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Chlorine in PDB 5oar: Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae

Enzymatic activity of Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae

All present enzymatic activity of Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae:
3.2.1.52;

Protein crystallography data

The structure of Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae, PDB code: 5oar was solved by J.Skerlova, P.Rezacova, J.Brynda, P.Pachl, Z.Otwinowski, O.Vanek, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 23.37 / 2.30
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 105.752, 105.752, 285.807, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 24.1

Other elements in 5oar:

The structure of Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae also contains other interesting chemical elements:

Bromine (Br) 12 atoms
Tantalum (Ta) 6 atoms

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae (pdb code 5oar). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae, PDB code: 5oar:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 5oar

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Chlorine binding site 1 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl708

b:69.3
occ:1.00
 N B:ALA548 3.7 56.2 1.0
CB B:ALA548 3.8 57.1 1.0
CB B:ASP547 3.8 56.2 1.0
CA B:ALA548 4.4 57.9 1.0
CA B:ASP547 4.5 53.6 1.0
C B:ASP547 4.6 53.5 1.0
CG B:ASP547 4.7 57.1 1.0
OE1 B:GLU556 4.9 49.0 1.0

Chlorine binding site 2 out of 12 in 5oar

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Chlorine binding site 2 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl709

b:42.8
occ:1.00
 OG B:SER179 3.5 34.5 1.0
NZ B:LYS177 3.8 58.5 1.0
CG B:LYS177 3.8 51.2 1.0
CB A:ARG28 3.9 41.5 1.0
C B:ASP178 4.1 36.5 1.0
N B:SER179 4.1 36.0 1.0
CG A:ARG28 4.1 42.4 1.0
N B:ASP178 4.2 39.1 1.0
CB B:SER179 4.2 35.8 1.0
CA B:ASP178 4.2 37.8 1.0
O B:LYS177 4.3 40.8 1.0
C B:LYS177 4.3 40.8 1.0
CE B:LYS177 4.3 57.8 1.0
NH1 A:ARG28 4.4 43.4 1.0
CZ A:ARG28 4.5 43.8 1.0
O B:ASP178 4.6 36.2 1.0
OE2 A:GLU29 4.6 61.3 1.0
CD B:LYS177 4.7 54.6 1.0
CA B:SER179 4.8 35.4 1.0
NH2 A:ARG28 4.8 44.4 1.0
NE A:ARG28 4.9 42.8 1.0
CB B:LYS177 4.9 47.1 1.0

Chlorine binding site 3 out of 12 in 5oar

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Chlorine binding site 3 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl710

b:59.2
occ:1.00
 NE B:ARG432 3.2 63.7 1.0
CD B:ARG432 3.6 65.4 1.0
NZ B:LYS412 4.0 67.8 1.0
CZ B:ARG432 4.2 61.6 1.0
CE B:LYS412 4.3 66.7 1.0
NH2 B:ARG432 4.4 58.3 1.0
CB B:ARG432 4.7 60.4 1.0
CG B:ARG432 4.8 63.2 1.0

Chlorine binding site 4 out of 12 in 5oar

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Chlorine binding site 4 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl711

b:47.7
occ:1.00
 NH1 B:ARG459 3.8 49.0 1.0
O B:GLY480 3.8 42.4 1.0
C B:GLY480 4.0 40.7 1.0
CA B:TRP482 4.0 39.6 1.0
N B:TRP482 4.0 38.9 1.0
OD1 B:ASN478 4.1 46.6 1.0
O B:HOH850 4.2 36.6 1.0
CA B:GLY480 4.3 40.7 1.0
CB B:TRP482 4.3 39.5 1.0
ND2 B:ASN478 4.3 44.0 1.0
C B:SER481 4.4 39.5 1.0
CG B:ASN478 4.5 44.6 1.0
N B:SER481 4.5 39.2 1.0
CE1 B:PHE473 4.8 44.2 1.0
CZ B:ARG459 4.8 50.0 1.0
O B:SER481 4.9 40.7 1.0
CA B:SER481 4.9 39.0 1.0
N B:GLY480 5.0 41.5 1.0

Chlorine binding site 5 out of 12 in 5oar

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Chlorine binding site 5 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl712

b:62.4
occ:1.00
 CB B:ASP119 3.7 41.7 1.0
N B:ASP119 3.7 40.9 1.0
CA B:ASP119 4.3 40.3 1.0
O B:ASP119 4.7 38.0 1.0
CA B:ALA118 4.7 43.3 1.0
C B:ALA118 4.7 41.4 1.0
CG B:GLN121 4.8 37.4 1.0
C B:ASP119 4.8 39.2 1.0
CG B:ASP119 5.0 43.8 1.0
O B:GLU117 5.0 43.6 1.0

Chlorine binding site 6 out of 12 in 5oar

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Chlorine binding site 6 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl713

b:76.0
occ:1.00
 NE B:ARG368 3.7 70.2 1.0
NH2 B:ARG368 3.8 67.6 1.0
CZ B:ARG368 4.2 68.7 1.0
CZ2 B:TRP361 4.2 67.5 1.0
CD B:ARG368 4.6 67.3 1.0
CG B:ARG368 4.6 69.1 1.0
CH2 B:TRP361 4.7 65.9 1.0
CB B:ASP372 4.8 64.5 1.0
CG B:ASP372 5.0 65.9 1.0

Chlorine binding site 7 out of 12 in 5oar

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Chlorine binding site 7 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl714

b:54.8
occ:1.00
 N B:PHE473 3.4 50.2 1.0
CA B:PHE473 3.6 47.9 1.0
C B:ASN472 3.7 54.4 1.0
ND2 B:ASN478 3.7 44.0 1.0
N B:ASN478 3.9 42.5 1.0
CA B:ASN472 4.0 57.2 1.0
CG B:ASN478 4.1 44.6 1.0
CA B:GLY477 4.2 48.6 1.0
O B:ASN472 4.3 56.1 1.0
CB B:PHE473 4.4 46.5 1.0
OD1 B:ASN478 4.5 46.6 1.0
C B:GLY477 4.6 44.4 1.0
CG D:PRO471 4.7 69.8 1.0
O B:PRO471 4.7 60.5 1.0
CD1 B:PHE473 4.7 45.2 1.0
CB B:ASN478 4.8 44.1 1.0
C B:PHE473 4.8 47.0 1.0
N B:ASN472 4.9 58.9 1.0
CA B:ASN478 4.9 43.3 1.0

Chlorine binding site 8 out of 12 in 5oar

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Chlorine binding site 8 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl707

b:37.6
occ:0.75
 CB D:ASP119 4.0 71.8 1.0
N D:ASP119 4.4 69.0 1.0
CG D:GLN121 4.6 62.0 1.0
CA D:ASP119 4.7 69.3 1.0
OD2 D:ASP119 4.8 74.2 1.0
CB D:GLN121 4.9 61.5 1.0
O D:ASP119 4.9 67.1 1.0
NE2 D:HIS338 5.0 69.1 1.0
CG D:ASP119 5.0 72.8 1.0

Chlorine binding site 9 out of 12 in 5oar

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Chlorine binding site 9 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl708

b:52.9
occ:1.00
 O D:GLY480 3.8 45.8 1.0
NH1 D:ARG459 3.8 51.9 1.0
C D:GLY480 3.9 46.3 1.0
N D:TRP482 3.9 49.5 1.0
CA D:GLY480 4.0 46.3 1.0
CA D:TRP482 4.0 51.5 1.0
ND2 D:ASN478 4.1 52.9 1.0
CB D:TRP482 4.2 52.4 1.0
C D:SER481 4.4 47.0 1.0
OD1 D:ASN478 4.5 53.0 1.0
N D:SER481 4.5 46.6 1.0
CG D:ASN478 4.5 52.5 1.0
CZ D:ARG459 4.7 51.9 1.0
NH2 D:ARG459 4.7 51.9 1.0
N D:GLY480 4.9 47.1 1.0
O D:SER481 4.9 47.1 1.0
CA D:SER481 4.9 46.7 1.0

Chlorine binding site 10 out of 12 in 5oar

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Chlorine binding site 10 out of 12 in the Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae


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 Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl709

b:52.9
occ:0.50
 CL D:CL709 0.0 52.9 0.5
CL D:CL709 2.4 54.3 0.5
NH1 D:ARG368 2.9 0.3 1.0
CG D:ASP372 4.0 89.3 1.0
CB D:ASP372 4.0 88.6 1.0
CZ D:ARG368 4.2 0.2 1.0
OD1 D:ASP372 4.2 87.9 1.0
CG D:ARG368 4.4 0.2 1.0
OD2 D:ASP372 4.4 88.1 1.0
NH2 D:ARG368 4.9 0.7 1.0
CD D:ARG368 4.9 0.4 1.0
NE D:ARG368 4.9 0.7 1.0

Reference:

J.Skerlova, J.Blaha, P.Pachl, K.Hofbauerova, Z.Kukacka, P.Man, P.Pompach, P.Novak, Z.Otwinowski, J.Brynda, O.Vanek, P.Rezacova. Crystal Structure of Native Beta-N-Acetylhexosaminidase Isolated From Aspergillus Oryzae Sheds Light Onto Its Substrate Specificity, High Stability, and Regulation By Propeptide. Febs J. V. 285 580 2018.
ISSN: ISSN 1742-4658
PubMed: 29239122
DOI: 10.1111/FEBS.14360
Page generated: Sat Dec 12 12:11:58 2020

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