Atomistry » Zinc » PDB 3m6o-3mhm » 3m99
Atomistry »
  Zinc »
    PDB 3m6o-3mhm »
      3m99 »

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

Go back to Zinc Binding Sites List in 3m99
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

Go back to Zinc Binding Sites List in 3m99
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

Go back to Zinc Binding Sites List in 3m99
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

Go back to Zinc Binding Sites List in 3m99
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

Go back to Zinc Binding Sites List in 3m99
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

Go back to Zinc Binding Sites List in 3m99
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

Go back to Zinc Binding Sites List in 3m99
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: Wed Dec 16 04:34:39 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy