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Zinc in PDB 4fk5: Structure of the Saga UBP8(S144N)/SGF11/SUS1/SGF73 Dub Module

Enzymatic activity of Structure of the Saga UBP8(S144N)/SGF11/SUS1/SGF73 Dub Module

All present enzymatic activity of Structure of the Saga UBP8(S144N)/SGF11/SUS1/SGF73 Dub Module:
3.4.19.12;

Protein crystallography data

The structure of Structure of the Saga UBP8(S144N)/SGF11/SUS1/SGF73 Dub Module, PDB code: 4fk5 was solved by N.L.Samara, A.E.Ringel, C.Wolberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 74.87 / 2.03
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.528, 104.775, 107.018, 90.00, 90.00, 90.00
R / Rfree (%) 17.5 / 21.2

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of the Saga UBP8(S144N)/SGF11/SUS1/SGF73 Dub Module (pdb code 4fk5). 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(S144N)/SGF11/SUS1/SGF73 Dub Module, PDB code: 4fk5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 4fk5

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Zinc binding site 1 out of 8 in the Structure of the Saga UBP8(S144N)/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(S144N)/SGF11/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:38.2
occ:1.00
 SG A:CYS99 2.1 38.9 1.0
ND1 A:HIS6 2.2 44.5 1.0
SG A:CYS4 2.2 37.5 1.0
SG A:CYS96 2.3 36.4 1.0
CE1 A:HIS6 3.0 46.5 1.0
CB A:CYS96 3.1 31.6 1.0
CG A:HIS6 3.3 45.0 1.0
CB A:CYS99 3.3 40.9 1.0
CB A:CYS4 3.5 36.4 1.0
N A:CYS99 3.7 42.0 1.0
CB A:HIS6 3.7 42.1 1.0
CA A:CYS99 4.1 40.5 1.0
CA A:CYS4 4.1 40.5 1.0
N A:HIS6 4.2 45.8 1.0
NE2 A:HIS6 4.2 46.3 1.0
CD A:PRO5 4.2 48.0 1.0
CD2 A:HIS6 4.4 45.1 1.0
N A:PRO5 4.5 46.2 1.0
C A:CYS4 4.5 44.1 1.0
CA A:CYS96 4.6 30.8 1.0
CA A:HIS6 4.6 42.0 1.0
CB A:LYS98 4.7 44.8 1.0
C A:LYS98 4.8 45.4 1.0
O A:HOH794 4.9 45.8 1.0
CE1 A:PHE85 4.9 38.8 1.0
CG A:PRO5 4.9 48.8 1.0

Zinc binding site 2 out of 8 in 4fk5

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Zinc binding site 2 out of 8 in the Structure of the Saga UBP8(S144N)/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(S144N)/SGF11/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:30.2
occ:1.00
 SG A:CYS49 2.2 29.4 1.0
ND1 A:HIS73 2.2 29.0 1.0
SG A:CYS68 2.3 30.7 1.0
SG A:CYS46 2.3 29.8 1.0
CB A:CYS46 3.0 28.6 1.0
CE1 A:HIS73 3.2 32.5 1.0
CG A:HIS73 3.2 31.9 1.0
CB A:CYS68 3.4 29.0 1.0
CB A:CYS49 3.4 30.7 1.0
CB A:HIS73 3.5 30.3 1.0
N A:CYS49 3.7 31.8 1.0
N A:CYS68 4.1 28.7 1.0
CA A:CYS49 4.1 30.1 1.0
CD2 A:HIS71 4.2 40.3 1.0
CB A:HIS71 4.3 38.2 1.0
CA A:CYS68 4.3 28.0 1.0
NE2 A:HIS73 4.4 31.8 1.0
CD2 A:HIS73 4.4 30.4 1.0
CA A:CYS46 4.5 26.9 1.0
OG A:SER54 4.6 30.0 1.0
CB A:THR48 4.6 33.2 1.0
CG A:HIS71 4.6 40.3 1.0
CB A:SER54 4.8 28.5 1.0
C A:THR48 4.8 33.5 1.0
CA A:HIS73 4.8 31.6 1.0
N A:HIS73 4.9 33.0 1.0
C A:CYS49 5.0 30.5 1.0

Zinc binding site 3 out of 8 in 4fk5

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Zinc binding site 3 out of 8 in the Structure of the Saga UBP8(S144N)/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(S144N)/SGF11/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:34.3
occ:1.00
 NE2 A:HIS77 2.0 30.2 1.0
ND1 A:HIS83 2.1 43.4 1.0
SG A:CYS63 2.1 33.0 1.0
SG A:CYS60 2.4 30.4 1.0
CE1 A:HIS77 2.9 33.1 1.0
CE1 A:HIS83 3.1 40.7 1.0
CD2 A:HIS77 3.1 31.0 1.0
CB A:CYS60 3.2 30.3 1.0
CG A:HIS83 3.2 42.4 1.0
CB A:CYS63 3.4 34.6 1.0
CB A:HIS83 3.5 39.0 1.0
N A:CYS63 3.8 36.9 1.0
CA A:CYS63 4.1 35.0 1.0
ND1 A:HIS77 4.1 32.1 1.0
CG A:HIS77 4.2 31.8 1.0
NE2 A:HIS83 4.2 43.2 1.0
CD2 A:HIS83 4.3 42.9 1.0
CB A:PHE65 4.4 30.3 1.0
C A:GLN62 4.5 40.6 1.0
C A:CYS63 4.6 34.9 1.0
CA A:CYS60 4.6 25.9 1.0
O A:CYS63 4.7 33.4 1.0
CB A:GLN62 4.7 41.6 1.0
N A:GLN62 4.8 39.1 1.0
CA A:GLN62 4.9 40.1 1.0
CG2 A:ILE81 4.9 49.8 1.0

Zinc binding site 4 out of 8 in 4fk5

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Zinc binding site 4 out of 8 in the Structure of the Saga UBP8(S144N)/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(S144N)/SGF11/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:34.0
occ:1.00
 NE2 A:HIS170 2.0 31.1 1.0
SG A:CYS185 2.1 31.8 1.0
SG A:CYS182 2.3 36.0 1.0
SG A:CYS174 2.4 35.0 1.0
CD2 A:HIS170 3.0 32.2 1.0
CE1 A:HIS170 3.1 30.8 1.0
CB A:CYS182 3.2 36.3 1.0
CB A:CYS185 3.3 31.1 1.0
CB A:CYS174 3.4 35.0 1.0
N A:CYS185 3.5 29.4 1.0
CA A:CYS185 3.8 28.7 1.0
ND1 A:HIS170 4.2 32.3 1.0
CG A:HIS170 4.2 32.7 1.0
O A:HOH630 4.3 53.0 1.0
C A:SER184 4.3 27.7 1.0
CB A:SER184 4.4 29.7 1.0
N A:ARG177 4.4 54.2 1.0
CA A:CYS182 4.6 36.4 1.0
CA A:CYS174 4.6 37.1 1.0
CA A:SER184 4.8 28.1 1.0
CA A:ARG177 4.9 57.0 1.0
O A:CYS182 4.9 32.9 1.0
N A:SER184 4.9 29.8 1.0
C A:CYS182 5.0 34.4 1.0
CB A:VAL176 5.0 46.9 1.0

Zinc binding site 5 out of 8 in 4fk5

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Zinc binding site 5 out of 8 in the Structure of the Saga UBP8(S144N)/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(S144N)/SGF11/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:23.4
occ:1.00
 ND1 A:HIS276 2.0 21.1 1.0
ND1 A:HIS250 2.1 22.8 1.0
SG A:CYS273 2.3 24.1 1.0
SG A:CYS271 2.3 26.9 1.0
CE1 A:HIS276 2.8 23.9 1.0
CE1 A:HIS250 2.9 24.3 1.0
CG A:HIS276 3.1 23.8 1.0
CG A:HIS250 3.2 22.6 1.0
CB A:CYS273 3.2 24.5 1.0
CB A:CYS271 3.3 28.0 1.0
CB A:HIS276 3.7 22.1 1.0
CB A:HIS250 3.7 22.0 1.0
NE2 A:HIS276 4.0 24.4 1.0
N A:CYS273 4.0 22.7 1.0
NE2 A:HIS250 4.1 24.3 1.0
CA A:CYS273 4.1 24.4 1.0
CA A:HIS250 4.2 22.7 1.0
CD2 A:HIS276 4.2 23.8 1.0
CD2 A:HIS250 4.3 23.4 1.0
N A:HIS276 4.3 22.0 1.0
CA A:CYS271 4.6 29.6 1.0
CA A:HIS276 4.6 22.1 1.0
C A:CYS271 4.8 27.3 1.0
C A:CYS273 4.8 23.1 1.0
O A:HIS250 4.8 24.2 1.0
CD2 A:TYR253 4.8 29.5 1.0
C A:HIS250 4.9 24.9 1.0
O A:CYS273 5.0 22.8 1.0
CB A:VAL275 5.0 21.4 1.0

Zinc binding site 6 out of 8 in 4fk5

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Zinc binding site 6 out of 8 in the Structure of the Saga UBP8(S144N)/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(S144N)/SGF11/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:59.5
occ:1.00
 SG A:CYS292 2.4 61.1 1.0
SG A:CYS289 2.4 63.4 1.0
SG A:CYS336 2.4 66.1 1.0
SG A:CYS339 2.9 83.3 1.0
CB A:CYS289 3.2 64.9 1.0
CB A:CYS336 3.4 70.5 1.0
CB A:CYS292 3.5 66.3 1.0
N A:CYS292 3.7 65.2 1.0
CA A:CYS339 4.0 98.4 1.0
N A:CYS339 4.0 0.9 1.0
N A:CYS336 4.1 72.6 1.0
CB A:CYS339 4.2 93.9 1.0
CA A:CYS292 4.2 65.0 1.0
CA A:CYS336 4.2 75.7 1.0
CB A:ASN294 4.3 68.2 1.0
ND2 A:ASN294 4.4 69.3 1.0
C A:CYS336 4.5 83.9 1.0
C A:GLY291 4.6 66.9 1.0
CA A:CYS289 4.6 65.1 1.0
CA A:GLY291 4.7 67.0 1.0
N A:GLY337 4.9 93.7 1.0
C A:CYS292 4.9 62.0 1.0
N A:ASN294 4.9 59.0 0.8
CG A:ASN294 4.9 74.8 1.0
O A:GLY337 4.9 0.1 1.0
O A:CYS336 4.9 79.0 1.0
N A:GLN293 4.9 58.7 0.7

Zinc binding site 7 out of 8 in 4fk5

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Zinc binding site 7 out of 8 in the Structure of the Saga UBP8(S144N)/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(S144N)/SGF11/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:35.9
occ:1.00
 NE2 C:HIS88 2.0 27.2 1.0
SG C:CYS76 2.3 40.7 1.0
SG C:CYS73 2.3 36.0 1.0
SG C:CYS92 2.5 38.5 1.0
CE1 C:HIS88 3.0 27.9 1.0
CD2 C:HIS88 3.0 26.2 1.0
CB C:CYS73 3.2 35.6 1.0
CB C:CYS92 3.3 37.8 1.0
CB C:CYS76 3.3 42.7 1.0
N C:CYS76 3.7 44.4 1.0
CA C:CYS76 4.1 42.7 1.0
ND1 C:HIS88 4.1 27.9 1.0
CG C:HIS88 4.1 25.5 1.0
CB C:ASN75 4.3 49.7 1.0
CA C:CYS73 4.6 35.9 1.0
C C:ASN75 4.6 48.8 1.0
CA C:CYS92 4.7 37.8 1.0
CA C:ASN75 4.8 47.7 1.0
C C:CYS73 4.9 41.8 1.0
CG2 C:VAL80 4.9 28.6 1.0
N C:ASN75 4.9 49.3 1.0
C C:CYS76 4.9 40.8 1.0
O C:CYS73 5.0 39.8 1.0

Zinc binding site 8 out of 8 in 4fk5

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Zinc binding site 8 out of 8 in the Structure of the Saga UBP8(S144N)/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 8 of Structure of the Saga UBP8(S144N)/SGF11/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:40.0
occ:1.00
 NE2 E:HIS93 1.9 36.0 1.0
SG E:CYS78 2.1 37.6 1.0
SG E:CYS81 2.1 46.7 1.0
CE1 E:HIS93 2.8 35.2 1.0
CD2 E:HIS93 3.0 35.8 1.0
CB E:CYS78 3.0 37.8 1.0
CB E:CYS81 3.3 41.0 1.0
N E:CYS81 3.7 38.5 1.0
ND1 E:HIS93 4.0 35.6 1.0
CA E:CYS81 4.1 39.0 1.0
CG E:HIS93 4.1 35.6 1.0
CB E:LYS80 4.1 49.7 1.0
CA E:CYS78 4.5 36.3 1.0
C E:LYS80 4.7 45.8 1.0
C E:CYS81 4.7 35.4 1.0
CE E:LYS80 4.8 60.5 1.0
N E:GLY82 4.8 33.0 1.0
NZ E:LYS80 4.8 63.0 1.0
CA E:LYS80 4.9 45.3 1.0
N E:LYS80 4.9 43.0 1.0
CB E:LYS83 4.9 31.7 1.0
C E:CYS78 5.0 38.0 1.0

Reference:

N.L.Samara, A.E.Ringel, C.Wolberger. A Role For Intersubunit Interactions in Maintaining Saga Deubiquitinating Module Structure and Activity. Structure V. 20 1414 2012.
ISSN: ISSN 0969-2126
PubMed: 22771212
DOI: 10.1016/J.STR.2012.05.015
Page generated: Sat Oct 26 22:39:49 2024

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