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Zinc in PDB 4w4u: Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution

Enzymatic activity of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution

All present enzymatic activity of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution:
3.4.19.12;

Protein crystallography data

The structure of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution, PDB code: 4w4u was solved by C.Wolberger, M.Yan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.02 / 2.80
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 80.739, 67.273, 137.145, 90.00, 106.84, 90.00
R / Rfree (%) 18.2 / 24.1

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Zinc atom in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution (pdb code 4w4u). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 13 binding sites of Zinc where determined in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution, PDB code: 4w4u:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 13 in 4w4u

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Zinc binding site 1 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:73.7
occ:1.00
 ND1 A:HIS6 2.2 74.9 1.0
SG A:CYS96 2.3 71.3 1.0
SG A:CYS4 2.3 75.0 1.0
SG A:CYS99 2.3 70.5 1.0
CE1 A:HIS6 2.9 73.3 1.0
CG A:HIS6 3.2 74.2 1.0
CB A:CYS96 3.2 64.7 1.0
CB A:CYS99 3.3 70.8 1.0
CB A:CYS4 3.4 76.6 1.0
N A:CYS99 3.7 72.1 1.0
CB A:HIS6 3.7 73.8 1.0
CA A:CYS4 4.0 76.8 1.0
NE2 A:HIS6 4.0 75.4 1.0
CA A:CYS99 4.0 69.5 1.0
CD2 A:HIS6 4.2 73.9 1.0
N A:HIS6 4.3 76.5 1.0
CD A:PRO5 4.5 77.8 1.0
C A:CYS4 4.5 77.8 1.0
N A:PRO5 4.6 78.2 1.0
CA A:CYS96 4.6 61.9 1.0
CA A:HIS6 4.6 74.0 1.0
C A:LYS98 4.6 71.7 1.0
CB A:LYS98 4.7 76.3 1.0
CE1 A:PHE85 4.9 61.2 1.0

Zinc binding site 2 out of 13 in 4w4u

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Zinc binding site 2 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:55.1
occ:1.00
 ND1 A:HIS73 2.1 59.1 1.0
SG A:CYS46 2.3 57.3 1.0
SG A:CYS49 2.3 57.2 1.0
SG A:CYS68 2.3 60.0 1.0
CG A:HIS73 3.1 57.5 1.0
CE1 A:HIS73 3.1 57.3 1.0
CB A:CYS46 3.2 59.8 1.0
CB A:CYS49 3.3 58.9 1.0
CB A:CYS68 3.3 54.4 1.0
CB A:HIS73 3.4 57.9 1.0
N A:CYS49 3.7 62.0 1.0
N A:CYS68 4.0 54.0 1.0
CA A:CYS49 4.1 59.2 1.0
NE2 A:HIS73 4.2 57.2 1.0
CD2 A:HIS73 4.2 55.8 1.0
CA A:CYS68 4.3 52.9 1.0
ND1 A:HIS71 4.4 61.2 1.0
CB A:HIS71 4.4 55.6 1.0
CB A:THR48 4.6 58.9 1.0
CA A:CYS46 4.7 58.9 1.0
C A:THR48 4.7 62.7 1.0
OG A:SER54 4.8 61.3 1.0
CA A:HIS73 4.8 57.0 1.0
CB A:SER54 4.8 60.6 1.0
CG A:HIS71 4.9 57.9 1.0
N A:THR48 4.9 59.0 1.0
C A:CYS68 4.9 51.4 1.0
C A:CYS49 4.9 60.0 1.0
N A:HIS73 5.0 54.5 1.0

Zinc binding site 3 out of 13 in 4w4u

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Zinc binding site 3 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:76.5
occ:1.00
 ND1 A:HIS276 2.1 73.2 1.0
ND1 A:HIS250 2.1 81.5 1.0
SG A:CYS271 2.3 74.5 1.0
SG A:CYS273 2.4 77.2 1.0
CE1 A:HIS250 2.9 80.7 1.0
CE1 A:HIS276 3.0 75.7 1.0
CG A:HIS276 3.1 74.5 1.0
CB A:CYS271 3.2 73.8 1.0
CG A:HIS250 3.2 82.0 1.0
CB A:CYS273 3.3 74.9 1.0
CB A:HIS276 3.5 73.5 1.0
CB A:HIS250 3.7 80.2 1.0
N A:CYS273 4.1 75.5 1.0
NE2 A:HIS250 4.1 83.0 1.0
NE2 A:HIS276 4.1 73.4 1.0
CD2 A:HIS276 4.2 73.3 1.0
N A:HIS276 4.2 66.9 1.0
CA A:CYS273 4.3 74.3 1.0
CD2 A:HIS250 4.3 83.4 1.0
CA A:HIS250 4.3 79.9 1.0
CA A:HIS276 4.5 69.3 1.0
CA A:CYS271 4.5 76.3 1.0
CD2 A:TYR253 4.7 82.5 1.0
C A:CYS271 4.8 78.2 1.0
C A:CYS273 4.8 73.2 1.0
O A:HIS250 4.9 78.5 1.0
N A:GLU272 4.9 79.4 1.0
CB A:VAL275 4.9 69.1 1.0
O A:ALA266 5.0 83.9 1.0
O A:CYS273 5.0 77.6 1.0

Zinc binding site 4 out of 13 in 4w4u

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Zinc binding site 4 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:65.6
occ:1.00
 NE2 A:HIS77 2.1 59.5 1.0
ND1 A:HIS83 2.1 72.2 1.0
SG A:CYS63 2.3 59.3 1.0
SG A:CYS60 2.3 59.2 1.0
CE1 A:HIS77 2.9 59.1 1.0
CG A:HIS83 3.1 71.5 1.0
CE1 A:HIS83 3.1 75.1 1.0
CB A:CYS60 3.3 61.0 1.0
CD2 A:HIS77 3.3 58.2 1.0
CB A:CYS63 3.4 62.1 1.0
CB A:HIS83 3.4 69.3 1.0
N A:CYS63 3.8 67.1 1.0
CA A:CYS63 4.1 63.5 1.0
ND1 A:HIS77 4.1 59.0 1.0
NE2 A:HIS83 4.2 77.4 1.0
CD2 A:HIS83 4.2 72.5 1.0
CG A:HIS77 4.3 58.9 1.0
CB A:PHE65 4.4 54.7 1.0
C A:CYS63 4.5 60.5 1.0
C A:GLN62 4.6 70.8 1.0
O A:CYS63 4.7 61.5 1.0
CA A:CYS60 4.7 61.9 1.0
CG2 A:ILE81 4.8 76.3 1.0
N A:GLN62 4.9 70.9 1.0
CA A:HIS83 4.9 67.5 1.0
CB A:GLN62 5.0 75.3 1.0

Zinc binding site 5 out of 13 in 4w4u

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Zinc binding site 5 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:90.9
occ:1.00
 NE2 A:HIS170 2.1 88.3 1.0
SG A:CYS185 2.3 85.6 1.0
SG A:CYS174 2.3 97.5 1.0
SG A:CYS182 2.3 79.5 1.0
CE1 A:HIS170 3.1 86.8 1.0
CD2 A:HIS170 3.1 86.0 1.0
CB A:CYS174 3.3 94.8 1.0
CB A:CYS182 3.3 85.1 1.0
CB A:CYS185 3.4 83.8 1.0
N A:CYS185 3.6 84.1 1.0
CA A:CYS185 3.9 83.0 1.0
ND1 A:HIS170 4.2 84.0 1.0
CG A:HIS170 4.2 84.4 1.0
CB A:SER184 4.4 84.3 1.0
N A:ARG177 4.5 0.5 1.0
C A:SER184 4.5 82.5 1.0
CA A:CYS174 4.6 94.6 1.0
CA A:CYS182 4.7 87.2 1.0
O A:CYS182 4.8 91.6 1.0
CA A:SER184 4.8 82.6 1.0
C A:CYS182 4.9 89.5 1.0
CA A:ARG177 4.9 0.3 1.0
N A:SER184 4.9 82.5 1.0

Zinc binding site 6 out of 13 in 4w4u

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Zinc binding site 6 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:0.2
occ:1.00
 SG A:CYS339 2.3 0.7 1.0
SG A:CYS336 2.3 0.8 1.0
SG A:CYS292 2.3 0.8 1.0
SG A:CYS289 2.4 0.4 1.0
CB A:CYS336 3.2 0.2 1.0
CB A:CYS339 3.3 0.5 1.0
CB A:CYS292 3.3 1.0 1.0
CB A:CYS289 3.4 0.0 1.0
N A:CYS292 3.5 0.1 1.0
N A:CYS339 3.9 0.6 1.0
CA A:CYS292 3.9 0.8 1.0
CA A:CYS339 4.1 0.8 1.0
C A:GLY291 4.3 0.5 1.0
CA A:GLY291 4.5 0.1 1.0
C A:CYS292 4.5 0.2 1.0
O A:CYS289 4.5 99.6 1.0
CB A:ASN294 4.6 0.3 1.0
CB A:SER341 4.6 0.9 1.0
CA A:CYS336 4.6 0.6 1.0
CA A:CYS289 4.7 0.5 1.0
N A:GLY291 4.7 0.6 1.0
CB A:GLU338 4.7 0.7 1.0
C A:CYS289 4.7 99.5 1.0
C A:GLU338 4.8 0.1 1.0
C A:CYS339 4.8 0.7 1.0
N A:GLN293 4.9 0.7 1.0
N A:ASN294 4.9 0.3 1.0

Zinc binding site 7 out of 13 in 4w4u

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Zinc binding site 7 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:0.7
occ:1.00
 NE2 E:HIS93 2.2 99.8 1.0
SG E:CYS81 2.3 97.4 1.0
SG E:CYS78 2.4 94.5 1.0
CE1 E:HIS93 3.0 0.2 1.0
CB E:CYS81 3.2 97.7 1.0
CD2 E:HIS93 3.3 0.1 1.0
CB E:CYS78 3.4 91.9 1.0
N E:CYS81 3.7 97.7 1.0
CA E:CYS81 4.1 94.1 1.0
ND1 E:HIS93 4.2 0.3 1.0
CG E:HIS93 4.3 99.9 1.0
CB E:LYS80 4.4 0.2 1.0
C E:LYS80 4.7 0.6 1.0
C E:CYS81 4.8 91.6 1.0
CA E:CYS78 4.8 88.7 1.0
CA E:LYS80 4.9 0.8 1.0

Zinc binding site 8 out of 13 in 4w4u

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Zinc binding site 8 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn501

b:76.0
occ:1.00
 ND1 D:HIS6 2.2 78.6 1.0
SG D:CYS4 2.3 73.7 1.0
SG D:CYS99 2.3 73.6 1.0
SG D:CYS96 2.3 74.5 1.0
CE1 D:HIS6 2.9 77.3 1.0
CB D:CYS96 3.2 70.6 1.0
CG D:HIS6 3.2 77.3 1.0
CB D:CYS99 3.3 73.2 1.0
CB D:CYS4 3.4 70.6 1.0
N D:CYS99 3.7 74.5 1.0
CB D:HIS6 3.7 76.4 1.0
CA D:CYS4 4.0 71.7 1.0
NE2 D:HIS6 4.0 78.4 1.0
CA D:CYS99 4.1 71.7 1.0
CD2 D:HIS6 4.2 77.3 1.0
N D:HIS6 4.3 74.2 1.0
CD D:PRO5 4.5 73.4 1.0
C D:CYS4 4.5 77.4 1.0
N D:PRO5 4.6 75.1 1.0
CA D:CYS96 4.6 66.7 1.0
CA D:HIS6 4.6 76.0 1.0
C D:LYS98 4.7 74.2 1.0
CB D:LYS98 4.7 78.1 1.0
CE1 D:PHE85 5.0 67.0 1.0

Zinc binding site 9 out of 13 in 4w4u

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Zinc binding site 9 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn502

b:80.4
occ:1.00
 NE2 D:HIS170 2.2 68.5 1.0
SG D:CYS185 2.3 75.4 1.0
SG D:CYS174 2.3 82.5 1.0
SG D:CYS182 2.4 83.1 1.0
CE1 D:HIS170 3.1 68.1 1.0
CD2 D:HIS170 3.2 66.4 1.0
CB D:CYS182 3.3 92.4 1.0
CB D:CYS174 3.3 84.1 1.0
CB D:CYS185 3.3 76.8 1.0
N D:CYS185 3.5 72.6 1.0
CA D:CYS185 3.8 73.6 1.0
ND1 D:HIS170 4.2 65.1 1.0
CG D:HIS170 4.3 61.3 1.0
N D:ARG177 4.4 0.7 1.0
CB D:SER184 4.4 76.8 1.0
C D:SER184 4.5 76.5 1.0
CA D:CYS182 4.6 99.4 1.0
CA D:CYS174 4.6 85.8 1.0
CA D:ARG177 4.8 0.5 1.0
C D:CYS182 4.8 94.1 1.0
O D:CYS182 4.8 81.8 1.0
CA D:SER184 4.9 80.0 1.0
N D:SER184 4.9 85.9 1.0
N D:SER178 4.9 0.3 1.0

Zinc binding site 10 out of 13 in 4w4u

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Zinc binding site 10 out of 13 in the Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Yeast Saga Dubm with SGF73 Y57A Mutant at 2.8 Angstroms Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn503

b:58.1
occ:1.00
 ND1 D:HIS276 2.1 61.2 1.0
ND1 D:HIS250 2.1 61.3 1.0
SG D:CYS273 2.3 55.0 1.0
SG D:CYS271 2.3 53.8 1.0
CE1 D:HIS250 3.0 61.4 1.0
CE1 D:HIS276 3.0 65.0 1.0
CG D:HIS276 3.1 60.0 1.0
CG D:HIS250 3.3 58.9 1.0
CB D:CYS271 3.3 55.3 1.0
CB D:CYS273 3.3 52.8 1.0
CB D:HIS276 3.5 57.9 1.0
CB D:HIS250 3.7 58.8 1.0
N D:CYS273 4.1 55.1 1.0
NE2 D:HIS276 4.1 68.9 1.0
NE2 D:HIS250 4.2 60.3 1.0
CA D:CYS273 4.2 52.9 1.0
N D:HIS276 4.2 53.8 1.0
CD2 D:HIS276 4.2 66.3 1.0
CA D:HIS250 4.2 60.6 1.0
CD2 D:HIS250 4.3 58.4 1.0
CA D:HIS276 4.5 54.5 1.0
CA D:CYS271 4.6 55.4 1.0
C D:CYS273 4.7 51.6 1.0
CD1 D:TYR253 4.7 55.2 1.0
C D:CYS271 4.8 54.6 1.0
O D:HIS250 4.8 63.4 1.0
N D:GLU272 4.9 56.9 1.0
CB D:VAL275 4.9 50.2 1.0
O D:CYS273 4.9 44.6 1.0

Reference:

M.Yan, C.Wolberger. Uncovering the Role of SGF73 in Maintaining Saga Deubiquitinating Module Structure and Activity. J.Mol.Biol. V. 427 1765 2015.
ISSN: ESSN 1089-8638
PubMed: 25526805
DOI: 10.1016/J.JMB.2014.12.004
Page generated: Wed Aug 20 22:55:54 2025

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