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Zinc in PDB 3mhh: Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module

Enzymatic activity of Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module

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

Protein crystallography data

The structure of Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module, PDB code: 3mhh 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) 50.00 / 2.45
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.577, 103.986, 106.076, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 27.3

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 3mhh

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Zinc binding site 1 out of 7 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn472

b:36.8
occ:1.00
 ND1 A:HIS6 2.1 44.7 1.0
SG A:CYS4 2.3 34.8 1.0
SG A:CYS99 2.3 42.4 1.0
SG A:CYS96 2.3 36.8 1.0
CE1 A:HIS6 3.0 41.7 1.0
CG A:HIS6 3.2 41.7 1.0
CB A:CYS4 3.3 36.6 1.0
CB A:CYS96 3.3 33.7 1.0
CB A:CYS99 3.4 43.2 1.0
CB A:HIS6 3.6 37.9 1.0
N A:CYS99 3.8 44.3 1.0
CA A:CYS4 4.0 37.8 1.0
NE2 A:HIS6 4.1 43.2 1.0
CA A:CYS99 4.1 43.7 1.0
N A:HIS6 4.1 38.9 1.0
CD2 A:HIS6 4.3 44.1 1.0
C A:CYS4 4.4 37.9 1.0
CD A:PRO5 4.5 39.8 1.0
N A:PRO5 4.5 38.8 1.0
CA A:HIS6 4.5 38.5 1.0
CB A:LYS98 4.6 46.7 1.0
CA A:CYS96 4.7 33.1 1.0
C A:LYS98 4.8 44.9 1.0
CE2 A:PHE85 4.9 40.8 1.0

Zinc binding site 2 out of 7 in 3mhh

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Zinc binding site 2 out of 7 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn473

b:33.8
occ:1.00
 ND1 A:HIS73 2.3 34.5 1.0
SG A:CYS49 2.3 34.3 1.0
SG A:CYS68 2.3 38.8 1.0
SG A:CYS46 2.3 30.9 1.0
CG A:HIS73 3.2 36.3 1.0
CB A:CYS46 3.3 33.4 1.0
CE1 A:HIS73 3.3 34.4 1.0
CB A:CYS49 3.4 32.4 1.0
CB A:HIS73 3.4 33.4 1.0
CB A:CYS68 3.4 30.6 1.0
N A:CYS49 3.7 31.9 1.0
CB A:HIS71 4.1 36.9 1.0
CA A:CYS49 4.1 32.3 1.0
N A:CYS68 4.2 30.2 1.0
CD2 A:HIS71 4.2 41.0 1.0
CD2 A:HIS73 4.3 37.2 1.0
CA A:CYS68 4.3 31.1 1.0
NE2 A:HIS73 4.4 39.0 1.0
CG A:HIS71 4.5 37.9 1.0
CB A:THR48 4.6 34.4 1.0
OG A:SER54 4.7 29.9 1.0
CA A:CYS46 4.7 31.6 1.0
CA A:HIS73 4.7 34.1 1.0
C A:THR48 4.7 33.8 1.0
CB A:SER54 4.9 30.1 1.0
N A:HIS73 4.9 34.3 1.0
C A:CYS49 4.9 32.3 1.0
C A:CYS68 5.0 32.1 1.0
N A:THR48 5.0 32.6 1.0
CA A:THR48 5.0 33.7 1.0

Zinc binding site 3 out of 7 in 3mhh

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Zinc binding site 3 out of 7 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn474

b:35.7
occ:1.00
 ND1 A:HIS83 2.1 46.4 1.0
NE2 A:HIS77 2.1 26.8 1.0
SG A:CYS63 2.3 33.9 1.0
SG A:CYS60 2.3 33.1 1.0
CE1 A:HIS77 2.8 31.3 1.0
CE1 A:HIS83 2.9 49.6 1.0
CG A:HIS83 3.0 45.9 1.0
CD2 A:HIS77 3.2 29.6 1.0
CB A:CYS60 3.3 33.0 1.0
CB A:HIS83 3.4 46.2 1.0
CB A:CYS63 3.4 35.6 1.0
N A:CYS63 3.7 34.5 1.0
NE2 A:HIS83 4.0 47.0 1.0
CD2 A:HIS83 4.0 47.6 1.0
CA A:CYS63 4.0 34.1 1.0
ND1 A:HIS77 4.0 32.0 1.0
CG A:HIS77 4.3 31.6 1.0
C A:CYS63 4.4 32.1 1.0
C A:GLN62 4.5 36.2 1.0
CB A:PHE65 4.5 29.3 1.0
O A:CYS63 4.6 31.7 1.0
CB A:GLN62 4.7 37.8 1.0
CA A:CYS60 4.8 30.9 1.0
N A:GLN62 4.8 35.5 1.0
CG2 A:ILE81 4.8 56.7 1.0
CA A:HIS83 4.9 46.7 1.0
CA A:GLN62 4.9 36.8 1.0

Zinc binding site 4 out of 7 in 3mhh

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Zinc binding site 4 out of 7 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn475

b:31.9
occ:1.00
 NE2 A:HIS170 2.0 36.6 1.0
SG A:CYS185 2.3 32.2 1.0
SG A:CYS182 2.3 34.0 1.0
SG A:CYS174 2.3 40.5 1.0
CE1 A:HIS170 2.8 34.7 1.0
CD2 A:HIS170 3.1 34.1 1.0
CB A:CYS182 3.3 38.9 1.0
CB A:CYS185 3.4 30.5 1.0
CB A:CYS174 3.4 41.3 1.0
N A:CYS185 3.5 27.6 1.0
CA A:CYS185 3.8 28.6 1.0
O A:HOH478 4.0 49.2 1.0
ND1 A:HIS170 4.0 32.8 1.0
CG A:HIS170 4.2 33.6 1.0
CB A:SER184 4.3 28.9 1.0
C A:SER184 4.4 27.7 1.0
N A:ARG177 4.6 51.6 1.0
CA A:CYS182 4.7 38.4 1.0
CA A:CYS174 4.7 41.8 1.0
CA A:SER184 4.7 28.6 1.0
O A:HOH654 4.8 29.5 1.0
O A:CYS182 4.9 34.8 1.0
N A:SER184 4.9 29.2 1.0
C A:CYS182 4.9 36.5 1.0

Zinc binding site 5 out of 7 in 3mhh

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Zinc binding site 5 out of 7 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn476

b:28.1
occ:1.00
 ND1 A:HIS276 2.0 22.5 1.0
ND1 A:HIS250 2.1 25.1 1.0
SG A:CYS273 2.3 26.6 1.0
SG A:CYS271 2.3 38.2 1.0
CE1 A:HIS276 2.7 23.1 1.0
CE1 A:HIS250 3.1 23.6 1.0
CG A:HIS250 3.1 25.3 1.0
CG A:HIS276 3.2 25.1 1.0
CB A:CYS273 3.3 30.8 1.0
CB A:CYS271 3.3 45.4 1.0
CB A:HIS250 3.4 25.5 1.0
CB A:HIS276 3.7 24.9 1.0
NE2 A:HIS276 3.9 26.5 1.0
CA A:HIS250 4.1 27.2 1.0
CD2 A:HIS276 4.2 24.2 1.0
NE2 A:HIS250 4.2 27.1 1.0
CD2 A:HIS250 4.2 26.1 1.0
CA A:CYS273 4.3 29.7 1.0
N A:CYS273 4.3 32.5 1.0
N A:HIS276 4.4 23.7 1.0
CA A:CYS271 4.7 46.2 1.0
CA A:HIS276 4.7 23.6 1.0
CD2 A:TYR253 4.7 27.5 1.0
O A:HIS250 4.8 29.5 1.0
C A:HIS250 4.8 28.4 1.0
C A:CYS273 4.9 28.5 1.0
C A:CYS271 4.9 42.9 1.0

Zinc binding site 6 out of 7 in 3mhh

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Zinc binding site 6 out of 7 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn100

b:34.4
occ:1.00
 NE2 C:HIS88 2.0 28.9 1.0
SG C:CYS76 2.3 40.1 1.0
SG C:CYS92 2.3 40.2 1.0
SG C:CYS73 2.4 34.8 1.0
CE1 C:HIS88 2.9 32.1 1.0
CD2 C:HIS88 3.0 25.7 1.0
CB C:CYS76 3.2 41.6 1.0
CB C:CYS92 3.2 40.2 1.0
CB C:CYS73 3.2 37.7 1.0
N C:CYS76 3.8 44.2 1.0
ND1 C:HIS88 4.0 30.3 1.0
CG C:HIS88 4.1 30.7 1.0
CA C:CYS76 4.1 43.0 1.0
CB C:ASN75 4.4 47.6 1.0
C C:ASN75 4.5 47.1 1.0
CA C:CYS92 4.7 41.7 1.0
CA C:CYS73 4.7 37.3 1.0
CA C:ASN75 4.9 47.4 1.0
C C:CYS76 4.9 42.1 1.0
C C:CYS73 4.9 40.3 1.0
N C:ASN75 4.9 46.9 1.0
CG2 C:VAL80 5.0 25.8 1.0
O C:CYS73 5.0 40.7 1.0

Zinc binding site 7 out of 7 in 3mhh

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Zinc binding site 7 out of 7 in the Structure of the Saga UBP8/SGF11/SUS1/SGF73 Dub Module


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn97

b:35.7
occ:1.00
 NE2 E:HIS93 2.1 41.0 1.0
SG E:CYS78 2.3 32.9 1.0
O E:HOH163 2.3 34.2 1.0
SG E:CYS81 2.3 40.5 1.0
CE1 E:HIS93 2.9 40.2 1.0
CD2 E:HIS93 3.2 40.3 1.0
CB E:CYS78 3.3 36.0 1.0
CB E:CYS81 3.4 39.4 1.0
N E:CYS81 3.7 40.0 1.0
ND1 E:HIS93 4.1 37.7 1.0
CA E:CYS81 4.1 38.9 1.0
CB E:LYS80 4.2 44.0 1.0
CG E:HIS93 4.3 41.8 1.0
C E:LYS80 4.7 41.9 1.0
CA E:CYS78 4.7 34.9 1.0
C E:CYS81 4.9 35.5 1.0
CA E:LYS80 4.9 43.0 1.0
CG E:LYS80 5.0 50.2 1.0
N E:GLY82 5.0 34.0 1.0
N E:LYS80 5.0 41.8 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 09:29:06 2024

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