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Zinc in PDB 4zux: Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome

Enzymatic activity of Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome

All present enzymatic activity of Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome:
3.4.19.12;

Protein crystallography data

The structure of Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome, PDB code: 4zux was solved by M.Morgan, C.Wolberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.50 / 3.82
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 178.804, 179.174, 353.819, 90.00, 90.00, 90.00
R / Rfree (%) 23.4 / 25.6

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 32;

Binding sites:

The binding sites of Zinc atom in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome (pdb code 4zux). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 32 binding sites of Zinc where determined in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome, PDB code: 4zux:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 32 in 4zux

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Zinc binding site 1 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to 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 UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn501

b:0.3
occ:1.00
 ND1 U:HIS73 2.0 0.8 1.0
SG U:CYS46 2.3 0.2 1.0
SG U:CYS49 2.3 0.3 1.0
SG U:CYS68 2.3 0.2 1.0
CE1 U:HIS73 2.8 0.1 1.0
CB U:CYS46 2.9 0.5 1.0
CB U:CYS68 3.0 0.7 1.0
CG U:HIS73 3.1 0.6 1.0
CB U:HIS73 3.6 0.9 1.0
CB U:CYS49 3.7 0.2 1.0
NE2 U:HIS73 4.0 1.0 1.0
N U:CYS68 4.0 0.7 1.0
CA U:CYS68 4.1 0.6 1.0
CD2 U:HIS71 4.1 0.6 1.0
CD2 U:HIS73 4.2 0.1 1.0
N U:CYS49 4.2 0.2 1.0
CB U:HIS71 4.3 0.3 1.0
CA U:CYS46 4.3 0.1 1.0
CA U:CYS49 4.5 0.4 1.0
CB U:SER54 4.6 1.0 1.0
CG U:HIS71 4.6 0.2 1.0
OG U:SER54 4.7 0.7 1.0
C U:CYS68 4.9 0.7 1.0

Zinc binding site 2 out of 32 in 4zux

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Zinc binding site 2 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to 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 UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn502

b:0.8
occ:1.00
 NE2 U:HIS77 2.0 0.1 1.0
SG U:CYS60 2.3 0.9 1.0
SG U:CYS63 2.3 0.9 1.0
CE1 U:HIS77 2.5 0.4 1.0
CD2 U:HIS83 2.8 0.4 1.0
CD2 U:HIS77 3.3 0.1 1.0
NE2 U:HIS83 3.3 0.1 1.0
CB U:CYS60 3.5 0.8 1.0
CB U:CYS63 3.5 0.2 1.0
ND1 U:HIS77 3.7 0.7 1.0
CG U:HIS83 3.7 0.9 1.0
N U:CYS63 4.0 0.7 1.0
CG U:HIS77 4.1 0.3 1.0
CE1 U:HIS83 4.3 0.1 1.0
CA U:CYS63 4.3 0.1 1.0
CB U:PHE65 4.4 0.1 1.0
CB U:HIS83 4.4 0.9 1.0
ND1 U:HIS83 4.5 0.0 1.0
CG2 U:ILE81 4.7 0.7 1.0
C U:GLN62 4.8 0.6 1.0
C U:CYS63 4.8 0.2 1.0
CB U:GLN62 4.9 0.4 1.0
CA U:CYS60 4.9 0.6 1.0

Zinc binding site 3 out of 32 in 4zux

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Zinc binding site 3 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to 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 UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn503

b:0.3
occ:1.00
 ND1 U:HIS6 2.0 0.1 1.0
SG U:CYS96 2.3 0.2 1.0
SG U:CYS99 2.3 0.3 1.0
SG U:CYS4 2.4 0.4 1.0
CE1 U:HIS6 2.7 0.1 1.0
CG U:HIS6 3.1 0.3 1.0
CB U:CYS4 3.3 0.4 1.0
CB U:CYS99 3.4 0.5 1.0
CB U:CYS96 3.4 0.2 1.0
N U:CYS99 3.6 0.7 1.0
CB U:HIS6 3.7 0.8 1.0
NE2 U:HIS6 3.8 0.1 1.0
CA U:CYS99 4.0 0.8 1.0
CD2 U:HIS6 4.0 0.4 1.0
CB U:LYS98 4.1 0.6 1.0
CA U:CYS4 4.1 0.6 1.0
CD U:PRO5 4.4 0.7 1.0
N U:HIS6 4.4 0.3 1.0
C U:LYS98 4.4 0.9 1.0
C U:CYS4 4.6 0.6 1.0
CA U:LYS98 4.7 0.3 1.0
CA U:HIS6 4.7 0.2 1.0
N U:PRO5 4.7 0.3 1.0
CA U:CYS96 4.8 0.8 1.0
N U:LYS98 4.9 0.8 1.0

Zinc binding site 4 out of 32 in 4zux

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Zinc binding site 4 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to 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 UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn504

b:0.4
occ:1.00
 NE2 U:HIS170 2.0 0.1 1.0
SG U:CYS182 2.2 0.0 1.0
SG U:CYS185 2.3 0.7 1.0
SG U:CYS174 2.3 0.7 1.0
CB U:CYS182 2.8 0.9 1.0
CE1 U:HIS170 2.8 0.9 1.0
CD2 U:HIS170 3.1 0.2 1.0
CB U:CYS174 3.5 0.8 1.0
CB U:CYS185 3.5 0.3 1.0
ND1 U:HIS170 3.9 0.8 1.0
N U:CYS185 4.0 0.5 1.0
N U:ARG177 4.1 0.4 1.0
CG U:HIS170 4.1 0.4 1.0
CG1 U:VAL176 4.3 0.1 1.0
CA U:CYS182 4.3 0.0 1.0
CA U:CYS185 4.3 0.7 1.0
CA U:ARG177 4.4 0.3 1.0
CG2 U:VAL176 4.5 0.4 1.0
N U:SER178 4.6 1.0 1.0
CA U:CYS174 4.7 0.4 1.0
O U:SER178 4.8 0.5 1.0
C U:CYS182 4.9 0.6 1.0
CB U:VAL176 4.9 0.9 1.0

Zinc binding site 5 out of 32 in 4zux

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Zinc binding site 5 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to 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 UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn505

b:0.9
occ:1.00
 ND1 U:HIS250 2.0 0.6 1.0
ND1 U:HIS276 2.0 0.8 1.0
SG U:CYS273 2.1 0.4 1.0
SG U:CYS271 2.2 0.7 1.0
CE1 U:HIS276 2.6 0.6 1.0
CB U:CYS273 2.9 0.0 1.0
CG U:HIS250 2.9 0.7 1.0
CE1 U:HIS250 3.0 0.3 1.0
CB U:HIS250 3.3 0.3 1.0
CG U:HIS276 3.3 0.2 1.0
CB U:CYS271 3.3 0.7 1.0
NE2 U:HIS276 3.8 0.6 1.0
CA U:HIS250 3.8 0.0 1.0
CB U:HIS276 4.0 0.5 1.0
NE2 U:HIS250 4.1 0.6 1.0
CD2 U:HIS250 4.1 0.5 1.0
CA U:CYS273 4.1 0.7 1.0
N U:CYS273 4.1 0.8 1.0
CD2 U:HIS276 4.2 0.7 1.0
N U:HIS276 4.4 0.3 1.0
O U:HIS250 4.6 0.3 1.0
C U:HIS250 4.7 0.7 1.0
CA U:CYS271 4.7 0.5 1.0
CB U:VAL275 4.7 0.6 1.0
C U:CYS273 4.8 0.4 1.0
CA U:HIS276 4.8 0.0 1.0
C U:CYS271 4.9 0.0 1.0
CD2 U:TYR253 4.9 0.4 1.0
N U:HIS250 5.0 0.3 1.0

Zinc binding site 6 out of 32 in 4zux

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Zinc binding site 6 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to 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 UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
U:Zn506

b:0.2
occ:1.00
 SG U:CYS289 2.2 0.6 1.0
SG U:CYS292 2.2 0.5 1.0
SG U:CYS336 2.2 0.9 1.0
SG U:CYS339 2.3 0.2 1.0
CB U:CYS289 3.1 0.4 1.0
CB U:CYS336 3.2 0.2 1.0
CB U:CYS339 3.2 0.7 1.0
CB U:CYS292 3.3 0.1 1.0
N U:CYS292 3.5 0.3 1.0
N U:CYS339 3.6 0.6 1.0
CA U:CYS339 4.0 0.6 1.0
CA U:CYS292 4.0 0.1 1.0
C U:GLU338 4.5 0.1 1.0
CA U:CYS289 4.6 0.1 1.0
C U:GLY291 4.6 0.9 1.0
CB U:GLU338 4.6 0.7 1.0
CA U:CYS336 4.7 0.1 1.0
CA U:GLY291 4.7 0.2 1.0
N U:GLU338 4.8 0.3 1.0
ND2 U:ASN295 4.8 0.3 1.0
N U:GLY291 4.8 0.3 1.0
CA U:GLU338 4.9 0.2 1.0
C U:CYS339 4.9 0.2 1.0
C U:CYS289 5.0 1.0 1.0

Zinc binding site 7 out of 32 in 4zux

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Zinc binding site 7 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to 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 UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
W:Zn101

b:0.0
occ:1.00
 SG W:CYS73 2.3 0.3 1.0
N W:CYS76 2.3 0.9 1.0
SG W:CYS92 2.3 0.7 1.0
CB W:ASN75 2.7 0.8 1.0
SG W:CYS76 2.8 0.4 1.0
CB W:CYS76 2.8 0.7 1.0
C W:ASN75 2.8 0.9 1.0
CA W:ASN75 3.0 0.9 1.0
CA W:CYS76 3.1 1.0 1.0
N W:ASN75 3.2 0.2 1.0
CG W:ASN75 3.7 0.9 1.0
ND2 W:ASN75 3.7 0.5 1.0
CB W:CYS73 3.8 0.1 1.0
O W:ASN75 3.8 0.9 1.0
NE2 W:HIS88 3.9 0.2 1.0
CB W:CYS92 3.9 0.0 1.0
O W:CYS73 4.2 0.1 1.0
C W:CYS76 4.2 0.8 1.0
C W:CYS73 4.3 0.6 1.0
N W:GLY77 4.3 0.2 1.0
C W:GLU74 4.4 1.0 1.0
CD2 W:HIS88 4.7 0.1 1.0
CA W:CYS73 4.7 0.2 1.0
N W:GLU74 4.7 0.8 1.0
CE1 W:HIS88 4.8 0.8 1.0
OD1 W:ASN75 4.8 0.7 1.0

Zinc binding site 8 out of 32 in 4zux

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Zinc binding site 8 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to 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 UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
Y:Zn201

b:0.3
occ:1.00
 NE2 Y:HIS93 2.0 0.9 1.0
SG Y:CYS81 2.3 0.3 1.0
SG Y:CYS98 2.3 0.1 1.0
SG Y:CYS78 2.4 0.6 1.0
CD2 Y:HIS93 2.9 0.4 1.0
CB Y:CYS98 2.9 0.1 1.0
CE1 Y:HIS93 3.0 0.8 1.0
CB Y:CYS78 3.1 0.3 1.0
CB Y:CYS81 3.4 0.3 1.0
CA Y:CYS98 3.9 0.1 1.0
N Y:CYS81 3.9 0.1 1.0
CG Y:HIS93 4.0 0.7 1.0
ND1 Y:HIS93 4.0 0.9 1.0
CA Y:CYS81 4.2 0.6 1.0
CA Y:CYS78 4.6 0.0 1.0
O Y:HIS93 4.6 0.5 1.0
N Y:CYS98 4.7 0.4 1.0
CD2 Y:LEU94 4.7 0.9 1.0
CB Y:LYS80 4.8 0.3 1.0
C Y:CYS81 4.9 0.1 1.0
C Y:LYS80 5.0 0.1 1.0

Zinc binding site 9 out of 32 in 4zux

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Zinc binding site 9 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn501

b:0.6
occ:1.00
 CB Z:CYS339 2.2 0.3 1.0
SG Z:CYS289 2.3 0.9 1.0
SG Z:CYS339 2.3 0.8 1.0
SG Z:CYS292 2.8 0.1 1.0
N Z:CYS292 3.1 0.4 1.0
CA Z:GLY291 3.5 0.1 1.0
CA Z:CYS339 3.5 0.7 1.0
C Z:GLY291 3.7 0.4 1.0
N Z:CYS339 3.8 0.3 1.0
CB Z:CYS292 3.8 0.5 1.0
N Z:GLY291 3.8 0.8 1.0
CB Z:CYS289 3.9 0.5 1.0
CA Z:CYS292 4.0 0.9 1.0
SG Z:CYS336 4.1 0.3 1.0
C Z:CYS339 4.6 0.5 1.0
C Z:GLU338 4.7 0.2 1.0
O Z:GLY291 4.8 0.9 1.0
CB Z:CYS336 4.8 0.9 1.0
CA Z:CYS289 5.0 1.0 1.0
C Z:CYS289 5.0 0.8 1.0

Zinc binding site 10 out of 32 in 4zux

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Zinc binding site 10 out of 32 in the Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Saga Dub Module UBP8/SGF11/SUS1/SGF73 Bound to Ubiqitinated Nucleosome within 5.0Å range:
probe atom residue distance (Å) B Occ
Z:Zn502

b:0.5
occ:1.00
 SG Z:CYS273 2.3 0.6 1.0
SG Z:CYS271 2.4 0.9 1.0
N Z:CYS273 2.5 0.8 1.0
CB Z:CYS273 2.8 0.4 1.0
CG Z:HIS276 2.8 0.8 1.0
CB Z:HIS276 2.8 0.6 1.0
CB Z:CYS271 2.8 0.9 1.0
CA Z:CYS273 3.0 0.4 1.0
C Z:CYS271 3.0 0.9 1.0
O Z:CYS271 3.1 0.1 1.0
CD2 Z:HIS276 3.2 0.6 1.0
N Z:GLU272 3.4 0.3 1.0
ND1 Z:HIS276 3.4 0.5 1.0
CA Z:CYS271 3.5 0.5 1.0
O Z:CYS273 3.5 0.2 1.0
C Z:GLU272 3.5 0.4 1.0
C Z:CYS273 3.6 0.6 1.0
N Z:HIS276 3.8 0.8 1.0
CA Z:HIS276 3.9 0.9 1.0
CA Z:GLU272 3.9 0.1 1.0
NE2 Z:HIS276 3.9 0.2 1.0
CE1 Z:HIS276 4.0 0.7 1.0
NE2 Z:HIS250 4.3 0.2 1.0
CD2 Z:HIS250 4.3 0.8 1.0
CE1 Z:HIS250 4.5 0.7 1.0
N Z:CYS271 4.5 0.6 1.0
O Z:GLU272 4.6 0.4 1.0
CG Z:HIS250 4.6 0.2 1.0
N Z:ILE274 4.6 0.4 1.0
ND1 Z:HIS250 4.7 0.1 1.0
C Z:HIS276 4.8 0.9 1.0
C Z:VAL275 5.0 0.7 1.0
N Z:VAL275 5.0 0.3 1.0

Reference:

M.T.Morgan, M.Haj-Yahya, A.E.Ringel, P.Bandi, A.Brik, C.Wolberger. Structural Basis For Histone H2B Deubiquitination By the Saga Dub Module. Science V. 351 725 2016.
ISSN: ESSN 1095-9203
PubMed: 26912860
DOI: 10.1126/SCIENCE.AAC5681
Page generated: Sun Oct 27 12:00:28 2024

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