Chlorine in PDB 7vi7: Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac

Enzymatic activity of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac

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

Protein crystallography data

The structure of Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac, PDB code: 7vi7 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) 37.79 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 79.243, 81.407, 125.836, 90, 90, 90
R / Rfree (%) 18 / 21.6

Other elements in 7vi7:

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

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac (pdb code 7vi7). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 9 binding sites of Chlorine where determined in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac, PDB code: 7vi7:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 7vi7

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Chlorine binding site 1 out of 9 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl504

b:61.5
occ:1.00
 N A:GLU17 3.1 51.6 1.0
N A:GLU16 3.3 46.4 1.0
CA A:GLY14 3.4 49.0 1.0
CB A:GLU16 3.5 58.5 1.0
CG A:GLU17 3.5 50.8 1.0
C A:GLY14 3.6 50.4 1.0
N A:ALA15 3.7 47.9 1.0
CA A:GLU16 3.7 50.1 1.0
CB A:GLU17 3.9 50.5 1.0
C A:GLU16 3.9 53.4 1.0
CD A:GLU17 3.9 49.6 1.0
CA A:GLU17 4.1 52.0 1.0
O A:GLY14 4.1 49.8 1.0
N A:GLY14 4.2 46.0 1.0
OE1 A:GLU17 4.2 47.1 1.0
C A:ALA15 4.2 47.3 1.0
OE2 A:GLU17 4.5 47.1 1.0
O A:HOH720 4.5 48.5 1.0
CA A:ALA15 4.5 53.2 1.0
CD1 A:LEU281 4.8 50.1 1.0
CG A:GLU16 4.8 65.5 1.0

Chlorine binding site 2 out of 9 in 7vi7

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Chlorine binding site 2 out of 9 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl505

b:51.6
occ:1.00
 N A:ALA138 3.1 36.8 1.0
O A:HOH674 3.1 42.5 1.0
CB A:ALA138 3.6 33.5 1.0
CG2 A:THR191 3.7 42.1 1.0
CA A:ASN137 3.8 38.0 1.0
C A:ASN137 3.9 36.9 1.0
CB A:THR191 3.9 46.0 1.0
CA A:ALA138 3.9 38.0 1.0
CB A:ASN137 4.1 40.6 1.0
CD1 A:ILE119 4.1 34.4 1.0
CA A:THR191 4.1 44.6 1.0
CE1 A:HIS121 4.2 56.8 1.0
OE1 A:GLN139 4.6 41.7 1.0
C A:THR191 4.7 42.4 1.0
O A:LYS190 4.8 43.0 1.0
ND1 A:HIS121 4.8 53.0 1.0
CG2 A:ILE119 4.8 41.0 1.0
O A:THR191 5.0 38.1 1.0

Chlorine binding site 3 out of 9 in 7vi7

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Chlorine binding site 3 out of 9 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl506

b:44.7
occ:1.00
 O A:HOH659 2.8 53.9 1.0
OG A:SER80 3.1 34.4 1.0
NH2 A:ARG86 3.4 47.0 1.0
NH1 A:ARG67 3.5 47.1 1.0
CA A:GLY131 3.7 41.9 1.0
CB A:SER80 3.9 32.0 1.0
NH1 A:ARG86 4.0 44.3 1.0
CZ A:ARG86 4.2 45.5 1.0
CB A:ALA82 4.3 37.2 1.0
N A:GLY131 4.4 45.1 1.0
N A:SER83 4.5 32.9 1.0
CZ A:ARG67 4.5 51.9 1.0
NH2 A:ARG67 4.6 46.5 1.0
CB A:SER83 4.7 35.0 1.0
O A:PRO130 4.7 48.2 1.0
C A:PRO130 4.8 54.3 1.0
C A:GLY131 4.9 38.9 1.0
O A:GLY131 4.9 36.1 1.0

Chlorine binding site 4 out of 9 in 7vi7

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Chlorine binding site 4 out of 9 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl507

b:51.7
occ:1.00
 O A:HOH733 3.1 37.0 1.0
N A:ARG240 3.1 34.3 1.0
NE A:ARG240 3.6 54.4 1.0
CD1 A:PHE239 3.7 36.7 1.0
CA A:PHE239 3.9 34.6 1.0
CB A:ARG240 3.9 42.3 1.0
O A:GLY238 4.0 36.3 1.0
C A:PHE239 4.0 35.4 1.0
CA A:ARG240 4.0 34.7 1.0
NH2 A:ARG240 4.0 46.5 1.0
CE1 A:PHE239 4.2 36.6 1.0
CB A:CYS200 4.2 34.4 1.0
CG A:ARG240 4.2 38.5 1.0
CZ A:ARG240 4.3 56.4 1.0
O A:HOH741 4.3 47.0 1.0
SG A:CYS200 4.3 41.3 1.0
O B:HOH667 4.4 40.7 1.0
N A:GLY241 4.4 33.9 1.0
CG A:PHE239 4.4 35.5 1.0
CD A:ARG240 4.5 44.8 1.0
C A:ARG240 4.6 38.3 1.0
O A:CYS200 4.7 38.9 1.0
CB A:PHE239 4.7 32.6 1.0
C A:GLY238 4.8 35.6 1.0
N A:PHE239 4.8 38.5 1.0
C A:CYS200 5.0 36.9 1.0

Chlorine binding site 5 out of 9 in 7vi7

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Chlorine binding site 5 out of 9 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl506

b:60.0
occ:1.00
 O B:HOH821 2.9 65.7 1.0
N B:ARG186 3.1 42.6 1.0
CB B:ARG186 3.5 45.2 1.0
N B:GLU185 3.6 44.1 1.0
CB B:ASP184 3.6 50.1 1.0
CA B:ARG186 3.9 39.3 1.0
C B:GLU185 4.0 39.7 1.0
CB B:GLU185 4.1 48.0 1.0
CA B:GLU185 4.1 42.7 1.0
C B:ASP184 4.1 42.2 1.0
O B:HOH714 4.3 42.4 1.0
CA B:ASP184 4.3 48.3 1.0
CG B:ASP184 4.5 59.7 1.0
OD2 B:ASP184 4.8 54.9 1.0
CG B:ARG186 4.9 48.1 1.0
O B:HOH624 5.0 55.4 1.0
O B:ASP184 5.0 41.4 1.0

Chlorine binding site 6 out of 9 in 7vi7

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Chlorine binding site 6 out of 9 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl507

b:44.4
occ:1.00
 OG B:SER80 2.9 34.5 1.0
O B:HOH737 3.3 47.4 1.0
NH2 B:ARG86 3.3 42.7 1.0
NH1 B:ARG67 3.4 45.3 1.0
CA B:GLY131 3.8 40.1 1.0
CB B:SER80 3.8 33.9 1.0
CZ B:ARG86 4.3 38.2 1.0
NH1 B:ARG86 4.4 42.9 1.0
N B:SER83 4.4 34.9 1.0
CZ B:ARG67 4.4 51.5 1.0
N B:GLY131 4.5 41.0 1.0
CB B:SER83 4.5 38.6 1.0
NH2 B:ARG67 4.5 42.3 1.0
CB B:ALA82 4.6 38.9 1.0
O B:PRO130 4.7 43.3 1.0
C B:PRO130 4.8 48.1 1.0
CA B:SER83 4.9 37.7 1.0
C B:GLY131 5.0 38.9 1.0

Chlorine binding site 7 out of 9 in 7vi7

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Chlorine binding site 7 out of 9 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl508

b:68.1
occ:1.00
 N B:GLU16 3.1 48.3 1.0
O B:HOH798 3.3 55.1 1.0
N B:GLU17 3.3 51.6 1.0
N B:ALA15 3.4 52.8 1.0
CB B:GLU16 3.4 58.3 1.0
CA B:GLY14 3.5 50.4 1.0
C B:GLY14 3.5 48.0 1.0
CA B:GLU16 3.7 57.0 1.0
CG B:GLU17 3.8 48.3 1.0
C B:GLU16 4.0 51.4 1.0
C B:ALA15 4.0 51.5 1.0
CG B:GLU16 4.1 63.6 1.0
CB B:GLU17 4.2 47.2 1.0
O B:GLY14 4.2 48.0 1.0
CD B:GLU17 4.3 50.9 1.0
CA B:ALA15 4.3 55.0 1.0
CA B:GLU17 4.4 52.9 1.0
N B:GLY14 4.4 52.5 1.0
OE1 B:GLU16 4.5 77.8 1.0
OE1 B:GLU17 4.6 53.1 1.0
CD B:GLU16 4.7 82.9 1.0
OE2 B:GLU17 4.8 46.7 1.0
CD1 B:LEU281 4.9 44.5 1.0
CB B:ALA15 5.0 48.8 1.0

Chlorine binding site 8 out of 9 in 7vi7

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Chlorine binding site 8 out of 9 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila in Complex with Glcnac


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl509

b:70.0
occ:1.00
 NE B:ARG144 3.5 40.5 1.0
O A:HOH711 3.6 50.2 1.0
O B:GLY88 3.8 46.3 1.0
CA B:GLY88 3.8 46.1 1.0
C B:GLY88 3.9 45.5 1.0
O A:HOH694 3.9 45.6 1.0
NH2 B:ARG144 4.2 34.9 1.0
CG B:ARG144 4.3 33.4 1.0
CZ B:ARG144 4.3 37.4 1.0
CD B:ARG144 4.4 36.5 1.0
CD1 B:ILE93 4.5 39.7 1.0
CG2 B:VAL90 4.6 38.4 1.0
N B:SER89 4.8 43.4 1.0
N B:GLY88 4.9 44.2 1.0

Chlorine binding site 9 out of 9 in 7vi7

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


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 in Complex with Glcnac within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl510

b:49.1
occ:1.00
 O A:HOH737 3.1 37.6 1.0
N B:ARG240 3.2 35.1 1.0
NE B:ARG240 3.5 46.1 1.0
CD1 B:PHE239 3.7 32.6 1.0
O B:HOH747 3.8 47.0 1.0
NH2 B:ARG240 3.8 53.6 1.0
CA B:PHE239 3.9 36.1 1.0
O B:GLY238 3.9 34.9 1.0
CB B:ARG240 4.0 38.9 1.0
C B:PHE239 4.1 33.9 1.0
CA B:ARG240 4.1 38.1 1.0
CB B:CYS200 4.1 34.0 1.0
CZ B:ARG240 4.1 51.3 1.0
CE1 B:PHE239 4.1 36.1 1.0
CG B:ARG240 4.3 39.5 1.0
O A:HOH677 4.3 40.5 1.0
SG B:CYS200 4.3 42.0 1.0
N B:GLY241 4.4 35.2 1.0
CG B:PHE239 4.4 32.4 1.0
CD B:ARG240 4.5 45.9 1.0
O B:CYS200 4.5 32.8 1.0
C B:ARG240 4.7 36.5 1.0
CB B:PHE239 4.7 33.3 1.0
C B:GLY238 4.7 40.6 1.0
N B:PHE239 4.8 38.6 1.0
C B:CYS200 4.9 33.7 1.0
CA B:CYS200 4.9 35.3 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 05:22:09 2024

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