Magnesium 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:

Chlorine (Cl) 9 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium 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 Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7vi7

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Magnesium binding site 1 out of 6 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 Magnesium with other atoms in the Mg 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:Mg502

b:53.7
occ:1.00
 O A:HOH765 2.2 49.9 1.0
O A:ASP37 2.3 41.0 1.0
O A:HOH756 2.5 55.3 1.0
O A:HOH779 2.6 62.8 1.0
O A:SER73 2.6 39.9 1.0
O A:HOH774 2.7 48.5 1.0
O A:HOH799 3.4 61.6 1.0
C A:ASP37 3.5 36.2 1.0
C A:SER73 3.7 43.2 1.0
O A:HOH764 3.9 54.0 1.0
CA A:SER38 4.3 36.2 1.0
N A:SER38 4.3 40.1 1.0
CB A:SER73 4.3 40.9 1.0
OD2 A:ASP37 4.4 41.6 1.0
O A:HOH752 4.4 29.2 1.0
CA A:SER73 4.5 39.4 1.0
CB A:SER38 4.5 42.4 1.0
CG A:ASP37 4.5 45.5 1.0
CA A:ASP37 4.5 41.6 1.0
OD1 A:ASP37 4.5 43.4 1.0
N A:LEU74 4.6 33.0 1.0
CA A:LEU74 4.7 35.4 1.0
CD2 A:LEU74 4.9 40.4 1.0

Magnesium binding site 2 out of 6 in 7vi7

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Magnesium binding site 2 out of 6 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 Magnesium with other atoms in the Mg 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:Mg503

b:61.5
occ:1.00
 O A:HOH794 2.4 53.3 1.0
O A:HOH642 2.5 58.3 1.0
O A:ARG50 2.6 52.6 1.0
O A:HIS55 2.8 43.8 1.0
O A:CYS53 2.9 52.6 1.0
C A:ARG50 3.6 52.7 1.0
C A:HIS55 3.6 47.8 1.0
O A:HOH787 3.8 51.1 1.0
C A:CYS53 3.9 44.8 1.0
CD A:PRO57 3.9 43.8 1.0
O A:LEU54 4.0 52.7 1.0
CA A:ARG50 4.0 43.9 0.5
CA A:ARG50 4.0 43.8 0.5
CA A:HIS56 4.1 44.0 1.0
N A:HIS56 4.2 47.4 1.0
C A:LEU54 4.3 48.5 1.0
CB A:ARG50 4.3 47.8 0.5
CB A:ARG50 4.3 47.8 0.5
CB A:CYS53 4.3 43.3 1.0
O A:HOH738 4.5 57.7 1.0
CA A:CYS53 4.6 46.5 1.0
N A:HIS55 4.6 49.6 1.0
CA A:HIS55 4.7 45.1 1.0
N A:LYS51 4.7 52.8 1.0
N A:LEU54 4.8 51.8 1.0
CG A:ARG50 4.8 45.9 0.5
N A:PRO57 4.8 40.8 1.0
N A:CYS53 4.8 49.8 1.0
CG A:ARG50 4.8 45.9 0.5
CA A:LEU54 4.9 48.5 1.0
CG A:PRO57 4.9 41.0 1.0
C A:HIS56 5.0 39.8 1.0

Magnesium binding site 3 out of 6 in 7vi7

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Magnesium binding site 3 out of 6 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 Magnesium with other atoms in the Mg 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
B:Mg502

b:49.1
occ:1.00
 O B:ASP173 2.2 44.5 1.0
O B:PHE176 2.2 47.7 1.0
O B:HOH776 2.4 47.9 1.0
O B:HOH663 2.5 40.1 1.0
O B:HOH720 2.7 54.5 1.0
O B:HOH782 2.9 57.1 1.0
C B:ASP173 3.3 46.6 1.0
C B:PHE176 3.4 48.3 1.0
N B:ASP173 3.7 42.5 1.0
CA B:ASP173 4.1 40.5 1.0
O B:HOH822 4.2 61.3 1.0
CA B:SER177 4.2 50.7 1.0
N B:PHE176 4.2 47.5 1.0
N B:SER177 4.3 53.2 1.0
N B:PRO174 4.3 46.8 1.0
C B:SER177 4.4 50.4 1.0
CA B:PHE176 4.4 48.4 1.0
CA B:PRO174 4.5 48.9 1.0
C B:PRO174 4.5 50.7 1.0
O B:PRO174 4.5 54.8 1.0
O B:LEU178 4.6 44.8 1.0
O B:SER177 4.6 50.2 1.0
O B:HOH799 4.6 44.5 1.0
CB B:ASP173 4.8 44.5 1.0
C B:ALA172 4.8 39.6 1.0
N B:LEU178 4.9 46.4 1.0
O B:HOH786 4.9 52.8 1.0
CB B:PHE176 5.0 42.4 1.0

Magnesium binding site 4 out of 6 in 7vi7

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Magnesium binding site 4 out of 6 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 Magnesium with other atoms in the Mg 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
B:Mg503

b:55.0
occ:1.00
 O B:SER73 2.3 44.5 1.0
O B:HOH627 2.3 52.0 1.0
O B:HOH739 2.4 47.7 1.0
O B:ASP37 2.5 42.9 1.0
O B:HOH781 2.8 58.4 1.0
C B:SER73 3.4 48.4 1.0
C B:ASP37 3.7 43.2 1.0
CB B:SER73 4.1 48.6 1.0
CA B:SER73 4.1 47.2 1.0
OD1 B:ASP37 4.2 44.0 1.0
N B:LEU74 4.5 37.8 1.0
O B:HOH784 4.5 61.3 1.0
CG B:ASP37 4.5 54.5 1.0
N B:SER38 4.6 39.4 1.0
CA B:SER38 4.6 44.2 1.0
CA B:ASP37 4.6 48.3 1.0
CA B:LEU74 4.7 40.3 1.0
O B:HOH761 4.7 31.6 1.0
OD2 B:ASP37 4.8 47.2 1.0
CB B:SER38 4.9 42.3 1.0

Magnesium binding site 5 out of 6 in 7vi7

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Magnesium binding site 5 out of 6 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 Magnesium with other atoms in the Mg 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:Mg504

b:54.2
occ:1.00
 O B:HOH805 2.5 54.2 1.0
O B:ARG50 2.6 56.3 1.0
O B:CYS53 2.6 51.8 1.0
O B:HIS55 2.6 47.1 1.0
O B:HOH613 2.6 58.3 1.0
C B:HIS55 3.5 46.3 1.0
C B:ARG50 3.6 48.8 1.0
C B:CYS53 3.6 50.1 1.0
O B:LEU54 3.9 54.8 1.0
CD B:PRO57 3.9 37.8 1.0
CA B:ARG50 4.0 45.2 1.0
C B:LEU54 4.1 50.5 1.0
CA B:HIS56 4.1 42.4 1.0
N B:HIS56 4.1 44.7 1.0
CB B:CYS53 4.2 44.6 1.0
O B:HOH817 4.2 54.8 1.0
CB B:ARG50 4.3 46.7 1.0
CA B:CYS53 4.3 49.0 1.0
N B:HIS55 4.4 49.4 1.0
N B:CYS53 4.5 47.9 1.0
N B:LEU54 4.5 49.1 1.0
O B:HOH819 4.5 55.1 1.0
CA B:HIS55 4.6 46.0 1.0
CA B:LEU54 4.6 51.1 1.0
N B:LYS51 4.7 52.2 1.0
CG B:ARG50 4.7 52.3 1.0
N B:PRO57 4.8 41.3 1.0
CG B:PRO57 5.0 38.8 1.0

Magnesium binding site 6 out of 6 in 7vi7

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Magnesium binding site 6 out of 6 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 Magnesium with other atoms in the Mg 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:Mg505

b:56.5
occ:1.00
 O B:HOH771 2.7 47.7 1.0
SG B:CYS120 2.9 60.8 1.0
SG B:CYS133 3.0 47.5 1.0
O B:HOH775 3.1 55.0 1.0
O B:HOH700 3.1 47.9 1.0
O B:HOH762 3.5 49.5 1.0
CB B:CYS120 3.6 45.4 1.0
CB B:CYS133 3.6 37.5 1.0
CA B:CYS120 4.3 41.5 1.0
ND2 B:ASN127 4.4 78.6 1.0
O B:HOH779 4.5 54.4 1.0
N B:CYS133 4.5 33.7 1.0
CA B:CYS133 4.7 37.0 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: Fri Dec 24 09:29:05 2021

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