Zinc in PDB 7l0b: Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme

Enzymatic activity of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme

All present enzymatic activity of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme:
3.1.2.6;

Protein crystallography data

The structure of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme, PDB code: 7l0b was solved by J.J.Miller, J.M.Jez, A.R.Odom John, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.96 / 1.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 93.672, 44.757, 105.041, 90, 96.73, 90
R / Rfree (%) 22.7 / 25.1

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme (pdb code 7l0b). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme, PDB code: 7l0b:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Zinc binding site 1 out of 8 in 7l0b

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Zinc binding site 1 out of 8 in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn301

b:32.2
occ:1.00
OD2 A:ASP153 2.2 27.3 1.0
NE2 A:HIS194 2.2 20.4 1.0
NE2 A:HIS63 2.3 26.1 1.0
O A:HOH404 2.3 32.0 1.0
OD2 A:ASP62 2.3 32.2 1.0
O4 A:SO4303 2.5 58.4 1.0
CD2 A:HIS63 3.1 29.0 1.0
CD2 A:HIS194 3.2 23.9 1.0
CG A:ASP153 3.2 28.5 1.0
CE1 A:HIS194 3.2 24.2 1.0
CG A:ASP62 3.3 36.9 1.0
CE1 A:HIS63 3.3 27.9 1.0
ZN A:ZN302 3.3 30.5 1.0
OD1 A:ASP153 3.4 25.8 1.0
S A:SO4303 3.5 44.7 1.0
OD1 A:ASP62 3.5 33.5 1.0
O2 A:SO4303 3.7 51.4 1.0
O1 A:SO4303 3.8 62.8 1.0
CG A:HIS63 4.3 24.5 1.0
ND1 A:HIS194 4.3 24.4 1.0
CG A:HIS194 4.3 21.6 1.0
NE2 A:HIS58 4.4 27.0 1.0
ND1 A:HIS63 4.4 29.5 1.0
CE1 A:HIS58 4.4 24.3 1.0
CB A:ASP153 4.5 26.1 1.0
CB A:ASP62 4.6 33.0 1.0
O3 A:SO4303 4.8 52.5 1.0
OG1 A:THR17 4.9 29.6 1.0

Zinc binding site 2 out of 8 in 7l0b

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Zinc binding site 2 out of 8 in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn302

b:30.5
occ:1.00
O A:HOH404 2.2 32.0 1.0
ND1 A:HIS60 2.3 28.1 1.0
NE2 A:HIS58 2.3 27.0 1.0
NE2 A:HIS136 2.3 29.7 1.0
OD2 A:ASP153 2.4 27.3 1.0
O2 A:SO4303 2.5 51.4 1.0
CE1 A:HIS60 3.2 30.1 1.0
CD2 A:HIS58 3.2 29.5 1.0
CD2 A:HIS136 3.2 27.7 1.0
CE1 A:HIS58 3.3 24.3 1.0
CG A:HIS60 3.3 32.9 1.0
ZN A:ZN301 3.3 32.2 1.0
CE1 A:HIS136 3.4 29.5 1.0
CG A:ASP153 3.4 28.5 1.0
S A:SO4303 3.6 44.7 1.0
CB A:HIS60 3.6 26.6 1.0
CB A:ASP153 3.7 26.1 1.0
O4 A:SO4303 3.8 58.4 1.0
O1 A:SO4303 3.9 62.8 1.0
NE2 A:HIS63 4.1 26.1 1.0
NE2 A:HIS60 4.3 30.8 1.0
CD2 A:HIS63 4.4 29.0 1.0
ND1 A:HIS58 4.4 27.6 1.0
CD2 A:HIS60 4.4 28.7 1.0
CG A:HIS58 4.4 28.2 1.0
CG A:HIS136 4.4 25.3 1.0
ND1 A:HIS136 4.4 32.5 1.0
OD1 A:ASP153 4.5 25.8 1.0
OD1 A:ASP62 4.6 33.5 1.0
CD1 A:LEU165 4.9 34.1 0.5
O3 A:SO4303 4.9 52.5 1.0
OD2 A:ASP62 4.9 32.2 1.0

Zinc binding site 3 out of 8 in 7l0b

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Zinc binding site 3 out of 8 in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn301

b:34.6
occ:1.00
ND1 B:HIS60 2.3 33.8 1.0
NE2 B:HIS136 2.4 31.4 1.0
NE2 B:HIS58 2.4 30.2 1.0
O B:HOH403 2.4 32.3 1.0
OD2 B:ASP153 2.4 25.9 1.0
O1 B:SO4303 2.4 50.1 1.0
CE1 B:HIS60 3.2 38.7 1.0
CD2 B:HIS136 3.3 26.9 1.0
CD2 B:HIS58 3.3 29.4 1.0
ZN B:ZN302 3.3 35.4 1.0
CG B:HIS60 3.3 35.5 1.0
CE1 B:HIS58 3.4 25.1 1.0
CE1 B:HIS136 3.4 26.4 1.0
CG B:ASP153 3.4 33.2 1.0
O4 B:SO4303 3.5 66.0 1.0
S B:SO4303 3.5 51.4 1.0
CB B:HIS60 3.7 27.0 1.0
CB B:ASP153 3.8 32.0 1.0
NE2 B:HIS63 4.3 30.7 1.0
O2 B:SO4303 4.3 58.2 1.0
NE2 B:HIS60 4.3 35.1 1.0
CD2 B:HIS63 4.4 31.2 1.0
CD2 B:HIS60 4.4 37.8 1.0
CG B:HIS136 4.4 26.1 1.0
OD1 B:ASP153 4.4 29.8 1.0
CG B:HIS58 4.4 28.7 1.0
ND1 B:HIS58 4.5 26.2 1.0
ND1 B:HIS136 4.5 30.6 1.0
O3 B:SO4303 4.5 45.2 1.0
OD1 B:ASP62 4.7 39.7 1.0
CD1 B:LEU165 5.0 29.6 1.0

Zinc binding site 4 out of 8 in 7l0b

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Zinc binding site 4 out of 8 in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn302

b:35.4
occ:1.00
NE2 B:HIS194 2.2 29.4 1.0
OD2 B:ASP153 2.2 25.9 1.0
O B:HOH403 2.3 32.3 1.0
O4 B:SO4303 2.4 66.0 1.0
NE2 B:HIS63 2.4 30.7 1.0
OD2 B:ASP62 2.4 37.9 1.0
CD2 B:HIS63 3.0 31.2 1.0
CD2 B:HIS194 3.1 29.5 1.0
CG B:ASP153 3.2 33.2 1.0
CE1 B:HIS194 3.3 30.9 1.0
ZN B:ZN301 3.3 34.6 1.0
CG B:ASP62 3.4 38.7 1.0
OD1 B:ASP153 3.4 29.8 1.0
CE1 B:HIS63 3.5 28.3 1.0
S B:SO4303 3.6 51.4 1.0
OD1 B:ASP62 3.6 39.7 1.0
O1 B:SO4303 3.8 50.1 1.0
O2 B:SO4303 4.3 58.2 1.0
CG B:HIS63 4.3 29.1 1.0
NE2 B:HIS58 4.3 30.2 1.0
CG B:HIS194 4.3 30.5 1.0
ND1 B:HIS194 4.4 36.1 1.0
CE1 B:HIS58 4.4 25.1 1.0
ND1 B:HIS63 4.5 30.0 1.0
CB B:ASP153 4.5 32.0 1.0
O3 B:SO4303 4.6 45.2 1.0
CB B:ASP62 4.7 34.0 1.0
OG1 B:THR17 4.9 35.1 1.0

Zinc binding site 5 out of 8 in 7l0b

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Zinc binding site 5 out of 8 in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn301

b:32.8
occ:1.00
NE2 C:HIS194 2.2 24.9 1.0
O C:HOH403 2.2 30.0 1.0
OD2 C:ASP153 2.3 27.6 1.0
NE2 C:HIS63 2.3 26.0 1.0
OD2 C:ASP62 2.3 34.5 1.0
O4 C:SO4303 2.4 55.1 1.0
CD2 C:HIS63 3.0 30.1 1.0
CD2 C:HIS194 3.1 26.2 1.0
CG C:ASP153 3.2 26.5 1.0
CE1 C:HIS194 3.2 25.7 1.0
CG C:ASP62 3.2 34.4 1.0
ZN C:ZN302 3.3 33.1 1.0
CE1 C:HIS63 3.4 18.6 1.0
OD1 C:ASP153 3.4 26.9 1.0
S C:SO4303 3.5 47.9 1.0
OD1 C:ASP62 3.5 34.5 1.0
O3 C:SO4303 3.6 45.0 1.0
CG C:HIS63 4.3 25.4 1.0
CG C:HIS194 4.3 23.3 1.0
ND1 C:HIS194 4.3 25.7 1.0
NE2 C:HIS58 4.3 28.6 1.0
CE1 C:HIS58 4.4 29.1 1.0
O1 C:SO4303 4.4 63.0 1.0
ND1 C:HIS63 4.4 21.9 1.0
O2 C:SO4303 4.5 57.0 1.0
CB C:ASP153 4.6 22.9 1.0
CB C:ASP62 4.6 31.2 1.0
OG1 C:THR17 4.7 35.5 1.0

Zinc binding site 6 out of 8 in 7l0b

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Zinc binding site 6 out of 8 in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn302

b:33.1
occ:1.00
O C:HOH403 2.2 30.0 1.0
NE2 C:HIS58 2.3 28.6 1.0
ND1 C:HIS60 2.3 27.8 1.0
NE2 C:HIS136 2.3 25.6 1.0
OD2 C:ASP153 2.4 27.6 1.0
O3 C:SO4303 2.4 45.0 1.0
CE1 C:HIS136 3.2 30.5 1.0
CE1 C:HIS60 3.2 33.1 1.0
CD2 C:HIS58 3.2 27.7 1.0
CE1 C:HIS58 3.2 29.1 1.0
CG C:HIS60 3.3 33.2 1.0
ZN C:ZN301 3.3 32.8 1.0
CD2 C:HIS136 3.4 25.7 1.0
CG C:ASP153 3.4 26.5 1.0
CB C:HIS60 3.6 30.0 1.0
S C:SO4303 3.6 47.9 1.0
CB C:ASP153 3.7 22.9 1.0
O4 C:SO4303 3.8 55.1 1.0
NE2 C:HIS63 4.1 26.0 1.0
CD2 C:HIS63 4.3 30.1 1.0
ND1 C:HIS136 4.3 29.0 1.0
NE2 C:HIS60 4.4 32.5 1.0
ND1 C:HIS58 4.4 26.8 1.0
CG C:HIS58 4.4 26.9 1.0
CD2 C:HIS60 4.4 33.9 1.0
OD1 C:ASP153 4.4 26.9 1.0
O2 C:SO4303 4.4 57.0 1.0
CG C:HIS136 4.5 27.9 1.0
OD1 C:ASP62 4.5 34.5 1.0
O1 C:SO4303 4.6 63.0 1.0
OD2 C:ASP62 4.9 34.5 1.0
CD1 C:LEU165 4.9 32.9 1.0

Zinc binding site 7 out of 8 in 7l0b

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Zinc binding site 7 out of 8 in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn301

b:33.4
occ:1.00
NE2 D:HIS136 2.3 27.1 1.0
ND1 D:HIS60 2.3 27.2 1.0
NE2 D:HIS58 2.3 27.5 1.0
O D:HOH401 2.4 30.2 1.0
O3 D:SO4303 2.4 40.2 1.0
OD2 D:ASP153 2.4 25.6 1.0
CE1 D:HIS60 3.2 30.9 1.0
CE1 D:HIS136 3.2 25.1 1.0
CD2 D:HIS58 3.3 26.6 1.0
CE1 D:HIS58 3.3 26.2 1.0
CD2 D:HIS136 3.3 24.3 1.0
CG D:HIS60 3.3 30.9 1.0
ZN D:ZN302 3.3 33.6 1.0
CG D:ASP153 3.4 29.4 1.0
S D:SO4303 3.6 46.1 1.0
CB D:HIS60 3.6 29.3 1.0
CB D:ASP153 3.7 24.7 1.0
O1 D:SO4303 3.8 61.5 1.0
NE2 D:HIS63 4.2 28.9 1.0
NE2 D:HIS60 4.3 29.4 1.0
ND1 D:HIS136 4.4 26.9 1.0
CD2 D:HIS63 4.4 29.3 1.0
ND1 D:HIS58 4.4 23.6 1.0
CG D:HIS58 4.4 24.6 1.0
CG D:HIS136 4.4 23.7 1.0
CD2 D:HIS60 4.4 31.1 1.0
O4 D:SO4303 4.4 58.0 1.0
OD1 D:ASP153 4.5 27.8 1.0
OD1 D:ASP62 4.6 33.5 1.0
O2 D:SO4303 4.6 51.1 1.0
CD1 D:LEU165 4.9 31.6 1.0
OD2 D:ASP62 5.0 34.6 1.0

Zinc binding site 8 out of 8 in 7l0b

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Zinc binding site 8 out of 8 in the Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Crystal Structure of Hydroxyacyl Glutathione Hydrolase (Glob) From Staphylococcus Aureus, Apoenzyme within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn302

b:33.6
occ:1.00
NE2 D:HIS194 2.2 26.4 1.0
OD2 D:ASP153 2.2 25.6 1.0
O D:HOH401 2.3 30.2 1.0
OD2 D:ASP62 2.3 34.6 1.0
NE2 D:HIS63 2.3 28.9 1.0
O1 D:SO4303 2.4 61.5 1.0
CD2 D:HIS63 3.0 29.3 1.0
CD2 D:HIS194 3.1 26.5 1.0
CG D:ASP153 3.2 29.4 1.0
CE1 D:HIS194 3.2 27.9 1.0
CG D:ASP62 3.3 33.6 1.0
ZN D:ZN301 3.3 33.4 1.0
OD1 D:ASP153 3.4 27.8 1.0
OD1 D:ASP62 3.5 33.5 1.0
CE1 D:HIS63 3.5 17.8 1.0
S D:SO4303 3.5 46.1 1.0
O3 D:SO4303 3.6 40.2 1.0
O4 D:SO4303 4.2 58.0 1.0
NE2 D:HIS58 4.3 27.5 1.0
CG D:HIS63 4.3 28.7 1.0
CG D:HIS194 4.3 23.5 1.0
ND1 D:HIS194 4.3 28.6 1.0
CE1 D:HIS58 4.3 26.2 1.0
ND1 D:HIS63 4.5 20.6 1.0
CB D:ASP153 4.5 24.7 1.0
CB D:ASP62 4.6 35.8 1.0
O2 D:SO4303 4.7 51.1 1.0
OG1 D:THR17 4.8 34.8 1.0

Reference:

J.J.Miller, I.T.Shah, J.Hatten, Y.Barekatain, E.A.Mueller, A.M.Moustafa, R.L.Edwaards, C.S.Dowd, P.J.Planet, F.L.Muller, J.M.Jez, A.R.Odom John. Structure-Guided Microbial Targeting of Antistaphylococcal Prodrugs Biorxiv 2020.
DOI: 10.1101/2020.12.15.408237
Page generated: Mon Jan 25 16:48:10 2021

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