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Zinc in PDB 3mhs: Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde

Enzymatic activity of Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde

All present enzymatic activity of Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde:
3.1.2.15;

Protein crystallography data

The structure of Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde, PDB code: 3mhs was solved by N.L.Samara, A.B.Datta, C.E.Berndsen, X.Zhang, T.Yao, R.E.Cohen, C.Wolberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.10 / 1.89
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.600, 102.084, 120.903, 90.00, 90.00, 90.00
R / Rfree (%) 15.9 / 20.8

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde (pdb code 3mhs). 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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde, PDB code: 3mhs:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 3mhs

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Zinc binding site 1 out of 8 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde


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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn472

b:45.0
occ:1.00
 ND1 A:HIS6 2.1 38.9 1.0
SG A:CYS4 2.3 51.0 1.0
SG A:CYS99 2.3 50.6 1.0
SG A:CYS96 2.3 49.9 1.0
CE1 A:HIS6 3.0 46.4 1.0
CG A:HIS6 3.2 47.2 1.0
CB A:CYS96 3.2 45.0 1.0
CB A:CYS4 3.4 50.2 1.0
CB A:CYS99 3.4 52.1 1.0
CB A:HIS6 3.6 47.8 1.0
N A:CYS99 3.8 53.9 1.0
CA A:CYS4 4.0 51.0 1.0
N A:HIS6 4.0 51.2 1.0
CD A:PRO5 4.1 52.8 1.0
NE2 A:HIS6 4.1 52.2 1.0
CA A:CYS99 4.2 52.8 1.0
CD2 A:HIS6 4.2 48.0 1.0
C A:CYS4 4.4 51.2 1.0
CA A:HIS6 4.4 50.0 1.0
N A:PRO5 4.4 53.3 1.0
CB A:LYS98 4.5 55.7 1.0
CA A:CYS96 4.7 44.2 1.0
O A:HOH583 4.7 48.1 1.0
C A:LYS98 4.7 54.1 1.0
N A:ILE7 4.9 49.9 1.0

Zinc binding site 2 out of 8 in 3mhs

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Zinc binding site 2 out of 8 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde


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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn473

b:44.4
occ:1.00
 ND1 A:HIS73 2.1 36.1 1.0
SG A:CYS46 2.3 45.4 1.0
SG A:CYS68 2.3 49.3 1.0
SG A:CYS49 2.3 50.2 1.0
CG A:HIS73 3.0 48.2 1.0
CE1 A:HIS73 3.2 48.5 1.0
CB A:CYS46 3.2 43.9 1.0
CB A:HIS73 3.3 47.8 1.0
CB A:CYS68 3.3 44.8 1.0
CB A:CYS49 3.4 52.7 1.0
N A:CYS49 3.9 52.2 1.0
CB A:HIS71 4.0 55.0 1.0
N A:CYS68 4.1 44.5 1.0
CD2 A:HIS71 4.1 61.1 1.0
CD2 A:HIS73 4.2 46.2 1.0
NE2 A:HIS73 4.2 47.2 1.0
CA A:CYS49 4.3 52.7 1.0
CA A:CYS68 4.3 44.3 1.0
CG A:HIS71 4.5 59.0 1.0
OG A:SER54 4.5 46.1 1.0
CB A:THR48 4.6 55.2 1.0
CA A:CYS46 4.6 44.4 1.0
CA A:HIS73 4.6 49.4 1.0
CB A:SER54 4.7 43.9 1.0
N A:HIS73 4.9 48.9 1.0
C A:THR48 4.9 54.5 1.0
C A:CYS68 5.0 44.7 1.0

Zinc binding site 3 out of 8 in 3mhs

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Zinc binding site 3 out of 8 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde


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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn474

b:48.5
occ:1.00
 NE2 A:HIS77 1.9 40.5 1.0
ND1 A:HIS83 2.1 58.1 1.0
SG A:CYS63 2.3 52.9 1.0
SG A:CYS60 2.3 46.0 1.0
CE1 A:HIS77 2.8 48.9 1.0
CD2 A:HIS77 3.0 51.6 1.0
CG A:HIS83 3.1 57.6 1.0
CE1 A:HIS83 3.1 57.4 1.0
CB A:CYS60 3.2 48.7 1.0
CB A:HIS83 3.4 54.2 1.0
CB A:CYS63 3.5 57.4 1.0
N A:CYS63 3.8 55.5 1.0
ND1 A:HIS77 3.9 48.6 1.0
CG A:HIS77 4.0 52.0 1.0
CA A:CYS63 4.1 55.2 1.0
NE2 A:HIS83 4.2 58.3 1.0
CD2 A:HIS83 4.2 60.2 1.0
CB A:PHE65 4.6 49.4 1.0
C A:GLN62 4.6 55.7 1.0
CA A:CYS60 4.6 44.9 1.0
C A:CYS63 4.7 53.7 1.0
CG2 A:ILE81 4.7 64.1 1.0
CB A:GLN62 4.7 56.5 1.0
N A:GLN62 4.8 53.1 1.0
CA A:HIS83 4.9 56.6 1.0
CA A:GLN62 4.9 55.6 1.0
O A:CYS63 5.0 50.8 1.0

Zinc binding site 4 out of 8 in 3mhs

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Zinc binding site 4 out of 8 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde


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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn475

b:33.0
occ:1.00
 NE2 A:HIS170 2.1 29.9 1.0
SG A:CYS185 2.2 36.2 1.0
SG A:CYS182 2.3 37.1 1.0
SG A:CYS174 2.4 34.1 1.0
CE1 A:HIS170 3.0 31.2 1.0
CD2 A:HIS170 3.1 26.2 1.0
CB A:CYS182 3.2 37.9 1.0
CB A:CYS174 3.3 36.4 1.0
CB A:CYS185 3.3 33.2 1.0
N A:CYS185 3.4 32.0 1.0
CA A:CYS185 3.8 30.7 1.0
O A:HOH984 4.1 44.6 1.0
ND1 A:HIS170 4.1 26.7 1.0
O A:HOH607 4.2 50.8 1.0
CG A:HIS170 4.2 29.4 1.0
C A:SER184 4.3 29.8 1.0
N A:ARG177 4.4 45.0 1.0
CB A:SER184 4.5 31.2 1.0
CA A:CYS182 4.6 38.3 1.0
CA A:CYS174 4.6 37.0 1.0
OG A:SER252 4.7 40.6 1.0
CA A:ARG177 4.8 46.8 1.0
CA A:SER184 4.8 31.3 1.0
O A:CYS182 4.9 32.9 1.0
C A:CYS182 4.9 35.6 1.0
N A:SER184 4.9 31.2 1.0

Zinc binding site 5 out of 8 in 3mhs

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Zinc binding site 5 out of 8 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde


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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn476

b:23.2
occ:1.00
 ND1 A:HIS276 2.1 24.3 1.0
ND1 A:HIS250 2.1 25.4 1.0
SG A:CYS273 2.3 23.6 1.0
SG A:CYS271 2.3 23.8 1.0
CE1 A:HIS250 2.9 28.4 1.0
CE1 A:HIS276 3.0 26.0 1.0
CG A:HIS276 3.2 21.9 1.0
CG A:HIS250 3.2 26.1 1.0
CB A:CYS271 3.3 29.3 1.0
CB A:CYS273 3.3 24.5 1.0
CB A:HIS276 3.6 21.8 1.0
CB A:HIS250 3.6 23.9 1.0
N A:CYS273 4.1 24.8 1.0
NE2 A:HIS250 4.1 24.6 1.0
NE2 A:HIS276 4.1 21.7 1.0
CA A:CYS273 4.2 24.4 1.0
CD2 A:HIS250 4.2 24.3 1.0
CA A:HIS250 4.2 26.3 1.0
CD2 A:HIS276 4.2 24.6 1.0
N A:HIS276 4.3 21.2 1.0
CA A:HIS276 4.6 20.1 1.0
CA A:CYS271 4.6 30.9 1.0
C A:CYS271 4.8 28.9 1.0
CD2 A:TYR253 4.8 26.4 1.0
C A:CYS273 4.8 25.0 1.0
O A:HIS250 4.9 26.0 1.0
CB A:VAL275 4.9 19.5 1.0
O A:CYS273 5.0 23.7 1.0
C A:HIS250 5.0 28.1 1.0

Zinc binding site 6 out of 8 in 3mhs

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Zinc binding site 6 out of 8 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde


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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn477

b:34.4
occ:1.00
 SG A:CYS336 2.3 38.6 1.0
SG A:CYS339 2.3 32.7 1.0
SG A:CYS289 2.3 29.8 1.0
SG A:CYS292 2.4 45.1 1.0
CB A:CYS336 3.1 35.4 1.0
CB A:CYS289 3.1 30.8 1.0
CB A:CYS339 3.3 40.5 1.0
CB A:CYS292 3.5 50.0 1.0
N A:CYS339 3.6 42.0 1.0
N A:CYS292 3.9 49.4 1.0
CA A:CYS339 4.0 39.5 1.0
O A:HOH609 4.2 42.0 1.0
CA A:CYS292 4.3 50.2 1.0
C A:GLU338 4.6 44.3 1.0
CA A:CYS289 4.6 27.4 1.0
CA A:CYS336 4.6 36.7 1.0
CB A:GLU338 4.7 44.6 1.0
CG A:GLN343 4.8 28.1 1.0
N A:GLU338 4.9 44.5 1.0
CA A:GLU338 5.0 44.1 1.0
C A:GLY291 5.0 49.3 1.0
C A:CYS339 5.0 38.1 1.0

Zinc binding site 7 out of 8 in 3mhs

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Zinc binding site 7 out of 8 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde


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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn100

b:32.9
occ:1.00
 NE2 C:HIS88 2.0 26.6 1.0
SG C:CYS73 2.1 34.3 1.0
SG C:CYS76 2.3 31.9 1.0
SG C:CYS92 2.4 35.4 1.0
CD2 C:HIS88 3.0 26.1 1.0
CE1 C:HIS88 3.0 31.8 1.0
CB C:CYS76 3.2 38.5 1.0
CB C:CYS73 3.2 35.4 1.0
CB C:CYS92 3.2 31.6 1.0
N C:CYS76 3.7 38.5 1.0
CA C:CYS76 4.0 38.9 1.0
ND1 C:HIS88 4.1 27.6 1.0
CG C:HIS88 4.1 25.9 1.0
O C:HOH296 4.2 50.5 1.0
CB C:ASN75 4.4 43.2 1.0
NH1 C:ARG78 4.5 43.3 0.5
C C:ASN75 4.5 41.9 1.0
CA C:CYS73 4.6 36.7 1.0
CA C:CYS92 4.7 31.9 1.0
CA C:ASN75 4.8 43.6 1.0
C C:CYS76 4.9 40.1 1.0
N C:ASN75 4.9 44.4 1.0
O C:CYS73 5.0 39.1 1.0
ND2 C:ASN75 5.0 45.8 1.0
C C:CYS73 5.0 38.7 1.0

Zinc binding site 8 out of 8 in 3mhs

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Zinc binding site 8 out of 8 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde


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 Saga UBP8/SGF11/SUS1/SGF73 Dub Module Bound to Ubiquitin Aldehyde within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn97

b:44.1
occ:1.00
 NE2 E:HIS93 2.0 46.8 1.0
OE2 E:GLU95 2.2 34.4 1.0
SG E:CYS81A 2.3 45.4 1.0
SG E:CYS78 2.3 44.0 1.0
CE1 E:HIS93 2.9 46.4 1.0
CD E:GLU95 3.1 55.0 1.0
CD2 E:HIS93 3.1 48.0 1.0
CB E:CYS78 3.2 40.5 1.0
CB E:CYS81A 3.2 45.5 1.0
OE1 E:GLU95 3.3 52.2 1.0
N E:CYS81A 3.7 45.1 1.0
O E:HOH855 3.9 61.6 1.0
CA E:CYS81A 4.0 44.3 1.0
ND1 E:HIS93 4.1 42.8 1.0
CG E:HIS93 4.2 43.3 1.0
CB E:LYS80 4.3 48.9 1.0
CG E:GLU95 4.5 58.0 1.0
CA E:CYS78 4.6 39.8 1.0
C E:LYS80 4.6 46.8 1.0
C E:CYS81A 4.7 41.3 1.0
O E:LEU94 4.9 58.0 1.0
CA E:LYS80 4.9 47.5 1.0
N E:LYS80 4.9 45.1 1.0
N E:GLY82 4.9 40.1 1.0
O E:HOH449 5.0 72.2 1.0

Reference:

N.L.Samara, A.B.Datta, C.E.Berndsen, X.Zhang, T.Yao, R.E.Cohen, C.Wolberger. Structural Insights Into the Assembly and Function of the Saga Deubiquitinating Module. Science V. 328 1025 2010.
ISSN: ISSN 0036-8075
PubMed: 20395473
DOI: 10.1126/SCIENCE.1190049
Page generated: Sat Oct 26 09:31:50 2024

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