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Zinc in PDB 6aqr: Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin

Enzymatic activity of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin

All present enzymatic activity of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin:
3.4.19.12;

Protein crystallography data

The structure of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin, PDB code: 6aqr was solved by M.E.Morrow, M.T.Morgan, C.Wolberger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 76.15 / 2.10
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.755, 103.177, 112.846, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.9

Zinc Binding Sites:

The binding sites of Zinc atom in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin (pdb code 6aqr). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin, PDB code: 6aqr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 6aqr

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Zinc binding site 1 out of 8 in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn501

b:28.9
occ:0.83
 ND1 A:HIS73 2.0 36.6 1.0
SG A:CYS49 2.3 37.0 1.0
SG A:CYS46 2.3 34.2 1.0
SG A:CYS68 2.3 33.8 1.0
CG A:HIS73 3.0 34.1 1.0
CE1 A:HIS73 3.0 36.3 1.0
CB A:CYS46 3.1 34.6 1.0
CB A:HIS73 3.3 34.1 1.0
CB A:CYS68 3.3 30.1 1.0
CB A:CYS49 3.4 38.7 1.0
OG1 A:THR48 3.7 54.3 1.0
N A:CYS49 3.7 35.4 1.0
N A:CYS68 4.1 19.9 1.0
NE2 A:HIS73 4.1 37.5 1.0
CD2 A:HIS73 4.1 37.7 1.0
CA A:CYS49 4.1 33.9 1.0
CA A:CYS68 4.3 26.4 1.0
CB A:HIS71 4.3 36.1 1.0
CD2 A:HIS71 4.3 40.1 1.0
CA A:CYS46 4.6 33.1 1.0
OG A:SER54 4.6 37.3 1.0
CG A:HIS71 4.7 38.1 1.0
CA A:HIS73 4.7 27.6 1.0
CB A:SER54 4.8 30.0 1.0
C A:THR48 4.8 41.0 1.0
N A:HIS73 4.9 27.0 1.0
C A:CYS49 5.0 35.4 1.0

Zinc binding site 2 out of 8 in 6aqr

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Zinc binding site 2 out of 8 in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn502

b:28.6
occ:0.86
 NE2 A:HIS77 1.9 30.7 1.0
ND1 A:HIS83 1.9 36.7 1.0
SG A:CYS63 2.3 34.2 1.0
SG A:CYS60 2.3 35.1 1.0
CE1 A:HIS77 2.8 33.2 1.0
CE1 A:HIS83 2.9 38.5 1.0
CG A:HIS83 2.9 36.0 1.0
CD2 A:HIS77 3.0 34.7 1.0
CB A:CYS60 3.2 29.2 1.0
CB A:HIS83 3.3 32.6 1.0
CB A:CYS63 3.4 32.8 1.0
N A:CYS63 3.7 38.7 1.0
ND1 A:HIS77 4.0 32.3 1.0
NE2 A:HIS83 4.0 41.2 1.0
CD2 A:HIS83 4.1 35.1 1.0
CA A:CYS63 4.1 37.8 1.0
CG A:HIS77 4.1 34.3 1.0
C A:CYS63 4.6 38.0 1.0
C A:GLN62 4.6 42.7 1.0
CB A:GLN62 4.6 46.7 1.0
O A:CYS63 4.6 44.0 1.0
CA A:CYS60 4.7 24.4 1.0
CB A:PHE65 4.8 30.1 1.0
CA A:HIS83 4.8 32.8 1.0
N A:GLN62 4.8 44.6 1.0
CA A:GLN62 4.9 45.0 1.0
CD1 A:PHE65 5.0 30.0 1.0

Zinc binding site 3 out of 8 in 6aqr

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Zinc binding site 3 out of 8 in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn503

b:26.9
occ:0.77
 ND1 A:HIS6 2.1 38.7 1.0
SG A:CYS99 2.2 32.0 1.0
SG A:CYS96 2.3 31.7 1.0
SG A:CYS4 2.3 33.1 1.0
CE1 A:HIS6 3.0 36.7 1.0
CG A:HIS6 3.2 36.9 1.0
CB A:CYS96 3.2 29.7 1.0
CB A:CYS99 3.4 35.9 1.0
CB A:CYS4 3.4 33.6 1.0
CB A:HIS6 3.6 31.9 1.0
N A:CYS99 3.7 39.6 1.0
CA A:CYS4 4.1 29.7 1.0
CA A:CYS99 4.1 38.8 1.0
N A:HIS6 4.1 32.4 1.0
NE2 A:HIS6 4.1 38.9 1.0
CD2 A:HIS6 4.2 41.9 1.0
CD A:PRO5 4.4 37.8 1.0
CA A:HIS6 4.5 33.7 1.0
C A:CYS4 4.5 33.5 1.0
N A:PRO5 4.5 36.5 1.0
CA A:CYS96 4.6 28.3 1.0
CB A:LYS98 4.7 49.2 1.0
C A:LYS98 4.7 41.6 1.0
CE1 A:PHE85 4.8 30.2 1.0
N A:ILE7 4.9 32.5 1.0

Zinc binding site 4 out of 8 in 6aqr

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Zinc binding site 4 out of 8 in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn504

b:24.4
occ:0.83
 NE2 A:HIS170 2.0 30.8 1.0
SG A:CYS185 2.3 31.7 1.0
SG A:CYS182 2.3 32.1 1.0
SG A:CYS174 2.4 34.5 1.0
CE1 A:HIS170 3.0 27.7 1.0
CD2 A:HIS170 3.1 25.0 1.0
CB A:CYS182 3.1 39.1 1.0
CB A:CYS174 3.4 31.7 1.0
CB A:CYS185 3.4 25.6 1.0
N A:CYS185 3.5 24.5 1.0
CA A:CYS185 3.9 23.7 1.0
O A:HOH667 4.0 35.6 0.8
ND1 A:HIS170 4.1 24.8 1.0
CG A:HIS170 4.2 28.9 1.0
CG1 A:VAL176 4.3 42.7 1.0
CB A:SER184 4.4 32.2 1.0
C A:SER184 4.4 27.9 1.0
CA A:CYS182 4.6 39.5 1.0
CA A:CYS174 4.7 28.3 1.0
N A:ARG177 4.8 72.7 1.0
CA A:SER184 4.8 28.5 1.0
O A:CYS182 4.9 37.1 1.0
N A:SER178 4.9 69.2 1.0
C A:CYS182 4.9 33.8 1.0

Zinc binding site 5 out of 8 in 6aqr

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Zinc binding site 5 out of 8 in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn505

b:19.3
occ:0.84
 ND1 A:HIS276 2.0 20.4 1.0
ND1 A:HIS250 2.1 18.6 1.0
SG A:CYS273 2.3 18.8 1.0
SG A:CYS271 2.3 24.4 1.0
CE1 A:HIS276 2.9 25.4 1.0
CE1 A:HIS250 3.0 20.2 1.0
CG A:HIS276 3.1 22.0 1.0
CG A:HIS250 3.2 20.0 1.0
CB A:CYS271 3.2 21.6 1.0
CB A:CYS273 3.3 21.4 1.0
CB A:HIS276 3.6 19.6 1.0
CB A:HIS250 3.6 16.9 1.0
N A:CYS273 4.0 25.2 1.0
NE2 A:HIS276 4.1 26.4 1.0
CA A:HIS250 4.1 19.2 1.0
CA A:CYS273 4.1 23.6 1.0
CD2 A:HIS276 4.2 23.9 1.0
NE2 A:HIS250 4.2 22.6 1.0
N A:HIS276 4.3 19.7 1.0
CD2 A:HIS250 4.3 21.6 1.0
CA A:HIS276 4.6 20.4 1.0
CA A:CYS271 4.6 26.1 1.0
C A:CYS271 4.7 24.1 1.0
O A:HIS250 4.8 24.7 1.0
C A:CYS273 4.8 22.1 1.0
C A:HIS250 4.9 21.6 1.0
CD1 A:TYR253 4.9 23.3 1.0

Zinc binding site 6 out of 8 in 6aqr

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Zinc binding site 6 out of 8 in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn506

b:28.1
occ:0.60
 SG A:CYS336 2.2 43.8 1.0
SG A:CYS292 2.3 50.8 1.0
SG A:CYS289 2.3 49.3 1.0
SG A:CYS339 2.3 43.5 1.0
CB A:CYS289 3.0 33.4 1.0
CB A:CYS336 3.0 44.2 1.0
CB A:CYS292 3.2 49.0 1.0
CB A:CYS339 3.2 42.3 1.0
N A:CYS292 3.3 43.7 1.0
N A:CYS339 3.6 51.1 1.0
CA A:CYS292 3.8 46.9 1.0
CA A:CYS339 4.0 51.0 1.0
C A:GLY291 4.3 53.1 1.0
CB A:ASN294 4.4 59.0 1.0
CA A:GLY291 4.4 57.5 1.0
CA A:CYS336 4.5 50.1 1.0
CA A:CYS289 4.5 39.2 1.0
C A:CYS292 4.6 50.9 1.0
CB A:SER341 4.6 49.6 1.0
C A:CYS339 4.7 49.8 1.0
CB A:GLU338 4.7 64.2 1.0
C A:GLU338 4.7 61.5 1.0
N A:ASN294 4.9 58.7 1.0
N A:GLY291 4.9 56.0 1.0
OH A:TYR334 4.9 53.9 1.0
N A:ASN340 4.9 49.9 1.0
N A:GLN293 4.9 57.3 1.0
N A:SER341 4.9 53.4 1.0

Zinc binding site 7 out of 8 in 6aqr

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Zinc binding site 7 out of 8 in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn101

b:28.4
occ:0.84
 NE2 C:HIS88 1.9 22.3 1.0
SG C:CYS73 2.3 33.6 1.0
SG C:CYS76 2.3 38.7 1.0
SG C:CYS92 2.4 36.6 1.0
CD2 C:HIS88 2.9 23.6 1.0
CE1 C:HIS88 2.9 25.8 1.0
CB C:CYS73 3.2 34.1 1.0
CB C:CYS92 3.3 29.3 1.0
CB C:CYS76 3.3 32.6 1.0
N C:CYS76 3.7 38.8 1.0
ND1 C:HIS88 4.0 24.3 1.0
CG C:HIS88 4.0 22.8 1.0
CA C:CYS76 4.1 33.4 1.0
CB C:ASN75 4.5 38.0 1.0
C C:ASN75 4.5 40.4 1.0
CA C:CYS73 4.7 37.9 1.0
CA C:CYS92 4.7 27.8 1.0
CA C:ASN75 4.8 40.4 1.0
N C:ASN75 4.9 41.6 1.0
ND2 C:ASN75 5.0 32.6 1.0

Zinc binding site 8 out of 8 in 6aqr

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Zinc binding site 8 out of 8 in the Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Saga Dub Module UBP8(C146A)/SGF11/SUS1/SGF73 Bound to Monoubiquitin within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn101

b:33.6
occ:0.78
 NE2 E:HIS93 1.9 30.4 1.0
SG E:CYS78 2.3 37.0 1.0
SG E:CYS81 2.3 41.2 1.0
CE1 E:HIS93 2.9 33.4 1.0
CD2 E:HIS93 2.9 31.2 1.0
CB E:CYS78 3.2 32.4 1.0
CB E:CYS81 3.4 40.1 1.0
N E:CYS81 3.7 38.9 1.0
ND1 E:HIS93 4.0 32.7 1.0
CG E:HIS93 4.1 32.9 1.0
CA E:CYS81 4.1 37.9 1.0
CB E:LYS80 4.6 48.9 1.0
CA E:CYS78 4.7 31.0 1.0
C E:LYS80 4.8 44.5 1.0
C E:CYS81 5.0 34.4 1.0

Reference:

M.E.Morrow, M.T.Morgan, M.Clerici, K.Growkova, M.Yan, D.Komander, T.K.Sixma, M.Simicek, C.Wolberger. Active Site Alanine Mutations Convert Deubiquitinases Into High-Affinity Ubiquitin-Binding Proteins. Embo Rep. V. 19 2018.
ISSN: ESSN 1469-3178
PubMed: 30150323
DOI: 10.15252/EMBR.201745680
Page generated: Mon Oct 28 17:37:45 2024

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