Zinc in PDB 6t9l: Saga Dub Module Bound to A Ubiqitinated Nucleosome

Enzymatic activity of Saga Dub Module Bound to A Ubiqitinated Nucleosome

All present enzymatic activity of Saga Dub Module Bound to A Ubiqitinated Nucleosome:
3.4.19.12;

Zinc Binding Sites:

The binding sites of Zinc atom in the Saga Dub Module Bound to A Ubiqitinated Nucleosome (pdb code 6t9l). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Saga Dub Module Bound to A Ubiqitinated Nucleosome, PDB code: 6t9l:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6t9l

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Zinc binding site 1 out of 8 in the Saga Dub Module Bound to A Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Saga Dub Module Bound to A Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn501

b:0.3
occ:1.01
 SG K:CYS46 2.5 0.1 1.0
SG K:CYS68 2.5 0.2 1.0
SG K:CYS49 2.5 0.9 1.0
CB K:CYS68 2.5 0.2 1.0
ND1 K:HIS73 2.7 1.0 1.0
CB K:CYS46 2.7 0.1 1.0
N K:CYS68 3.3 0.2 1.0
CE1 K:HIS73 3.5 1.0 1.0
CA K:CYS68 3.5 0.2 1.0
CG K:HIS73 3.7 1.0 1.0
CB K:CYS49 4.0 0.9 1.0
CB K:HIS73 4.0 1.0 1.0
CA K:CYS46 4.2 0.1 1.0
N K:CYS49 4.3 0.9 1.0
C K:GLY67 4.4 0.6 1.0
OG K:SER54 4.5 0.2 1.0
C K:CYS68 4.6 0.2 1.0
CA K:CYS49 4.6 0.9 1.0
NE2 K:HIS73 4.6 1.0 1.0
N K:HIS50 4.7 0.9 1.0
CB K:SER54 4.7 0.2 1.0
N K:GLU51 4.7 0.8 1.0
CD2 K:HIS73 4.8 1.0 1.0
CA K:GLY67 4.8 0.6 1.0
CB K:GLU51 4.9 0.8 1.0
C K:CYS49 5.0 0.9 1.0
O K:GLU51 5.0 0.8 1.0

Zinc binding site 2 out of 8 in 6t9l

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Zinc binding site 2 out of 8 in the Saga Dub Module Bound to A Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Saga Dub Module Bound to A Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn502

b:0.2
occ:1.01
 NE2 K:HIS83 2.3 0.3 1.0
CD2 K:HIS83 2.4 0.3 1.0
SG K:CYS60 2.5 0.4 1.0
CE1 K:HIS83 2.5 0.3 1.0
SG K:CYS63 2.8 0.8 1.0
CG K:HIS83 2.8 0.3 1.0
ND1 K:HIS83 2.8 0.3 1.0
NE2 K:HIS77 3.0 0.8 1.0
N K:CYS63 3.8 0.8 1.0
CB K:HIS83 3.8 0.3 1.0
CD2 K:HIS77 3.9 0.8 1.0
CE1 K:HIS77 4.0 0.8 1.0
CB K:CYS63 4.0 0.8 1.0
CB K:GLN62 4.0 0.8 1.0
CB K:CYS60 4.2 0.4 1.0
N K:GLN62 4.3 0.8 1.0
C K:GLN62 4.4 0.8 1.0
CA K:GLN62 4.4 0.8 1.0
CA K:CYS63 4.5 0.8 1.0
OE1 K:GLN62 4.6 0.8 1.0
CG K:GLN62 4.8 0.8 1.0

Zinc binding site 3 out of 8 in 6t9l

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Zinc binding site 3 out of 8 in the Saga Dub Module Bound to A Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Saga Dub Module Bound to A Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn503

b:0.0
occ:1.01
 ND1 K:HIS6 2.3 0.8 1.0
N K:CYS99 2.3 0.7 1.0
CE1 K:HIS6 2.5 0.8 1.0
SG K:CYS99 2.5 0.7 1.0
SG K:CYS96 2.6 0.4 1.0
C K:LYS98 2.7 0.9 1.0
CB K:LYS98 2.9 0.9 1.0
CB K:CYS99 3.0 0.7 1.0
CA K:CYS99 3.1 0.7 1.0
CA K:LYS98 3.2 0.9 1.0
CG K:HIS6 3.2 0.8 1.0
NE2 K:HIS6 3.4 0.8 1.0
O K:LYS98 3.4 0.9 1.0
N K:LYS98 3.5 0.9 1.0
CD2 K:HIS6 3.7 0.8 1.0
CB K:HIS6 4.0 0.8 1.0
CB K:CYS96 4.1 0.4 1.0
CG K:LYS98 4.3 0.9 1.0
SG K:CYS4 4.3 0.0 1.0
CD1 K:ILE84 4.5 0.7 1.0
C K:CYS99 4.5 0.7 1.0
C K:PHE97 4.5 0.9 1.0
C K:CYS96 4.8 0.4 1.0
CD K:LYS98 4.9 0.9 1.0
N K:GLU100 4.9 0.8 1.0
N K:PHE97 4.9 0.9 1.0

Zinc binding site 4 out of 8 in 6t9l

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Zinc binding site 4 out of 8 in the Saga Dub Module Bound to A Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Saga Dub Module Bound to A Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn504

b:0.7
occ:1.00
 NE2 K:HIS170 2.3 0.1 1.0
CE1 K:HIS170 2.5 0.1 1.0
SG K:CYS185 2.5 0.5 1.0
SG K:CYS182 2.6 0.3 1.0
SG K:CYS174 2.7 0.2 1.0
CB K:CYS182 2.9 0.3 1.0
CD2 K:HIS170 3.6 0.1 1.0
ND1 K:HIS170 3.8 0.1 1.0
CB K:CYS185 3.9 0.5 1.0
CB K:CYS174 3.9 0.2 1.0
N K:CYS185 4.1 0.5 1.0
CG K:HIS170 4.4 0.1 1.0
CA K:CYS182 4.4 0.3 1.0
CG1 K:VAL176 4.4 0.0 1.0
OD2 K:ASP256 4.5 0.3 1.0
CA K:CYS185 4.5 0.5 1.0
CB K:SER184 4.6 0.6 1.0
N K:ARG177 4.9 0.9 1.0
C K:SER184 4.9 0.6 1.0
CA K:CYS174 5.0 0.2 1.0
C K:CYS182 5.0 0.3 1.0

Zinc binding site 5 out of 8 in 6t9l

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Zinc binding site 5 out of 8 in the Saga Dub Module Bound to A Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Saga Dub Module Bound to A Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn505

b:0.3
occ:1.00
 ND1 K:HIS250 2.2 0.4 1.0
ND1 K:HIS276 2.2 0.6 1.0
CE1 K:HIS276 2.5 0.6 1.0
SG K:CYS273 2.5 0.0 1.0
CB K:CYS271 2.5 0.7 1.0
SG K:CYS271 2.6 0.7 1.0
CG K:HIS276 2.7 0.6 1.0
CE1 K:HIS250 2.7 0.4 1.0
CG K:HIS250 3.0 0.4 1.0
NE2 K:HIS276 3.0 0.6 1.0
CD2 K:HIS276 3.1 0.6 1.0
CB K:HIS276 3.5 0.6 1.0
NE2 K:HIS250 3.6 0.4 1.0
CB K:HIS250 3.6 0.4 1.0
CB K:CYS273 3.7 0.0 1.0
CD2 K:HIS250 3.7 0.4 1.0
CA K:CYS271 4.0 0.7 1.0
N K:CYS273 4.3 0.0 1.0
CA K:HIS250 4.4 0.4 1.0
C K:CYS271 4.4 0.7 1.0
N K:HIS276 4.5 0.6 1.0
CA K:CYS273 4.6 0.0 1.0
CA K:HIS276 4.6 0.6 1.0
N K:CYS271 4.6 0.7 1.0
N K:GLU272 4.8 0.8 1.0
O K:HIS250 4.8 0.4 1.0
O K:CYS271 5.0 0.7 1.0

Zinc binding site 6 out of 8 in 6t9l

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Zinc binding site 6 out of 8 in the Saga Dub Module Bound to A Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Saga Dub Module Bound to A Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
K:Zn506

b:0.8
occ:1.01
 N K:CYS339 2.8 0.0 1.0
SG K:CYS339 2.8 0.0 1.0
CB K:CYS339 2.8 0.0 1.0
SG K:CYS292 3.0 0.2 1.0
N K:CYS292 3.0 0.2 1.0
CB K:GLU338 3.2 0.2 1.0
SG K:CYS336 3.3 0.9 1.0
CA K:GLY291 3.3 0.2 1.0
CA K:CYS339 3.3 0.0 1.0
OE1 K:GLU338 3.4 0.2 1.0
C K:GLY291 3.5 0.2 1.0
C K:GLU338 3.6 0.2 1.0
CB K:CYS292 3.7 0.2 1.0
CA K:GLU338 3.9 0.2 1.0
CA K:CYS292 3.9 0.2 1.0
N K:GLY291 4.0 0.2 1.0
SG K:CYS289 4.1 1.0 1.0
CD K:GLU338 4.2 0.2 1.0
CG K:GLU338 4.2 0.2 1.0
N K:GLU338 4.4 0.2 1.0
O K:GLU338 4.5 0.2 1.0
O K:GLY291 4.5 0.2 1.0
CB K:CYS336 4.5 0.9 1.0
C K:CYS339 4.6 0.0 1.0
OD1 K:ASN295 4.9 0.2 1.0
N K:ASN340 4.9 0.7 1.0
C K:CYS292 4.9 0.2 1.0

Zinc binding site 7 out of 8 in 6t9l

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Zinc binding site 7 out of 8 in the Saga Dub Module Bound to A Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Saga Dub Module Bound to A Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
M:Zn101

b:0.9
occ:1.00
 N M:CYS76 2.4 0.2 1.0
SG M:CYS76 2.5 0.2 1.0
SG M:CYS73 2.6 0.4 1.0
CB M:ASN75 2.7 0.8 1.0
C M:ASN75 3.0 0.8 1.0
CB M:CYS76 3.0 0.2 1.0
CA M:ASN75 3.1 0.8 1.0
CA M:CYS76 3.2 0.2 1.0
N M:ASN75 3.4 0.8 1.0
CG M:ASN75 3.6 0.8 1.0
NE2 M:HIS88 3.7 0.9 1.0
ND2 M:ASN75 3.8 0.8 1.0
CB M:CYS73 3.8 0.4 1.0
SG M:CYS92 3.9 0.4 1.0
O M:ASN75 3.9 0.8 1.0
CB M:CYS92 4.0 0.4 1.0
C M:CYS76 4.3 0.2 1.0
N M:GLY77 4.4 0.8 1.0
CD2 M:HIS88 4.5 0.9 1.0
C M:GLU74 4.6 0.5 1.0
OD1 M:ASN75 4.6 0.8 1.0
CE1 M:HIS88 4.6 0.9 1.0
N M:GLU74 4.8 0.5 1.0
C M:CYS73 4.9 0.4 1.0
CA M:CYS73 5.0 0.4 1.0

Zinc binding site 8 out of 8 in 6t9l

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Zinc binding site 8 out of 8 in the Saga Dub Module Bound to A Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Saga Dub Module Bound to A Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
N:Zn701

b:0.8
occ:1.00
 NE2 N:HIS93 2.3 1.0 1.0
SG N:CYS81 2.5 0.5 1.0
CD2 N:HIS93 2.6 1.0 1.0
SG N:CYS98 2.6 0.2 1.0
SG N:CYS78 2.7 0.7 1.0
CB N:CYS98 3.1 0.2 1.0
CB N:CYS78 3.5 0.7 1.0
CE1 N:HIS93 3.6 1.0 1.0
CA N:CYS98 3.7 0.2 1.0
CB N:CYS81 3.8 0.5 1.0
CG N:HIS93 3.9 1.0 1.0
N N:CYS81 4.1 0.5 1.0
CD2 N:LEU94 4.2 0.0 1.0
ND1 N:HIS93 4.3 1.0 1.0
CA N:CYS81 4.6 0.5 1.0
N N:CYS98 4.7 0.2 1.0
C N:CYS98 4.7 0.2 1.0
O N:HIS93 4.7 1.0 1.0
CB N:LYS80 4.9 0.1 1.0
CA N:CYS78 4.9 0.7 1.0
CD1 N:LEU85 5.0 0.2 1.0

Reference:

H.Wang, C.Dienemann, A.Stuetzer, H.Urlaub, A.Cheung, P.Cramer. Structure of the Transcription Coactivator Saga Nature 2020.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-020-1933-5
Page generated: Wed Dec 16 12:52:12 2020

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