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Zinc in PDB 4fip: Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module

Enzymatic activity of Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module

All present enzymatic activity of Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module:
3.4.19.12;

Protein crystallography data

The structure of Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module, PDB code: 4fip 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) 47.18 / 2.69
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.973, 79.975, 274.259, 90.00, 90.00, 90.00
R / Rfree (%) 18.3 / 26.4

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Zinc atom in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module (pdb code 4fip). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 14 binding sites of Zinc where determined in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module, PDB code: 4fip:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 14 in 4fip

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Zinc binding site 1 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/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(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:39.8
occ:1.00
ND1 A:HIS6 1.9 39.3 1.0
SG A:CYS4 2.1 39.8 1.0
SG A:CYS96 2.2 34.7 1.0
SG A:CYS99 2.3 39.6 1.0
CE1 A:HIS6 2.5 40.0 1.0
CG A:HIS6 3.1 39.7 1.0
CB A:CYS96 3.2 33.3 1.0
CB A:CYS99 3.3 39.8 1.0
CB A:CYS4 3.5 43.3 1.0
N A:CYS99 3.7 40.6 1.0
CB A:HIS6 3.7 40.4 1.0
NE2 A:HIS6 3.8 40.9 1.0
CA A:CYS99 4.0 39.4 1.0
CD2 A:HIS6 4.0 39.6 1.0
CA A:CYS4 4.1 44.2 1.0
N A:HIS6 4.3 42.9 1.0
CD A:PRO5 4.3 41.0 1.0
C A:CYS4 4.5 43.1 1.0
CA A:HIS6 4.6 41.1 1.0
N A:PRO5 4.6 41.2 1.0
CA A:CYS96 4.7 34.1 1.0
C A:LYS98 4.7 41.3 1.0
CB A:LYS98 4.9 44.0 1.0
N A:ILE7 4.9 41.8 1.0
CE1 A:PHE85 5.0 43.0 1.0

Zinc binding site 2 out of 14 in 4fip

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Zinc binding site 2 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/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(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:41.0
occ:1.00
SG A:CYS46 2.1 34.6 1.0
ND1 A:HIS73 2.1 45.9 1.0
SG A:CYS68 2.2 37.8 1.0
SG A:CYS49 2.3 44.8 1.0
CE1 A:HIS73 3.0 44.3 1.0
CB A:CYS46 3.1 36.6 1.0
CG A:HIS73 3.2 43.0 1.0
CB A:CYS68 3.3 35.6 1.0
CB A:CYS49 3.3 44.0 1.0
CB A:HIS73 3.6 40.8 1.0
N A:CYS49 3.8 43.7 1.0
N A:CYS68 4.0 36.4 1.0
ND1 A:HIS71 4.1 41.6 1.0
CA A:CYS49 4.1 44.3 1.0
NE2 A:HIS73 4.2 42.8 1.0
CA A:CYS68 4.2 35.5 1.0
CD2 A:HIS73 4.3 42.2 1.0
CB A:HIS71 4.4 38.8 1.0
CA A:CYS46 4.5 37.3 1.0
CB A:THR48 4.7 39.1 1.0
OG A:SER54 4.7 35.3 1.0
CG A:HIS71 4.7 41.1 1.0
C A:THR48 4.8 41.1 1.0
CB A:SER54 4.8 35.3 1.0
CA A:HIS73 4.8 40.1 1.0
N A:HIS73 4.9 41.1 1.0
C A:CYS49 4.9 46.5 1.0
C A:CYS68 4.9 35.1 1.0

Zinc binding site 3 out of 14 in 4fip

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Zinc binding site 3 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/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(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:35.5
occ:1.00
CE1 A:HIS77 2.0 31.6 1.0
SG A:CYS60 2.2 32.5 1.0
ND1 A:HIS83 2.2 40.4 1.0
SG A:CYS63 2.2 33.2 1.0
NE2 A:HIS77 2.9 31.7 1.0
CE1 A:HIS83 3.1 40.4 1.0
ND1 A:HIS77 3.1 32.5 1.0
CG A:HIS83 3.1 40.1 1.0
CB A:CYS60 3.2 32.6 1.0
CB A:HIS83 3.5 39.6 1.0
CB A:CYS63 3.5 33.4 1.0
N A:CYS63 3.7 36.5 1.0
CD2 A:HIS77 4.1 32.8 1.0
CA A:CYS63 4.1 34.8 1.0
NE2 A:HIS83 4.1 39.2 1.0
CG A:HIS77 4.2 33.5 1.0
CD2 A:HIS83 4.2 40.5 1.0
CB A:PHE65 4.2 30.5 1.0
C A:GLN62 4.5 37.6 1.0
C A:CYS63 4.6 33.3 1.0
CA A:CYS60 4.6 31.3 1.0
O A:CYS63 4.7 34.0 1.0
CG2 A:ILE81 4.7 42.6 1.0
N A:GLN62 4.8 33.9 1.0
CB A:GLN62 4.9 36.9 1.0
N A:PHE65 4.9 31.0 1.0
CA A:GLN62 5.0 37.1 1.0

Zinc binding site 4 out of 14 in 4fip

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Zinc binding site 4 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/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(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:42.4
occ:1.00
CD2 A:HIS250 2.0 37.7 1.0
SG A:CYS271 2.1 42.5 1.0
SG A:CYS273 2.2 36.1 1.0
CD2 A:HIS276 2.3 35.4 1.0
NE2 A:HIS250 3.0 38.6 1.0
CG A:HIS250 3.1 37.9 1.0
CB A:CYS271 3.1 48.2 1.0
CG A:HIS276 3.1 36.0 1.0
NE2 A:HIS276 3.2 35.7 1.0
CB A:CYS273 3.3 36.4 1.0
CB A:HIS250 3.6 38.1 1.0
CB A:HIS276 3.7 35.0 1.0
ND1 A:HIS276 4.1 38.5 1.0
CE1 A:HIS250 4.1 40.6 1.0
CE1 A:HIS276 4.1 36.9 1.0
N A:CYS273 4.1 41.1 1.0
ND1 A:HIS250 4.1 40.0 1.0
CA A:HIS250 4.2 38.8 1.0
CA A:CYS273 4.2 37.4 1.0
N A:HIS276 4.4 31.3 1.0
CA A:CYS271 4.5 51.1 1.0
CA A:HIS276 4.7 33.3 1.0
C A:CYS271 4.7 47.5 1.0
O A:HIS250 4.8 41.6 1.0
CD1 A:TYR253 4.9 40.8 1.0
O A:ALA266 4.9 78.0 1.0
C A:CYS273 4.9 35.4 1.0
C A:HIS250 4.9 41.7 1.0

Zinc binding site 5 out of 14 in 4fip

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Zinc binding site 5 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/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(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:56.1
occ:1.00
SG A:CYS185 2.1 48.5 1.0
SG A:CYS182 2.2 63.9 1.0
SG A:CYS174 2.3 52.3 1.0
CE1 A:HIS170 2.5 43.8 1.0
CB A:CYS185 3.2 43.8 1.0
ND1 A:HIS170 3.2 43.3 1.0
N A:CYS185 3.2 40.9 1.0
CB A:CYS182 3.2 60.6 1.0
CB A:CYS174 3.3 56.2 1.0
CA A:CYS185 3.6 41.9 1.0
NE2 A:HIS170 3.7 44.9 1.0
C A:SER184 4.2 42.7 1.0
CB A:SER184 4.4 45.6 1.0
CG A:HIS170 4.4 43.0 1.0
CA A:CYS182 4.6 59.7 1.0
CA A:CYS174 4.6 58.1 1.0
CA A:SER184 4.6 44.0 1.0
CD2 A:HIS170 4.7 44.0 1.0
N A:SER184 4.7 45.9 1.0
N A:ARG177 4.7 78.5 1.0
C A:CYS182 4.8 52.4 1.0
O A:CYS182 4.8 52.9 1.0

Zinc binding site 6 out of 14 in 4fip

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Zinc binding site 6 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/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(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:80.4
occ:1.00
SG A:CYS292 2.2 72.7 1.0
SG A:CYS336 2.3 71.0 1.0
SG A:CYS289 2.3 74.2 1.0
SG A:CYS339 2.4 82.7 1.0
CB A:CYS292 2.8 74.5 1.0
CB A:CYS336 3.2 74.3 1.0
CB A:CYS289 3.2 72.5 1.0
CB A:CYS339 3.4 85.3 1.0
N A:CYS292 3.5 75.0 1.0
CA A:CYS292 3.7 74.4 1.0
N A:CYS339 4.0 84.6 1.0
CA A:CYS339 4.2 86.1 1.0
CG A:GLU338 4.4 86.1 1.0
C A:CYS292 4.6 72.3 1.0
N A:GLN293 4.6 75.5 1.0
CA A:CYS336 4.6 78.4 1.0
CA A:CYS289 4.7 70.7 1.0
C A:GLY291 4.7 81.0 1.0
C A:CYS339 4.8 87.8 1.0
CB A:ASN294 4.8 80.5 1.0
CB A:SER341 4.8 91.7 1.0

Zinc binding site 7 out of 14 in 4fip

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Zinc binding site 7 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/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(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn101

b:48.0
occ:1.00
NE2 D:HIS93 2.2 39.3 1.0
SG D:CYS78 2.3 35.4 1.0
SG D:CYS81 2.3 36.5 1.0
CE1 D:HIS93 3.1 40.8 1.0
CD2 D:HIS93 3.2 41.4 1.0
CB D:CYS81 3.2 35.6 1.0
CB D:CYS78 3.5 35.4 1.0
N D:CYS81 3.6 39.0 1.0
CA D:CYS81 4.0 36.3 1.0
CD D:LYS80 4.0 55.4 1.0
ND1 D:HIS93 4.2 40.8 1.0
CB D:LYS80 4.3 45.9 1.0
CG D:HIS93 4.3 40.5 1.0
CG D:LYS80 4.4 50.8 1.0
C D:LYS80 4.6 41.2 1.0
CA D:LYS80 4.9 43.1 1.0
N D:LYS80 4.9 42.1 1.0
CA D:CYS78 4.9 34.3 1.0
C D:CYS81 5.0 34.1 1.0

Zinc binding site 8 out of 14 in 4fip

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Zinc binding site 8 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/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(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn501

b:55.3
occ:1.00
SG E:CYS185 2.1 41.9 1.0
CE1 E:HIS170 2.1 45.1 1.0
SG E:CYS174 2.3 49.7 1.0
SG E:CYS182 2.3 45.2 1.0
NE2 E:HIS170 2.8 43.3 1.0
CB E:CYS174 3.1 51.4 1.0
ND1 E:HIS170 3.3 47.2 1.0
CB E:CYS182 3.3 48.6 1.0
CB E:CYS185 3.4 39.4 1.0
N E:CYS185 3.5 38.5 1.0
CA E:CYS185 3.9 38.8 1.0
CD2 E:HIS170 4.0 41.8 1.0
CG E:HIS170 4.3 44.5 1.0
CB E:SER184 4.3 42.9 1.0
C E:SER184 4.3 40.7 1.0
CA E:CYS174 4.4 53.3 1.0
N E:ARG177 4.5 71.9 1.0
CA E:CYS182 4.7 52.1 1.0
CA E:SER184 4.7 42.9 1.0
C E:CYS182 4.9 51.2 1.0
CB E:VAL176 4.9 65.5 1.0
O E:CYS182 5.0 48.4 1.0
N E:SER184 5.0 43.9 1.0

Zinc binding site 9 out of 14 in 4fip

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Zinc binding site 9 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn502

b:39.8
occ:1.00
ND1 E:HIS250 2.1 40.5 1.0
CD2 E:HIS276 2.2 39.5 1.0
SG E:CYS271 2.3 43.2 1.0
SG E:CYS273 2.3 36.6 1.0
CE1 E:HIS250 2.8 41.0 1.0
CB E:CYS271 2.9 51.0 1.0
CG E:HIS276 3.1 38.9 1.0
NE2 E:HIS276 3.2 42.2 1.0
CG E:HIS250 3.2 41.3 1.0
CB E:CYS273 3.4 38.0 1.0
CB E:HIS276 3.5 37.3 1.0
CB E:HIS250 3.8 41.3 1.0
NE2 E:HIS250 4.1 41.0 1.0
ND1 E:HIS276 4.2 40.9 1.0
N E:CYS273 4.2 41.5 1.0
CD2 E:HIS250 4.3 40.4 1.0
CA E:HIS250 4.3 39.9 1.0
CE1 E:HIS276 4.3 40.3 1.0
CA E:CYS271 4.3 56.0 1.0
CA E:CYS273 4.4 39.2 1.0
N E:HIS276 4.4 35.8 1.0
CA E:HIS276 4.6 36.4 1.0
C E:CYS271 4.7 51.6 1.0
CD2 E:TYR253 4.8 46.4 1.0
O E:HIS250 4.9 37.7 1.0
C E:CYS273 5.0 39.3 1.0
O E:CYS271 5.0 46.1 1.0

Zinc binding site 10 out of 14 in 4fip

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Zinc binding site 10 out of 14 in the Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of the Saga UBP8(S144N)/SGF11(1-72, Delta-Znf)/SUS1/SGF73 Dub Module within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn503

b:61.4
occ:1.00
ND1 E:HIS73 2.0 67.8 1.0
SG E:CYS68 2.0 62.5 1.0
SG E:CYS49 2.4 58.7 1.0
SG E:CYS46 2.4 51.0 1.0
CE1 E:HIS73 2.9 68.1 1.0
CG E:HIS73 2.9 66.7 1.0
CB E:CYS68 3.1 59.2 1.0
CB E:CYS46 3.3 53.8 1.0
CB E:HIS73 3.3 63.8 1.0
CB E:CYS49 3.5 62.6 1.0
N E:CYS68 3.9 56.1 1.0
NE2 E:HIS73 4.0 68.9 1.0
CA E:CYS68 4.0 56.9 1.0
CD2 E:HIS73 4.0 66.6 1.0
N E:CYS49 4.1 61.3 1.0
CB E:HIS71 4.1 65.2 1.0
ND1 E:HIS71 4.2 68.4 1.0
CA E:CYS49 4.4 62.5 1.0
OG E:SER54 4.4 59.8 1.0
CB E:SER54 4.6 57.9 1.0
C E:CYS68 4.6 56.5 1.0
CG E:HIS71 4.6 67.2 1.0
CA E:HIS73 4.7 60.4 1.0
CB E:THR48 4.7 58.7 1.0
CA E:CYS46 4.8 55.5 1.0
N E:HIS73 4.8 58.6 1.0
O E:CYS68 4.8 56.0 1.0
N E:HIS71 4.9 63.3 1.0
CA E:HIS71 4.9 65.8 1.0
O E:HIS71 4.9 64.2 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: Wed Dec 16 05:17:39 2020

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