3.6 45.2 1.0
CB B:CYS477 3.6 41.1 1.0
CB B:CYS479 3.6 43.6 1.0
HB3 B:CYS479 3.6 52.4 1.0
H B:ARG485 3.7 62.7 1.0
CA B:CYS484 3.7 50.0 1.0
N B:CYS412 3.9 44.0 1.0
H B:GLY486 3.9 69.1 1.0
N B:CYS479 4.0 31.9 1.0
HB3 B:CYS484 4.1 57.8 1.0
HB2 B:CYS477 4.1 49.4 1.0
HB2 B:SER481 4.1 54.9 1.0
HE2 B:HIS410 4.2 52.6 1.0
N B:ARG485 4.2 52.2 1.0
HA B:SER411 4.3 35.5 1.0
HB3 B:CYS412 4.3 54.3 1.0
HB2 B:CYS479 4.3 52.4 1.0
CA B:CYS479 4.4 35.7 1.0
HD2 B:HIS410 4.4 46.5 1.0
CA B:CYS412 4.4 35.2 1.0
H B:SER481 4.4 57.3 1.0
C B:CYS484 4.5 52.4 1.0
HN61 B:SAM505 4.5 33.1 1.0
H B:LYS478 4.6 37.9 1.0
N B:LYS478 4.7 31.6 1.0
NE2 B:HIS410 4.7 43.9 1.0
C B:CYS477 4.7 32.2 1.0
CA B:CYS477 4.8 40.6 1.0
HG B:SER481 4.8 57.7 1.0
N B:GLY486 4.8 57.6 1.0
CD2 B:HIS410 4.8 38.8 1.0
HA B:CYS412 4.9 42.3 1.0
C B:SER411 4.9 41.5 1.0
H B:GLY480 4.9 41.6 1.0
N B:CYS484 5.0 56.0 1.0
C B:CYS479 5.0 36.6 1.0

Zinc binding site 2 out of 8 in 6bp4

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Zinc binding site 2 out of 8 in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn502

b:40.9
occ:1.00
SG B:CYS311 2.3 39.2 1.0
SG B:CYS260 2.3 34.4 1.0
SG B:CYS307 2.3 44.3 1.0
SG B:CYS278 2.4 34.2 1.0
HA B:CYS307 2.8 41.1 1.0
HB3 B:CYS307 3.0 45.2 1.0
CB B:CYS307 3.0 37.6 1.0
HB3 B:CYS311 3.2 61.4 1.0
ZN B:ZN504 3.2 46.8 1.0
HB3 B:CYS260 3.3 65.3 1.0
CA B:CYS307 3.4 34.2 1.0
CB B:CYS311 3.4 51.2 1.0
HB2 B:CYS278 3.4 38.9 1.0
CB B:CYS260 3.5 54.5 1.0
CB B:CYS278 3.6 32.4 1.0
HB2 B:CYS311 3.8 61.4 1.0
ZN B:ZN503 3.8 42.2 1.0
SG B:CYS276 3.8 31.1 1.0
H B:ASN308 3.9 69.8 1.0
H B:CYS260 3.9 46.0 1.0
HB2 B:CYS307 3.9 45.2 1.0
HB3 B:CYS278 4.1 38.9 1.0
H B:CYS278 4.2 56.5 1.0
HB2 B:CYS260 4.2 65.3 1.0
N B:CYS307 4.3 28.3 1.0
N B:CYS260 4.3 38.4 1.0
HD22 B:ASN319 4.4 32.7 1.0
N B:ASN308 4.5 58.2 1.0
C B:CYS307 4.5 41.7 1.0
CA B:CYS260 4.5 50.4 1.0
SG B:CYS268 4.5 49.5 1.0
H B:CYS307 4.6 34.0 1.0
SG B:CYS313 4.6 46.3 1.0
HA2 B:GLY259 4.6 46.9 1.0
HA B:CYS311 4.7 54.1 1.0
CA B:CYS311 4.7 45.0 1.0
N B:CYS278 4.8 47.1 1.0
CA B:CYS278 4.8 43.3 1.0
HG B:CYS262 4.8 47.3 1.0
O B:GLU306 5.0 34.8 1.0
C B:GLU306 5.0 30.4 1.0

Zinc binding site 3 out of 8 in 6bp4

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Zinc binding site 3 out of 8 in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn503

b:42.2
occ:1.00
SG B:CYS313 2.2 46.3 1.0
SG B:CYS307 2.3 44.3 1.0
SG B:CYS317 2.3 33.1 1.0
SG B:CYS268 2.4 49.5 1.0
HB2 B:CYS317 3.1 56.6 1.0
CB B:CYS317 3.3 47.2 1.0
HB2 B:CYS268 3.4 69.3 1.0
H B:CYS268 3.5 75.2 1.0
CB B:CYS307 3.5 37.6 1.0
HB3 B:CYS317 3.5 56.6 1.0
ZN B:ZN504 3.6 46.8 1.0
CB B:CYS313 3.6 60.6 1.0
CB B:CYS268 3.6 57.8 1.0
HB2 B:CYS307 3.6 45.2 1.0
HB3 B:CYS307 3.6 45.2 1.0
HB3 B:CYS313 3.6 72.8 1.0
HB2 B:CYS313 3.8 72.8 1.0
ZN B:ZN502 3.8 40.9 1.0
HB3 B:ASN319 3.8 35.0 1.0
HE B:ARG320 4.1 61.1 1.0
HB3 B:CYS311 4.2 61.4 1.0
N B:CYS268 4.2 62.7 1.0
HB3 B:CYS268 4.3 69.3 1.0
SG B:CYS260 4.3 34.4 1.0
HG3 B:ARG320 4.4 56.5 1.0
CA B:CYS268 4.5 59.2 1.0
H B:ASN319 4.6 39.9 1.0
HH21 B:ARG320 4.6 52.8 1.0
HD22 B:ASN319 4.7 32.7 1.0
CA B:CYS317 4.7 44.8 1.0
CB B:ASN319 4.7 29.2 1.0
NE B:ARG320 4.7 50.9 1.0
HB2 B:ASN319 4.8 35.0 1.0
HB2 B:CYS311 4.8 61.4 1.0
HA B:CYS317 4.8 53.7 1.0
CB B:CYS311 4.9 51.2 1.0
HA2 B:GLY267 4.9 81.3 1.0
CA B:CYS307 4.9 34.2 1.0
CA B:CYS313 4.9 65.8 1.0
HA B:CYS268 4.9 71.1 1.0
H B:CYS307 5.0 34.0 1.0
HB2 B:CYS262 5.0 86.0 1.0

Zinc binding site 4 out of 8 in 6bp4

Go back to Zinc Binding Sites List in 6bp4
Zinc binding site 4 out of 8 in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn504

b:46.8
occ:1.00
SG B:CYS262 2.2 39.4 1.0
SG B:CYS276 2.3 31.1 1.0
SG B:CYS268 2.3 49.5 1.0
SG B:CYS260 2.3 34.4 1.0
HG B:CYS262 2.5 47.3 1.0
ZN B:ZN502 3.2 40.9 1.0
HB2 B:CYS276 3.3 58.8 1.0
HB2 B:CYS260 3.4 65.3 1.0
HB2 B:CYS262 3.4 86.0 1.0
CB B:CYS276 3.4 49.0 1.0
CB B:CYS262 3.4 71.7 1.0
HB3 B:CYS268 3.4 69.3 1.0
CB B:CYS260 3.5 54.5 1.0
ZN B:ZN503 3.6 42.2 1.0
CB B:CYS268 3.6 57.8 1.0
HA B:CYS276 3.6 56.6 1.0
HB3 B:CYS262 3.7 86.0 1.0
HB3 B:CYS260 3.8 65.3 1.0
SG B:CYS307 3.8 44.3 1.0
HZ B:PHE288 4.0 49.0 1.0
HB2 B:CYS268 4.1 69.3 1.0
CA B:CYS276 4.1 47.2 1.0
HB3 B:CYS276 4.2 58.8 1.0
HE1 B:PHE288 4.2 44.9 1.0
H B:CYS278 4.5 56.5 1.0
HB2 B:CYS278 4.5 38.9 1.0
SG B:CYS313 4.6 46.3 1.0
H B:GLU277 4.6 54.9 1.0
HA B:CYS268 4.7 71.1 1.0
CA B:CYS262 4.7 76.0 1.0
CZ B:PHE288 4.7 40.9 1.0
CA B:CYS268 4.8 59.2 1.0
HB3 B:CYS311 4.8 61.4 1.0
CE1 B:PHE288 4.8 37.4 1.0
SG B:CYS278 4.8 34.2 1.0
CA B:CYS260 4.9 50.4 1.0
C B:CYS276 4.9 45.7 1.0
N B:CYS262 5.0 73.3 1.0
HA B:CYS262 5.0 91.2 1.0
N B:GLU277 5.0 45.8 1.0

Zinc binding site 5 out of 8 in 6bp4

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Zinc binding site 5 out of 8 in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:31.9
occ:1.00
SG A:CYS477 2.2 30.6 1.0
SG A:CYS479 2.3 25.6 1.0
SG A:CYS412 2.3 41.5 1.0
SG A:CYS484 2.4 37.1 1.0
HB2 A:CYS484 3.1 66.3 1.0
HA A:CYS484 3.2 60.5 1.0
HB3 A:CYS477 3.2 58.8 1.0
CB A:CYS484 3.2 55.3 1.0
CB A:CYS477 3.3 49.0 1.0
H A:CYS479 3.3 40.6 1.0
H A:CYS412 3.4 58.6 1.0
H A:GLY486 3.7 79.8 1.0
CA A:CYS484 3.7 50.4 1.0
HB2 A:CYS412 3.7 49.0 1.0
HB2 A:CYS477 3.7 58.8 1.0
CB A:CYS412 3.8 40.9 1.0
CB A:CYS479 3.8 42.6 1.0
HB3 A:CYS479 3.8 51.1 1.0
H A:ARG485 3.8 67.9 1.0
HE2 A:HIS410 4.0 46.3 1.0
HB3 A:CYS484 4.1 66.3 1.0
N A:CYS412 4.1 48.8 1.0
N A:CYS479 4.1 33.9 1.0
HD2 A:HIS410 4.3 42.9 1.0
N A:ARG485 4.3 56.6 1.0
HG2 A:ARG485 4.4 83.7 1.0
HA A:SER411 4.4 36.4 1.0
C A:CYS484 4.4 57.6 1.0
HB3 A:CYS412 4.4 49.0 1.0
HB2 A:CYS479 4.5 51.1 1.0
NE2 A:HIS410 4.5 38.6 1.0
N A:GLY486 4.5 66.5 1.0
CA A:CYS479 4.5 40.7 1.0
H A:LYS478 4.5 50.7 1.0
CA A:CYS477 4.6 51.0 1.0
CA A:CYS412 4.6 33.8 1.0
HB2 A:SER481 4.6 55.9 1.0
C A:CYS477 4.6 43.8 1.0
N A:LYS478 4.7 42.3 1.0
CD2 A:HIS410 4.7 35.8 1.0
HN61 A:SAM505 4.7 41.4 1.0
O A:CYS479 4.8 62.7 1.0
HA2 A:GLY486 4.8 82.8 1.0
N A:CYS484 4.9 45.2 1.0
HA A:CYS477 4.9 61.2 1.0
HA A:CYS412 5.0 40.6 1.0

Zinc binding site 6 out of 8 in 6bp4

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Zinc binding site 6 out of 8 in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:38.8
occ:1.00
SG A:CYS276 2.2 25.6 1.0
SG A:CYS268 2.3 44.7 1.0
SG A:CYS262 2.4 62.0 1.0
SG A:CYS260 2.4 40.4 1.0
HG A:CYS262 2.6 74.5 1.0
HB2 A:CYS276 2.9 57.4 1.0
CB A:CYS276 3.1 47.8 1.0
HB2 A:CYS260 3.2 70.6 1.0
HA A:CYS276 3.2 59.8 1.0
CB A:CYS260 3.4 58.9 1.0
HB3 A:CYS268 3.4 54.2 1.0
HB2 A:CYS262 3.4 70.8 1.0
CB A:CYS262 3.5 59.0 1.0
CB A:CYS268 3.5 45.2 1.0
ZN A:ZN503 3.6 42.9 1.0
CA A:CYS276 3.7 49.8 1.0
HB3 A:CYS260 3.7 70.6 1.0
HB3 A:CYS262 3.8 70.8 1.0
ZN A:ZN504 3.9 40.5 1.0
HB3 A:CYS276 3.9 57.4 1.0
HZ A:PHE288 4.1 51.5 1.0
HB2 A:CYS268 4.2 54.2 1.0
HA A:CYS268 4.3 62.8 1.0
SG A:CYS307 4.3 23.0 1.0
H A:GLU277 4.4 58.7 1.0
HE1 A:PHE288 4.5 44.8 1.0
H A:CYS278 4.5 55.7 1.0
CA A:CYS268 4.5 52.3 1.0
C A:CYS276 4.6 47.3 1.0
N A:GLU277 4.7 48.9 1.0
N A:CYS276 4.8 49.0 1.0
CA A:CYS260 4.8 56.9 1.0
HB2 A:CYS278 4.8 44.5 1.0
HB3 A:CYS313 4.9 50.7 1.0
CA A:CYS262 4.9 73.5 1.0
CZ A:PHE288 4.9 42.9 1.0
HB3 A:CYS311 4.9 51.8 1.0
H A:CYS276 4.9 58.8 1.0
H A:ASN261 5.0 70.2 1.0

Zinc binding site 7 out of 8 in 6bp4

Go back to Zinc Binding Sites List in 6bp4
Zinc binding site 7 out of 8 in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:42.9
occ:1.00
SG A:CYS311 2.2 33.0 1.0
SG A:CYS260 2.3 40.4 1.0
SG A:CYS307 2.3 23.0 1.0
SG A:CYS278 2.3 33.6 1.0
HB3 A:CYS311 2.9 51.8 1.0
HB3 A:CYS307 3.1 36.1 1.0
HA A:CYS307 3.1 39.2 1.0
CB A:CYS307 3.2 30.1 1.0
CB A:CYS311 3.2 43.2 1.0
HB3 A:CYS260 3.3 70.6 1.0
CB A:CYS260 3.5 58.9 1.0
HB2 A:CYS311 3.6 51.8 1.0
ZN A:ZN502 3.6 38.8 1.0
HB2 A:CYS278 3.6 44.5 1.0
CA A:CYS307 3.6 32.6 1.0
H A:CYS260 3.7 56.8 1.0
ZN A:ZN504 3.7 40.5 1.0
CB A:CYS278 3.7 37.1 1.0
SG A:CYS276 3.8 25.6 1.0
HB2 A:CYS307 4.0 36.1 1.0
N A:CYS260 4.1 47.4 1.0
H A:ASN308 4.1 47.3 1.0
HB2 A:CYS260 4.2 70.6 1.0
H A:CYS278 4.2 55.7 1.0
HB3 A:CYS278 4.2 44.5 1.0
SG A:CYS313 4.3 33.2 1.0
SG A:CYS268 4.3 44.7 1.0
CA A:CYS260 4.4 56.9 1.0
HD22 A:ASN319 4.4 53.2 1.0
N A:CYS307 4.5 32.0 1.0
CA A:CYS311 4.5 46.4 1.0
HA A:CYS311 4.5 55.6 1.0
HA2 A:GLY259 4.6 38.6 1.0
N A:ASN308 4.7 39.4 1.0
H A:CYS307 4.8 38.4 1.0
C A:CYS307 4.8 30.0 1.0
N A:CYS278 4.8 46.4 1.0
CA A:CYS278 4.8 40.8 1.0
C A:GLY259 4.9 43.9 1.0

Zinc binding site 8 out of 8 in 6bp4

Go back to Zinc Binding Sites List in 6bp4
Zinc binding site 8 out of 8 in the Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of the S. Pombe CLR4 Catalytic Domain Bound to Sam within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:40.5
occ:1.00
SG A:CYS307 2.3 23.0 1.0
SG A:CYS268 2.3 44.7 1.0
SG A:CYS313 2.3 33.2 1.0
SG A:CYS317 2.4 34.1 1.0
HB3 A:CYS313 3.2 50.7 1.0
CB A:CYS313 3.2 42.2 1.0
HB2 A:CYS268 3.3 54.2 1.0
HB2 A:CYS313 3.3 50.7 1.0
CB A:CYS268 3.4 45.2 1.0
H A:CYS268 3.5 74.9 1.0
HB2 A:CYS317 3.5 48.7 1.0
CB A:CYS307 3.5 30.1 1.0
HB2 A:CYS307 3.6 36.1 1.0
CB A:CYS317 3.6 40.6 1.0
HB3 A:ASN319 3.6 40.5 1.0
ZN A:ZN503 3.7 42.9 1.0
HB3 A:CYS307 3.7 36.1 1.0
HB3 A:CYS317 3.9 48.7 1.0
ZN A:ZN502 3.9 38.8 1.0
HE A:ARG320 4.1 40.6 1.0
HB3 A:CYS268 4.1 54.2 1.0
N A:CYS268 4.2 62.4 1.0
HB3 A:CYS311 4.2 51.8 1.0
SG A:CYS260 4.3 40.4 1.0
HG3 A:ARG320 4.4 49.3 1.0
HD22 A:ASN319 4.4 53.2 1.0
HH21 A:ARG320 4.4 46.7 1.0
CA A:CYS268 4.4 52.3 1.0
CB A:ASN319 4.5 33.8 1.0
H A:ASN319 4.5 44.5 1.0
HB2 A:ASN319 4.6 40.5 1.0
NE A:ARG320 4.6 33.9 1.0
CA A:CYS313 4.7 44.5 1.0
HB2 A:CYS311 4.7 51.8 1.0
CB A:CYS311 4.9 43.2 1.0
HA A:CYS268 4.9 62.8 1.0
CA A:CYS307 4.9 32.6 1.0
SG A:CYS276 4.9 25.6 1.0
HE1 A:PHE288 4.9 44.8 1.0
H A:CYS307 4.9 38.4 1.0
NH2 A:ARG320 5.0 38.9 1.0
CA A:CYS317 5.0 35.5 1.0

Reference:

N.Iglesias, M.A.Currie, G.Jih, J.A.Paulo, N.Siuti, M.Kalocsay, S.P.Gygi, D.Moazed. Automethylation-Induced Conformational Switch in CLR4 (SUV39H) Maintains Epigenetic Stability. Nature V. 560 504 2018.
ISSN: ESSN 1476-4687
PubMed: 30051891
DOI: 10.1038/S41586-018-0398-2
Page generated: Wed Dec 16 11:32:55 2020

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