Chlorine in PDB 7pug: GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose

Enzymatic activity of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose

All present enzymatic activity of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose:
3.2.1.131;

Protein crystallography data

The structure of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose, PDB code: 7pug was solved by C.Wilkens, J.P.Morth, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 65.26 / 2.66
Space group P 61 2 2
Cell size a, b, c (Å), α, β, γ (°) 148.63, 148.63, 272.79, 90, 90, 120
R / Rfree (%) 17.4 / 21

Other elements in 7pug:

The structure of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Chlorine Binding Sites:

Pages:

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

Binding sites:

The binding sites of Chlorine atom in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose (pdb code 7pug). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 13 binding sites of Chlorine where determined in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose, PDB code: 7pug:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 13 in 7pug

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Chlorine binding site 1 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl901

b:131.5
occ:1.00
 O A:HOH1009 2.6 118.6 1.0
O A:ASP289 2.9 132.0 1.0
C A:ASP289 3.9 131.0 1.0
OD1 A:ASP291 4.2 109.5 1.0
OD1 A:ASP236 4.6 113.5 1.0
CA A:ASP289 4.6 141.3 1.0
CA A:THR290 4.7 116.8 1.0
N A:THR290 4.7 117.5 1.0
CG A:ASP291 4.9 107.0 1.0
OD2 A:ASP291 4.9 98.7 1.0

Chlorine binding site 2 out of 13 in 7pug

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Chlorine binding site 2 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl902

b:115.0
occ:1.00
 O A:GLY506 2.9 84.3 1.0
CA A:ARG507 3.4 71.6 1.0
O A:ARG507 3.6 75.2 1.0
C A:GLY506 3.7 76.6 1.0
C A:ARG507 3.8 73.9 1.0
N A:ARG507 4.0 73.9 1.0
O A:HOH1092 4.2 75.8 1.0
O A:HOH1147 4.3 75.8 1.0
CB A:ARG507 4.5 73.2 1.0
CG A:ARG507 4.9 72.8 1.0
N A:VAL508 4.9 77.5 1.0
CA A:GLY506 4.9 73.7 1.0

Chlorine binding site 3 out of 13 in 7pug

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Chlorine binding site 3 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl903

b:128.8
occ:1.00
 O A:HOH1238 3.2 107.1 1.0
OD2 A:ASP465 3.2 97.7 1.0
O A:ALA163 3.3 88.5 1.0
OD2 A:ASP164 3.9 100.0 1.0
CG A:ASP465 4.0 97.3 1.0
C A:ALA163 4.1 88.5 1.0
CB A:ASP465 4.3 90.3 1.0
CB A:ASP164 4.4 83.9 1.0
CA A:ALA163 4.6 84.8 1.0
CG A:ASP164 4.7 103.8 1.0
NE1 A:TRP464 4.8 78.1 1.0
CD1 A:TRP464 4.8 77.7 1.0
OD1 A:ASP465 5.0 99.8 1.0
N A:ASP164 5.0 87.7 1.0

Chlorine binding site 4 out of 13 in 7pug

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Chlorine binding site 4 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl904

b:127.8
occ:1.00
 O A:ASP227 4.1 99.5 1.0
CE1 A:TYR194 4.2 88.9 1.0
CD1 A:TYR194 4.3 88.0 1.0
OD2 A:ASP227 4.4 113.7 1.0
CZ A:TYR194 4.5 92.4 1.0
CA A:ASP227 4.5 102.8 1.0
CG A:TYR194 4.6 86.9 1.0
CB A:ASP227 4.7 99.0 1.0
CE2 A:TYR194 4.8 84.9 1.0
C A:ASP227 4.8 103.2 1.0
CD2 A:TYR194 4.8 84.5 1.0
CG A:ASP227 4.8 108.2 1.0

Chlorine binding site 5 out of 13 in 7pug

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Chlorine binding site 5 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl905

b:128.1
occ:1.00
 O A:HOH1295 2.5 101.9 1.0
CB A:ASN758 4.4 101.8 1.0
CD1 A:TRP761 4.4 115.3 1.0
CG A:TRP761 4.5 115.0 1.0
NE1 A:TRP761 4.6 113.6 1.0
CD2 A:TRP761 4.7 119.4 1.0
CE2 A:TRP761 4.8 117.3 1.0
CG A:ASN758 4.9 113.8 1.0
CB A:TRP761 5.0 114.6 1.0

Chlorine binding site 6 out of 13 in 7pug

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Chlorine binding site 6 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl906

b:145.3
occ:1.00
 CE A:MET701 4.4 97.3 1.0

Chlorine binding site 7 out of 13 in 7pug

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Chlorine binding site 7 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl907

b:152.2
occ:1.00
 NZ A:LYS684 2.7 144.3 1.0
OD1 A:ASP679 3.6 114.1 1.0
OD2 A:ASP679 3.6 127.3 1.0
CG A:ASP679 4.0 120.6 1.0
CE A:LYS684 4.1 147.8 1.0
O A:TRP685 4.4 108.6 1.0
CG A:LYS684 4.5 124.3 1.0
CB A:TRP685 4.6 101.7 1.0
O A:ALA677 4.7 132.7 1.0
OH A:TYR674 4.7 99.0 1.0
CD A:LYS684 4.8 137.3 1.0
N A:TRP685 5.0 102.2 1.0

Chlorine binding site 8 out of 13 in 7pug

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Chlorine binding site 8 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl908

b:150.2
occ:1.00
 OE2 A:GLU472 2.9 128.2 1.0
OD2 A:ASP476 3.5 95.8 1.0
OD1 A:ASP476 3.6 86.6 1.0
CD A:GLU472 3.9 128.7 1.0
CG A:ASP476 4.0 89.9 1.0
OE1 A:GLU472 4.2 126.9 1.0

Chlorine binding site 9 out of 13 in 7pug

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Chlorine binding site 9 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl909

b:114.4
occ:1.00
 O A:HOH1281 2.9 90.1 1.0
O A:HOH1290 3.2 89.5 1.0
OH A:TYR690 3.9 83.3 1.0
CD1 A:TYR591 4.0 65.8 1.0
CE1 A:TYR591 4.3 72.7 1.0
CG A:TYR591 4.3 80.1 1.0
SD A:MET588 4.3 105.0 1.0
O A:HOH1280 4.4 74.8 1.0
CE A:MET588 4.5 84.6 1.0
CE1 A:TYR690 4.5 73.5 1.0
CZ A:TYR690 4.5 85.2 1.0
CB A:TYR591 4.7 73.8 1.0
CZ A:TYR591 4.8 82.5 1.0
CD2 A:TYR591 4.8 79.5 1.0

Chlorine binding site 10 out of 13 in 7pug

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Chlorine binding site 10 out of 13 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl910

b:136.2
occ:1.00
 OG1 A:THR342 3.8 162.8 1.0
OE2 A:GLU344 3.8 159.1 1.0
OG1 A:THR349 3.9 111.4 1.0
O A:LYS348 4.1 127.5 1.0
O A:HOH1008 4.4 139.3 1.0
N A:ASP289 4.7 130.0 1.0
O A:THR290 4.8 103.7 1.0
CD A:GLU344 4.8 162.6 1.0
C A:LYS348 4.9 129.4 1.0
OE1 A:GLU344 5.0 167.7 1.0

Reference:

C.Wilkens, M.Vuillemin, B.Pilgaard, I.Polikarpov, J.P.Morth. A GH115 Alpha-Glucuronidase Structure Reveals Dimerization-Mediated Substrate Binding and A Proton Wire Potentially Important For Catalysis. Acta Crystallogr D Struct V. 78 658 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35503213
DOI: 10.1107/S2059798322003527
Page generated: Tue Jul 30 02:43:12 2024

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