Chlorine in PDB 7vi6: Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila

Enzymatic activity of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila

All present enzymatic activity of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila:
3.2.1.52;

Protein crystallography data

The structure of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila, PDB code: 7vi6 was solved by K.Qian, W.Yang, X.Chen, Y.Wang, M.Zhang, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.46 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 78.926, 81.105, 126.991, 90, 90, 90
R / Rfree (%) 18.3 / 22.6

Other elements in 7vi6:

The structure of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila also contains other interesting chemical elements:

Magnesium (Mg) 5 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila (pdb code 7vi6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 10 binding sites of Chlorine where determined in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila, PDB code: 7vi6:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 10 in 7vi6

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Chlorine binding site 1 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:55.5
occ:1.00
 N A:GLU17 3.4 44.8 1.0
N A:GLU16 3.4 42.1 1.0
CA A:GLY14 3.5 44.5 1.0
C A:GLY14 3.5 44.0 1.0
CB A:GLU16 3.6 53.3 1.0
CG A:GLU17 3.6 45.3 1.0
N A:ALA15 3.6 47.1 1.0
CA A:GLU16 3.9 45.8 1.0
CD A:GLU17 3.9 45.7 1.0
O A:GLY14 4.1 43.5 1.0
C A:GLU16 4.1 44.6 1.0
CB A:GLU17 4.1 40.7 1.0
OE1 A:GLU17 4.1 41.3 1.0
N A:GLY14 4.2 42.8 1.0
C A:ALA15 4.3 41.6 1.0
CA A:GLU17 4.3 42.5 1.0
OE2 A:GLU17 4.5 44.0 1.0
CA A:ALA15 4.5 39.4 1.0
O A:HOH655 4.6 46.0 1.0
CG A:GLU16 4.8 61.2 1.0
CD1 A:LEU281 4.9 48.5 1.0
O A:HOH732 4.9 56.2 1.0

Chlorine binding site 2 out of 10 in 7vi6

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Chlorine binding site 2 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:43.8
occ:1.00
 N A:ALA138 3.2 32.9 1.0
O A:HOH592 3.3 38.9 1.0
CG2 A:THR191 3.7 43.1 1.0
CA A:ASN137 3.8 35.8 1.0
CB A:ALA138 3.8 28.8 1.0
CB A:THR191 3.9 41.1 1.0
O A:HOH646 3.9 55.9 1.0
CE1 A:HIS121 4.0 48.7 1.0
C A:ASN137 4.0 35.0 1.0
CA A:THR191 4.1 38.8 1.0
CB A:ASN137 4.1 35.4 1.0
CA A:ALA138 4.1 33.9 1.0
CD1 A:ILE119 4.1 32.5 1.0
ND1 A:HIS121 4.6 46.9 1.0
C A:THR191 4.7 36.4 1.0
OE1 A:GLN139 4.8 37.9 1.0
CG2 A:ILE119 4.9 39.3 1.0
O A:LYS190 4.9 42.2 1.0
O A:THR191 5.0 32.9 1.0

Chlorine binding site 3 out of 10 in 7vi6

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Chlorine binding site 3 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:49.2
occ:1.00
 O A:HOH663 2.9 56.8 1.0
OG A:SER80 3.1 34.5 1.0
NH2 A:ARG86 3.3 48.8 1.0
NH1 A:ARG67 3.6 50.0 1.0
CB A:SER80 3.8 33.5 1.0
CA A:GLY131 3.8 41.9 1.0
NH1 A:ARG86 4.3 49.0 1.0
CZ A:ARG86 4.3 47.6 1.0
CB A:ALA82 4.4 34.4 1.0
N A:SER83 4.5 34.1 1.0
N A:GLY131 4.5 43.9 1.0
CB A:SER83 4.6 34.5 1.0
CZ A:ARG67 4.7 56.2 1.0
NH2 A:ARG67 4.7 52.1 1.0
O A:PRO130 4.7 54.3 1.0
C A:PRO130 4.9 53.6 1.0
C A:GLY131 4.9 36.2 1.0
O A:GLY131 5.0 36.1 1.0
CA A:SER83 5.0 38.8 1.0

Chlorine binding site 4 out of 10 in 7vi6

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Chlorine binding site 4 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:45.8
occ:1.00
 O A:HOH676 2.9 35.7 1.0
N A:ARG240 3.1 36.4 1.0
NE A:ARG240 3.5 48.7 1.0
CB A:ARG240 3.8 38.1 1.0
CD1 A:PHE239 3.8 37.1 1.0
CA A:PHE239 3.9 32.0 1.0
O A:HOH512 3.9 44.1 1.0
CA A:ARG240 4.0 36.8 1.0
O A:GLY238 4.0 31.4 1.0
C A:PHE239 4.0 33.3 1.0
NH2 A:ARG240 4.1 42.8 1.0
CB A:CYS200 4.2 33.9 1.0
CG A:ARG240 4.2 41.2 1.0
O B:HOH614 4.2 36.1 1.0
CZ A:ARG240 4.3 47.0 1.0
N A:GLY241 4.3 34.1 1.0
CE1 A:PHE239 4.3 37.4 1.0
SG A:CYS200 4.4 41.1 1.0
O A:HOH632 4.4 45.0 1.0
CD A:ARG240 4.5 44.0 1.0
CG A:PHE239 4.5 32.3 1.0
O A:HOH726 4.5 47.3 1.0
C A:ARG240 4.5 39.0 1.0
O A:CYS200 4.7 35.1 1.0
CB A:PHE239 4.7 30.7 1.0
C A:GLY238 4.8 32.2 1.0
N A:PHE239 4.8 33.3 1.0
O A:HOH656 5.0 57.3 1.0
C A:CYS200 5.0 35.9 1.0

Chlorine binding site 5 out of 10 in 7vi6

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Chlorine binding site 5 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:42.3
occ:1.00
 O A:HOH527 3.0 39.7 1.0
O A:HOH661 3.1 55.4 1.0
N A:VAL39 3.2 38.6 1.0
CG2 A:VAL39 3.6 43.4 1.0
CA A:SER38 3.7 39.1 1.0
CB A:SER38 4.0 38.9 1.0
CB A:VAL39 4.0 42.3 1.0
C A:SER38 4.0 34.0 1.0
CD2 A:LEU74 4.2 35.8 1.0
CA A:VAL39 4.2 40.1 1.0
O A:HOH596 4.2 42.8 1.0
O A:HOH739 4.4 51.8 1.0
MG A:MG401 4.5 51.0 1.0
CA A:LEU74 4.5 34.6 1.0
CB A:LEU74 4.6 35.3 1.0
O A:ASP37 4.8 37.7 1.0
O A:LEU74 4.8 36.9 1.0
NE1 A:TRP324 5.0 40.8 1.0

Chlorine binding site 6 out of 10 in 7vi6

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Chlorine binding site 6 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl404

b:55.2
occ:1.00
 N B:ARG186 3.2 38.5 1.0
N B:GLU185 3.6 39.1 1.0
CB B:ARG186 3.6 44.0 1.0
CB B:ASP184 3.6 46.8 1.0
CA B:ARG186 4.0 38.5 1.0
O B:HOH650 4.0 43.6 1.0
CB B:GLU185 4.1 48.0 1.0
C B:GLU185 4.1 42.5 1.0
CA B:GLU185 4.1 40.4 1.0
C B:ASP184 4.2 39.7 1.0
CA B:ASP184 4.3 48.6 1.0
CG B:ASP184 4.4 54.1 1.0
OD2 B:ASP184 4.9 52.2 1.0
O B:ASP184 5.0 36.2 1.0

Chlorine binding site 7 out of 10 in 7vi6

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Chlorine binding site 7 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl405

b:46.9
occ:1.00
 OG B:SER80 3.0 35.7 1.0
O B:HOH657 3.0 51.5 1.0
O B:HOH664 3.1 51.2 1.0
NH1 B:ARG67 3.4 46.5 1.0
NH2 B:ARG86 3.7 45.7 1.0
CB B:SER80 3.8 35.1 1.0
CA B:GLY131 3.8 41.2 1.0
NH1 B:ARG86 4.3 43.8 1.0
CZ B:ARG67 4.4 46.0 1.0
NH2 B:ARG67 4.5 43.5 1.0
CZ B:ARG86 4.5 41.0 1.0
N B:GLY131 4.5 43.2 1.0
N B:SER83 4.5 35.5 1.0
CB B:SER83 4.6 37.8 1.0
CB B:ALA82 4.6 38.3 1.0
O B:PRO130 4.7 43.4 1.0
C B:PRO130 4.8 45.4 1.0
C B:GLY131 5.0 36.6 1.0
CA B:SER83 5.0 34.0 1.0

Chlorine binding site 8 out of 10 in 7vi6

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Chlorine binding site 8 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl406

b:68.9
occ:1.00
 N B:GLU16 3.2 52.8 1.0
N B:GLU17 3.4 52.0 1.0
CB B:GLU16 3.4 58.9 1.0
N B:ALA15 3.5 48.2 1.0
CA B:GLY14 3.6 51.7 1.0
CG B:GLU16 3.6 65.1 1.0
C B:GLY14 3.6 52.8 1.0
OE1 B:GLU16 3.6 76.6 1.0
CG B:GLU17 3.7 49.4 1.0
CA B:GLU16 3.7 54.8 1.0
CD B:GLU16 3.8 78.1 1.0
C B:GLU16 4.0 52.5 1.0
C B:ALA15 4.1 50.8 1.0
CD B:GLU17 4.2 49.6 1.0
CB B:GLU17 4.2 50.5 1.0
O B:GLY14 4.3 48.8 1.0
CA B:GLU17 4.4 49.9 1.0
N B:GLY14 4.4 51.7 1.0
CA B:ALA15 4.4 53.9 1.0
OE1 B:GLU17 4.5 47.6 1.0
OE2 B:GLU17 4.7 50.2 1.0
OE2 B:GLU16 4.8 82.9 1.0
O B:HOH618 4.8 55.6 1.0
CD1 B:LEU281 4.9 49.7 1.0

Chlorine binding site 9 out of 10 in 7vi6

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Chlorine binding site 9 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl407

b:64.1
occ:1.00
 NE B:ARG144 3.2 38.4 1.0
O A:HOH614 3.4 39.2 1.0
O B:HOH511 3.5 53.2 1.0
NH2 B:ARG144 3.6 37.3 1.0
O A:HOH588 3.7 43.3 1.0
CZ B:ARG144 3.9 38.8 1.0
CA B:GLY88 3.9 48.5 1.0
CG B:ARG144 4.1 33.3 1.0
O B:GLY88 4.2 43.3 1.0
CD B:ARG144 4.2 35.3 1.0
C B:GLY88 4.2 50.0 1.0
O A:HOH694 4.4 54.9 1.0
O B:ALA85 4.8 39.1 1.0
CD1 B:ILE93 4.8 34.1 1.0
CG2 B:VAL90 4.9 41.9 1.0
N B:GLY88 5.0 44.4 1.0
O B:HOH521 5.0 53.1 1.0
N B:SER89 5.0 44.0 1.0

Chlorine binding site 10 out of 10 in 7vi6

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Chlorine binding site 10 out of 10 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl408

b:47.4
occ:1.00
 O B:HOH631 3.1 39.9 1.0
N B:ARG240 3.2 36.4 1.0
NE B:ARG240 3.5 43.0 1.0
CD1 B:PHE239 3.7 30.7 1.0
O B:HOH518 3.7 49.2 1.0
CA B:PHE239 3.9 34.0 1.0
NH2 B:ARG240 3.9 47.3 1.0
O B:GLY238 3.9 35.9 1.0
O B:HOH663 4.0 44.4 1.0
CB B:ARG240 4.0 38.3 1.0
C B:PHE239 4.0 33.5 1.0
CA B:ARG240 4.1 38.5 1.0
CB B:CYS200 4.1 32.1 1.0
CE1 B:PHE239 4.1 33.0 1.0
CZ B:ARG240 4.2 46.2 1.0
SG B:CYS200 4.3 44.6 1.0
N B:GLY241 4.3 32.7 1.0
CG B:ARG240 4.3 38.5 1.0
CG B:PHE239 4.4 32.5 1.0
O B:CYS200 4.5 36.5 1.0
O A:HOH536 4.5 41.3 1.0
CD B:ARG240 4.5 43.1 1.0
C B:ARG240 4.6 35.6 1.0
CB B:PHE239 4.7 31.0 1.0
C B:GLY238 4.7 40.6 1.0
N B:PHE239 4.8 39.9 1.0
C B:CYS200 4.9 34.6 1.0
CA B:CYS200 4.9 35.2 1.0

Reference:

K.Qian, W.Yang, X.Chen, Y.Wang, M.Zhang, M.Wang. Functional and Structural Characterization of A GH3 Beta-N-Acetylhexosaminidase From Akkermansia Muciniphila Involved in Mucin Degradation Biochem.Biophys.Res.Commun. V. 589 186 2022.
ISSN: ESSN 1090-2104
DOI: 10.1016/J.BBRC.2021.12.022
Page generated: Tue Jul 30 05:21:54 2024

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