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Zinc in PDB 3m99: Structure of the UBP8-SGF11-SGF73-SUS1 Saga Dub Module

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

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

Protein crystallography data

The structure of Structure of the UBP8-SGF11-SGF73-SUS1 Saga Dub Module, PDB code: 3m99 was solved by A.Kohler, E.Zimmerman, M.Schneider, E.Hurt, N.Zheng, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.12 / 2.70
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 64.424, 103.519, 70.350, 90.00, 108.09, 90.00
R / Rfree (%) 23.4 / 30

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the UBP8-SGF11-SGF73-SUS1 Saga Dub Module (pdb code 3m99). 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 UBP8-SGF11-SGF73-SUS1 Saga Dub Module, PDB code: 3m99:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 3m99

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Zinc binding site 1 out of 7 in the Structure of the UBP8-SGF11-SGF73-SUS1 Saga 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 UBP8-SGF11-SGF73-SUS1 Saga Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn472

b:0.5
occ:1.00
 SG A:CYS96 1.9 0.4 1.0
SG A:CYS99 2.4 87.2 1.0
SG A:CYS4 2.5 84.4 1.0
ND1 A:HIS6 2.6 75.1 1.0
N A:CYS99 2.6 68.9 1.0
CE1 A:HIS6 2.9 76.1 1.0
CB A:CYS99 3.2 54.5 1.0
CG A:HIS6 3.2 75.7 1.0
CB A:CYS96 3.3 60.0 1.0
CB A:LYS98 3.4 70.7 1.0
CA A:CYS99 3.4 68.1 1.0
NE2 A:HIS6 3.6 76.9 1.0
C A:LYS98 3.6 70.4 1.0
CA A:LYS98 3.7 69.2 1.0
N A:LYS98 3.8 65.4 1.0
CD2 A:HIS6 3.8 76.6 1.0
CB A:HIS6 4.0 75.4 1.0
CB A:CYS4 4.1 88.7 1.0
CA A:CYS96 4.2 58.6 1.0
C A:CYS96 4.2 59.3 1.0
O A:CYS96 4.4 60.2 1.0
CA A:CYS4 4.6 90.3 1.0
CG A:LYS98 4.7 72.3 1.0
N A:PHE97 4.7 59.5 1.0
O A:LYS98 4.7 72.6 1.0
C A:CYS99 4.7 67.9 1.0
N A:GLU100 4.8 67.4 1.0
C A:PHE97 5.0 63.4 1.0
CE2 A:PHE85 5.0 65.4 1.0

Zinc binding site 2 out of 7 in 3m99

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Zinc binding site 2 out of 7 in the Structure of the UBP8-SGF11-SGF73-SUS1 Saga 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 UBP8-SGF11-SGF73-SUS1 Saga Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn473

b:89.9
occ:1.00
 ND1 A:HIS73 2.4 64.1 1.0
SG A:CYS49 2.4 67.5 1.0
SG A:CYS68 2.4 64.0 1.0
SG A:CYS46 2.5 61.8 1.0
CB A:CYS49 2.7 69.5 1.0
CE1 A:HIS73 3.1 65.2 1.0
CB A:CYS46 3.1 64.1 1.0
CB A:CYS68 3.3 59.1 1.0
CG A:HIS73 3.3 63.3 1.0
N A:CYS49 3.5 68.5 1.0
CA A:CYS49 3.7 69.3 1.0
CB A:HIS73 3.8 61.9 1.0
ND1 A:HIS71 3.8 72.8 1.0
NE2 A:HIS73 4.1 65.7 1.0
N A:CYS68 4.2 57.3 1.0
CB A:HIS71 4.2 72.5 1.0
CD2 A:HIS73 4.3 64.8 1.0
CA A:CYS68 4.3 58.7 1.0
CG A:HIS71 4.4 73.2 1.0
C A:CYS49 4.6 68.4 1.0
CA A:CYS46 4.6 63.2 1.0
OG A:SER54 4.6 65.5 1.0
N A:HIS50 4.7 68.5 1.0
C A:THR48 4.7 68.7 1.0
CB A:THR48 4.7 64.4 1.0
CB A:SER54 4.8 65.6 1.0
CE1 A:HIS71 4.9 73.3 1.0

Zinc binding site 3 out of 7 in 3m99

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Zinc binding site 3 out of 7 in the Structure of the UBP8-SGF11-SGF73-SUS1 Saga 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 UBP8-SGF11-SGF73-SUS1 Saga Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn474

b:93.3
occ:1.00
 NE2 A:HIS77 2.1 55.5 1.0
ND1 A:HIS83 2.2 76.9 1.0
SG A:CYS63 2.3 0.7 1.0
CE1 A:HIS77 2.3 56.5 1.0
SG A:CYS60 2.4 72.4 1.0
CE1 A:HIS83 2.9 77.4 1.0
CB A:CYS63 3.1 58.6 1.0
CG A:HIS83 3.2 77.3 1.0
CD2 A:HIS77 3.5 55.8 1.0
CB A:CYS60 3.6 57.6 1.0
CB A:HIS83 3.6 76.3 1.0
ND1 A:HIS77 3.7 57.4 1.0
NE2 A:HIS83 4.0 78.4 1.0
CD2 A:HIS83 4.1 78.6 1.0
N A:CYS63 4.1 63.0 1.0
CG A:HIS77 4.2 57.4 1.0
CA A:CYS63 4.2 60.1 1.0
CG2 A:ILE81 4.5 79.2 1.0
CB A:PHE65 4.6 53.6 1.0
CA A:CYS60 5.0 55.9 1.0

Zinc binding site 4 out of 7 in 3m99

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Zinc binding site 4 out of 7 in the Structure of the UBP8-SGF11-SGF73-SUS1 Saga 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 UBP8-SGF11-SGF73-SUS1 Saga Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn475

b:0.2
occ:1.00
 SG A:CYS174 1.8 0.8 1.0
NE2 A:HIS170 2.0 66.8 1.0
CE1 A:HIS170 2.4 67.1 1.0
SG A:CYS182 2.7 86.2 1.0
SG A:CYS185 2.8 65.7 1.0
CB A:CYS174 2.9 98.3 1.0
CD2 A:HIS170 3.3 65.3 1.0
CA A:CYS174 3.5 98.2 1.0
ND1 A:HIS170 3.7 66.0 1.0
N A:CYS185 3.7 63.5 1.0
CB A:CYS182 3.8 87.8 1.0
CB A:CYS185 4.0 64.3 1.0
CG A:HIS170 4.1 64.6 1.0
CB A:SER184 4.1 66.0 1.0
CA A:CYS185 4.2 63.4 1.0
C A:CYS174 4.3 0.5 1.0
C A:SER184 4.5 63.7 1.0
O A:CYS174 4.7 0.1 1.0
N A:CYS174 4.7 95.8 1.0
CG2 A:VAL176 4.7 0.5 1.0
CA A:SER184 4.8 66.3 1.0
CB A:SER252 4.8 64.6 1.0
O A:HOH480 4.9 57.3 1.0
N A:SER184 5.0 70.0 1.0

Zinc binding site 5 out of 7 in 3m99

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Zinc binding site 5 out of 7 in the Structure of the UBP8-SGF11-SGF73-SUS1 Saga 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 UBP8-SGF11-SGF73-SUS1 Saga Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn476

b:81.3
occ:1.00
 ND1 A:HIS250 2.2 65.5 1.0
ND1 A:HIS276 2.3 55.3 1.0
SG A:CYS273 2.5 50.9 1.0
SG A:CYS271 2.6 0.4 1.0
CB A:CYS271 2.7 0.7 1.0
CE1 A:HIS250 2.8 66.7 1.0
CE1 A:HIS276 3.0 55.7 1.0
CB A:CYS273 3.3 62.2 1.0
CG A:HIS250 3.4 65.5 1.0
CG A:HIS276 3.5 54.9 1.0
CB A:HIS276 4.0 53.9 1.0
NE2 A:HIS250 4.0 67.3 1.0
CB A:HIS250 4.0 65.0 1.0
CA A:CYS271 4.2 0.4 1.0
NE2 A:HIS276 4.2 55.9 1.0
N A:CYS273 4.3 66.0 1.0
CD2 A:HIS250 4.3 66.5 1.0
CA A:CYS273 4.3 61.5 1.0
CD2 A:HIS276 4.4 55.4 1.0
CA A:HIS250 4.6 65.2 1.0
N A:HIS276 4.6 53.5 1.0
C A:CYS271 4.8 97.3 1.0
CD2 A:TYR253 4.8 68.9 1.0
O A:CYS273 4.8 56.5 1.0
N A:GLU272 4.9 93.3 1.0
C A:CYS273 4.9 58.1 1.0
O A:HIS250 4.9 67.5 1.0
CA A:HIS276 5.0 53.7 1.0

Zinc binding site 6 out of 7 in 3m99

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Zinc binding site 6 out of 7 in the Structure of the UBP8-SGF11-SGF73-SUS1 Saga 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 UBP8-SGF11-SGF73-SUS1 Saga Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn100

b:0.0
occ:1.00
 SG B:CYS76 1.6 0.8 1.0
NE2 B:HIS88 2.1 59.1 1.0
SG B:CYS73 2.2 99.9 1.0
CB B:CYS76 2.6 0.5 1.0
SG B:CYS92 2.7 0.7 1.0
CB B:CYS73 2.7 91.3 1.0
CD2 B:HIS88 3.1 58.2 1.0
CE1 B:HIS88 3.1 58.6 1.0
N B:CYS76 3.4 0.4 1.0
CA B:CYS76 3.6 0.7 1.0
CB B:CYS92 3.9 84.4 1.0
CA B:CYS73 4.2 90.6 1.0
ND1 B:HIS88 4.2 58.0 1.0
CG B:HIS88 4.3 63.0 1.0
C B:CYS73 4.5 93.0 1.0
C B:CYS76 4.5 0.0 1.0
CG2 B:VAL80 4.5 56.4 1.0
C B:ASN75 4.6 0.0 1.0
O B:CYS73 4.6 92.7 1.0
O B:CYS76 4.7 0.4 1.0
N B:ASN75 5.0 0.9 1.0

Zinc binding site 7 out of 7 in 3m99

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Zinc binding site 7 out of 7 in the Structure of the UBP8-SGF11-SGF73-SUS1 Saga 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 UBP8-SGF11-SGF73-SUS1 Saga Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn105

b:0.4
occ:1.00
 NE2 D:HIS93 2.2 75.6 1.0
SG D:CYS78 2.3 83.9 1.0
SG D:CYS98 2.5 69.0 1.0
SG D:CYS81 2.7 78.5 1.0
CB D:CYS98 3.0 80.2 1.0
CB D:CYS78 3.1 68.7 1.0
CE1 D:HIS93 3.2 75.3 1.0
CB D:CYS81 3.2 74.4 1.0
CD2 D:HIS93 3.2 75.0 1.0
N D:CYS81 3.8 76.9 1.0
CA D:CYS98 3.9 80.6 1.0
CA D:CYS81 4.1 75.3 1.0
ND1 D:HIS93 4.3 74.8 1.0
CG D:HIS93 4.4 74.8 1.0
CA D:CYS78 4.6 68.6 1.0
N D:GLY82 4.9 72.2 1.0
C D:CYS81 4.9 73.8 1.0
C D:CYS98 4.9 81.7 1.0
N D:CYS98 4.9 80.8 1.0
C D:LYS80 5.0 79.0 1.0

Reference:

A.Kohler, E.Zimmerman, M.Schneider, E.Hurt, N.Zheng. Structural Basis For Assembly and Activation of the Heterotetrameric Saga Histone H2B Deubiquitinase Module. Cell(Cambridge,Mass.) V. 141 606 2010.
ISSN: ISSN 0092-8674
PubMed: 20434206
DOI: 10.1016/J.CELL.2010.04.026
Page generated: Sat Oct 26 09:18:15 2024

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