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Magnesium 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:

Chlorine (Cl) 10 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila, PDB code: 7vi6:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in 7vi6

Go back to Magnesium Binding Sites List in 7vi6
Magnesium binding site 1 out of 5 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:51.0
occ:1.00
 O A:HOH661 2.1 55.4 1.0
O A:HOH669 2.2 52.2 1.0
O A:ASP37 2.4 37.7 1.0
O A:HOH695 2.4 57.0 1.0
O A:SER73 2.6 40.7 1.0
O A:HOH699 2.8 55.0 1.0
C A:ASP37 3.6 39.2 1.0
O A:HOH736 3.7 56.8 1.0
C A:SER73 3.7 43.8 1.0
CA A:SER38 4.2 39.1 1.0
CB A:SER38 4.4 38.9 1.0
N A:SER38 4.4 37.8 1.0
O A:HOH706 4.4 56.7 1.0
OD1 A:ASP37 4.4 40.8 1.0
CB A:SER73 4.4 36.9 1.0
CL A:CL407 4.5 42.3 1.0
CG A:ASP37 4.5 44.3 1.0
N A:LEU74 4.5 37.1 1.0
CA A:SER73 4.6 37.7 1.0
OD2 A:ASP37 4.6 44.1 1.0
CA A:ASP37 4.6 41.1 1.0
CA A:LEU74 4.6 34.6 1.0
CD2 A:LEU74 4.9 35.8 1.0

Magnesium binding site 2 out of 5 in 7vi6

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Magnesium binding site 2 out of 5 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:53.4
occ:1.00
 O A:HOH713 2.3 49.7 1.0
O A:HIS55 2.4 38.2 1.0
O A:CYS53 2.6 46.7 1.0
O A:ARG50 2.6 47.9 1.0
O A:HOH535 2.8 50.5 1.0
C A:HIS55 3.4 39.4 1.0
C A:CYS53 3.5 44.3 1.0
C A:ARG50 3.6 42.9 1.0
CD A:PRO57 3.6 37.5 1.0
CB A:CYS53 3.9 38.0 1.0
CA A:ARG50 3.9 42.0 0.5
CA A:ARG50 3.9 42.1 0.5
CA A:HIS56 4.0 36.9 1.0
N A:HIS56 4.0 37.5 1.0
O A:LEU54 4.0 48.5 1.0
O A:HOH728 4.1 52.0 1.0
C A:LEU54 4.1 45.4 1.0
CA A:CYS53 4.1 39.2 1.0
CB A:ARG50 4.3 41.6 0.5
CB A:ARG50 4.3 41.9 0.5
N A:HIS55 4.4 41.2 1.0
N A:CYS53 4.4 42.4 1.0
CA A:HIS55 4.5 40.7 1.0
N A:LEU54 4.5 41.8 1.0
N A:PRO57 4.6 32.6 1.0
CG A:PRO57 4.6 37.7 1.0
CA A:LEU54 4.7 48.0 1.0
CG A:ARG50 4.7 41.1 0.5
O A:HOH688 4.7 52.3 1.0
N A:LYS51 4.8 46.0 1.0
C A:HIS56 4.8 33.7 1.0

Magnesium binding site 3 out of 5 in 7vi6

Go back to Magnesium Binding Sites List in 7vi6
Magnesium binding site 3 out of 5 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg401

b:46.2
occ:1.00
 O B:ASP173 2.3 42.1 1.0
O B:HOH582 2.3 48.9 1.0
O B:HOH693 2.4 44.2 1.0
O B:PHE176 2.4 44.1 1.0
O B:HOH557 2.5 38.6 1.0
O B:HOH680 2.7 48.7 1.0
C B:ASP173 3.4 45.2 1.0
C B:PHE176 3.7 45.1 1.0
N B:ASP173 3.8 37.1 1.0
CA B:ASP173 4.2 42.1 1.0
O B:SER177 4.3 42.7 1.0
N B:PRO174 4.4 44.5 1.0
CA B:SER177 4.4 47.3 1.0
O B:HOH721 4.5 51.9 1.0
C B:SER177 4.5 47.6 1.0
N B:PHE176 4.5 45.2 1.0
O B:HOH720 4.5 43.1 1.0
CA B:PRO174 4.5 48.1 1.0
N B:SER177 4.5 49.1 1.0
C B:PRO174 4.6 47.1 1.0
CA B:PHE176 4.6 44.6 1.0
O B:PRO174 4.7 47.7 1.0
O B:HOH691 4.7 52.3 1.0
O B:LEU178 4.8 42.4 1.0
C B:ALA172 4.8 39.7 1.0
CB B:ASP173 4.9 43.0 1.0

Magnesium binding site 4 out of 5 in 7vi6

Go back to Magnesium Binding Sites List in 7vi6
Magnesium binding site 4 out of 5 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg402

b:53.9
occ:1.00
 O B:SER73 2.4 37.8 1.0
O B:HOH678 2.5 48.9 1.0
O B:ASP37 2.5 40.9 1.0
O B:HOH569 2.5 54.3 1.0
O B:HOH636 2.9 52.1 1.0
C B:SER73 3.4 41.4 1.0
C B:ASP37 3.7 40.5 1.0
CB B:SER73 4.0 41.0 1.0
CA B:SER73 4.1 42.3 1.0
N B:LEU74 4.3 36.6 1.0
OD1 B:ASP37 4.5 46.9 1.0
CA B:ASP37 4.5 44.6 1.0
CG B:ASP37 4.6 46.0 1.0
CA B:LEU74 4.6 36.3 1.0
N B:SER38 4.6 37.9 1.0
OD2 B:ASP37 4.7 44.0 1.0
CA B:SER38 4.7 39.5 1.0
O B:HOH677 4.9 29.9 1.0
CD2 B:LEU74 4.9 39.8 1.0

Magnesium binding site 5 out of 5 in 7vi6

Go back to Magnesium Binding Sites List in 7vi6
Magnesium binding site 5 out of 5 in the Crystal Structure of GH3 Beta-N-Acetylhexosaminidase AMUC_2109 From Akkermansia Muciniphila


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 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg403

b:56.1
occ:1.00
 O B:HOH719 2.3 45.4 1.0
O B:HOH604 2.5 58.4 1.0
O B:HIS55 2.6 45.0 1.0
O B:CYS53 2.6 48.8 1.0
O B:ARG50 2.7 53.9 1.0
C B:HIS55 3.4 49.8 1.0
C B:CYS53 3.6 50.0 1.0
C B:ARG50 3.7 49.0 1.0
CD B:PRO57 3.9 43.0 1.0
O B:LEU54 3.9 47.2 1.0
CA B:HIS56 4.0 41.8 1.0
N B:HIS56 4.0 43.5 1.0
O B:HOH528 4.0 56.7 1.0
C B:LEU54 4.1 52.7 1.0
CB B:CYS53 4.2 43.7 1.0
CA B:ARG50 4.2 47.1 1.0
N B:HIS55 4.4 48.7 1.0
CA B:CYS53 4.4 47.5 1.0
O B:HOH731 4.4 47.5 1.0
CG B:ARG50 4.4 54.9 1.0
CA B:HIS55 4.5 49.5 1.0
CB B:ARG50 4.5 48.2 1.0
N B:LEU54 4.5 51.0 1.0
CA B:LEU54 4.6 53.0 1.0
N B:CYS53 4.7 51.0 1.0
N B:PRO57 4.8 39.9 1.0
N B:LYS51 4.8 51.8 1.0
C B:HIS56 4.9 43.8 1.0
CB B:HIS56 4.9 37.8 1.0
CG B:PRO57 5.0 40.8 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: Thu Oct 3 10:31:13 2024

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