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Zinc in PDB 8bpa: Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom

Enzymatic activity of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom

All present enzymatic activity of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom:
3.5.1.98;

Other elements in 8bpa:

The structure of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom also contains other interesting chemical elements:

Calcium (Ca) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom (pdb code 8bpa). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 5 binding sites of Zinc where determined in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom, PDB code: 8bpa:
Jump to Zinc binding site number: 1; 2; 3; 4; 5;

Zinc binding site 1 out of 5 in 8bpa

Go back to Zinc Binding Sites List in 8bpa
Zinc binding site 1 out of 5 in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn501

b:92.6
occ:1.00
 CD2 B:HIS179 1.3 77.4 1.0
OD2 B:ASP265 2.1 84.8 1.0
NE2 B:HIS179 2.3 77.4 1.0
OD1 B:ASP177 2.4 69.9 1.0
CG B:HIS179 2.4 77.4 1.0
OD2 B:ASP177 2.7 69.9 1.0
CG B:ASP177 2.9 69.9 1.0
CB B:HIS179 3.2 77.4 1.0
CG B:ASP265 3.3 84.8 1.0
CE1 B:HIS179 3.4 77.4 1.0
ND1 B:HIS179 3.4 77.4 1.0
N B:HIS179 3.8 77.4 1.0
OH B:TYR304 3.9 88.3 1.0
OD1 B:ASP265 4.0 84.8 1.0
CG2 B:ILE178 4.1 74.7 1.0
CA B:HIS179 4.1 77.4 1.0
CE1 B:HIS142 4.1 74.1 1.0
CB B:ASP177 4.3 69.9 1.0
OE2 A:GLU436 4.5 99.4 1.0
CB B:ASP265 4.5 84.8 1.0
CE1 B:HIS141 4.6 73.8 1.0
CA B:GLY302 4.6 83.4 1.0
N B:ILE178 4.7 74.7 1.0
NE2 B:HIS141 4.7 73.8 1.0
CZ B:TYR304 4.8 88.3 1.0
C B:ILE178 4.9 74.7 1.0
NE2 B:HIS142 5.0 74.1 1.0

Zinc binding site 2 out of 5 in 8bpa

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Zinc binding site 2 out of 5 in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1101

b:136.4
occ:1.00
 NE2 C:HIS318 2.1 122.4 1.0
CD2 C:HIS318 2.1 122.4 1.0
SG C:CYS292 2.3 124.8 1.0
SG C:CYS315 2.3 117.2 1.0
SG C:CYS289 2.3 125.9 1.0
CB C:CYS315 2.7 117.2 1.0
CB C:CYS289 3.2 125.9 1.0
CE1 C:HIS318 3.3 122.4 1.0
CG C:HIS318 3.4 122.4 1.0
CB C:CYS292 3.6 124.8 1.0
N C:CYS292 3.8 124.8 1.0
CA C:CYS315 3.9 117.2 1.0
N C:CYS315 4.0 117.2 1.0
ND1 C:HIS318 4.0 122.4 1.0
CA C:CYS292 4.2 124.8 1.0
CD2 C:TYR291 4.3 125.0 1.0
O C:CYS292 4.4 124.8 1.0
CB C:TYR291 4.4 125.0 1.0
CB C:HIS318 4.6 122.4 1.0
C C:CYS315 4.6 117.2 1.0
C C:TYR291 4.6 125.0 1.0
CA C:CYS289 4.7 125.9 1.0
O C:CYS315 4.7 117.2 1.0
C C:CYS292 4.7 124.8 1.0
N C:TYR291 4.8 125.0 1.0
CA C:TYR291 4.9 125.0 1.0
CG C:TYR291 4.9 125.0 1.0
CB C:LEU294 5.0 120.7 1.0

Zinc binding site 3 out of 5 in 8bpa

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Zinc binding site 3 out of 5 in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1102

b:138.3
occ:1.00
 ND1 C:HIS297 2.1 104.7 1.0
SG C:CYS300 2.3 86.9 1.0
SG C:CYS277 2.3 113.2 1.0
SG C:CYS274 2.3 110.1 1.0
CE1 C:HIS297 2.8 104.7 1.0
OG1 C:THR276 3.0 101.3 1.0
CB C:CYS277 3.2 113.2 1.0
CG C:HIS297 3.3 104.7 1.0
CB C:CYS274 3.3 110.1 1.0
CB C:CYS300 3.6 86.9 1.0
CB C:HIS297 3.8 104.7 1.0
N C:CYS277 3.8 113.2 1.0
NH1 C:ARG279 4.0 111.4 1.0
NE2 C:HIS297 4.1 104.7 1.0
CA C:CYS277 4.2 113.2 1.0
CD2 C:HIS297 4.3 104.7 1.0
CB C:THR276 4.3 101.3 1.0
C C:THR276 4.5 101.3 1.0
CZ C:ARG279 4.6 111.4 1.0
NH2 C:ARG279 4.6 111.4 1.0
CA C:CYS274 4.7 110.1 1.0
CA C:THR276 4.8 101.3 1.0
N C:THR276 4.8 101.3 1.0
N C:HIS297 4.9 104.7 1.0
CA C:CYS300 4.9 86.9 1.0
CA C:HIS297 5.0 104.7 1.0

Zinc binding site 4 out of 5 in 8bpa

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Zinc binding site 4 out of 5 in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1103

b:200.1
occ:1.00
 SG C:CYS99 2.3 187.6 1.0
SG C:CYS102 2.3 184.1 1.0
SG C:CYS74 2.3 205.4 1.0
SG C:CYS71 2.3 204.7 1.0
CB C:CYS99 2.9 187.6 1.0
CB C:CYS102 2.9 184.1 1.0
CB C:CYS71 3.2 204.7 1.0
CB C:CYS74 3.3 205.4 1.0
N C:CYS74 3.6 205.4 1.0
N C:CYS99 3.7 187.6 1.0
CA C:CYS99 3.9 187.6 1.0
N C:CYS102 3.9 184.1 1.0
CA C:CYS74 4.0 205.4 1.0
CA C:CYS102 4.0 184.1 1.0
O C:CYS74 4.3 205.4 1.0
C C:HIS73 4.4 207.3 1.0
CB C:HIS73 4.5 207.3 1.0
ND1 C:HIS73 4.5 207.3 1.0
C C:CYS74 4.6 205.4 1.0
C C:CYS99 4.6 187.6 1.0
CA C:CYS71 4.7 204.7 1.0
N C:HIS73 4.8 207.3 1.0
CA C:HIS73 4.8 207.3 1.0
O C:CYS99 4.8 187.6 1.0
CG C:HIS73 5.0 207.3 1.0
C C:MET98 5.0 184.2 1.0

Zinc binding site 5 out of 5 in 8bpa

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Zinc binding site 5 out of 5 in the Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Cryo-Em Structure of the Human SIN3B Histone Deacetylase Complex at 3.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1104

b:215.8
occ:1.00
 ND1 C:HIS79 2.1 191.1 1.0
SG C:CYS62 2.3 189.0 1.0
SG C:CYS59 2.3 204.4 1.0
SG C:CYS82 2.3 181.0 1.0
OG C:SER61 2.7 195.1 1.0
CG C:HIS79 2.8 191.1 1.0
CB C:HIS79 3.0 191.1 1.0
CB C:CYS59 3.1 204.4 1.0
CE1 C:HIS79 3.2 191.1 1.0
CB C:CYS82 3.5 181.0 1.0
N C:HIS79 3.5 191.1 1.0
CB C:CYS62 3.7 189.0 1.0
N C:CYS62 3.7 189.0 1.0
CA C:HIS79 3.8 191.1 1.0
CD2 C:HIS79 4.1 191.1 1.0
CB C:SER61 4.1 195.1 1.0
NE2 C:HIS79 4.2 191.1 1.0
NZ D:LYS275 4.3 152.7 1.0
CA C:CYS62 4.3 189.0 1.0
CA C:CYS59 4.6 204.4 1.0
C C:PHE78 4.6 204.0 1.0
C C:SER61 4.7 195.1 1.0
N C:SER61 4.8 195.1 1.0
CA C:SER61 4.8 195.1 1.0
CA C:CYS82 4.8 181.0 1.0
O C:GLU64 4.9 191.7 1.0
CA C:PHE78 5.0 204.0 1.0

Reference:

M.S.M.Wan, R.Muhammad, M.G.Koliopoulos, T.I.Roumeliotis, J.S.Choudhary, C.Alfieri. Mechanism of Assembly, Activation and Lysine Selection By the SIN3B Histone Deacetylase Complex Nat Commun V. 14 2556 2023.
ISSN: ESSN 2041-1723
DOI: 10.1038/S41467-023-38276-0
Page generated: Wed Oct 30 18:23:25 2024

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