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Chlorine in PDB 5a94: Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1

Enzymatic activity of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1

All present enzymatic activity of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1:
3.2.1.73;

Protein crystallography data

The structure of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1, PDB code: 5a94 was solved by G.Sulzenbacher, M.Lafond, T.Freyd, B.Henrissat, R.M.Coutinho, J.G.Berrin, M.L.Garron, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.42 / 1.99
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 188.643, 132.753, 131.352, 90.00, 133.78, 90.00
R / Rfree (%) 17.9 / 19

Other elements in 5a94:

The structure of Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 also contains other interesting chemical elements:

Magnesium (Mg) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 (pdb code 5a94). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1, PDB code: 5a94:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 5a94

Go back to Chlorine Binding Sites List in 5a94
Chlorine binding site 1 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


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 Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:21.4
occ:1.00
O A:HOH2166 2.9 22.4 1.0
O A:HOH2177 3.1 27.0 1.0
N A:ASN231 3.1 17.8 1.0
NE A:ARG200 3.1 21.2 1.0
N A:THR192 3.4 16.3 1.0
CB A:PHE230 3.6 19.2 1.0
CA A:THR191 3.7 16.9 1.0
CA A:ASN231 3.7 17.5 1.0
NH2 A:ARG200 3.8 23.9 1.0
OG1 A:THR191 3.8 16.4 1.0
OG1 A:THR192 3.8 15.9 1.0
CZ A:ARG200 3.9 22.7 1.0
C A:THR191 4.0 17.0 1.0
CD A:ARG200 4.1 21.1 1.0
C A:PHE230 4.1 17.7 1.0
CB A:THR191 4.2 16.6 1.0
CA A:PHE230 4.3 18.3 1.0
CG A:PHE230 4.4 20.1 1.0
CA A:THR192 4.5 16.2 1.0
CB A:THR192 4.6 16.4 1.0
CB A:ASN231 4.6 17.5 1.0
O A:PRO190 4.6 15.4 1.0
CB A:ARG200 4.7 20.1 1.0
N A:THR191 4.7 16.9 1.0
N A:MET193 4.8 16.3 1.0
CG2 A:THR192 4.8 16.3 1.0
CD1 A:PHE230 4.8 20.8 1.0
C A:ASN231 4.9 17.8 1.0
N A:TRP232 5.0 17.7 1.0

Chlorine binding site 2 out of 6 in 5a94

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Chlorine binding site 2 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


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 Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:21.2
occ:1.00
O B:HOH2154 3.0 20.1 1.0
NE B:ARG200 3.1 21.7 1.0
O B:HOH2142 3.1 26.9 1.0
N B:ASN231 3.2 16.3 1.0
N B:THR192 3.4 18.6 1.0
NH2 B:ARG200 3.6 21.9 1.0
CB B:PHE230 3.7 17.9 1.0
OG1 B:THR192 3.8 18.3 1.0
CA B:THR191 3.8 17.9 1.0
OG1 B:THR191 3.8 18.5 1.0
CZ B:ARG200 3.8 22.0 1.0
CA B:ASN231 3.8 16.4 1.0
CD B:ARG200 4.0 21.2 1.0
C B:THR191 4.1 18.9 1.0
CB B:THR191 4.3 18.8 1.0
C B:PHE230 4.3 16.8 1.0
CA B:PHE230 4.4 17.2 1.0
CA B:THR192 4.5 18.6 1.0
CG B:PHE230 4.5 19.1 1.0
CB B:THR192 4.5 18.4 1.0
CB B:ASN231 4.7 16.9 1.0
N B:MET193 4.7 18.9 1.0
CB B:ARG200 4.7 20.9 1.0
O B:PRO190 4.8 18.8 1.0
CG2 B:THR192 4.8 17.6 1.0
N B:THR191 4.8 18.2 1.0
CD1 B:PHE230 5.0 20.4 1.0

Chlorine binding site 3 out of 6 in 5a94

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Chlorine binding site 3 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


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 Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl403

b:23.4
occ:1.00
O C:HOH2143 3.1 20.9 1.0
O C:HOH2149 3.2 26.0 1.0
NE C:ARG200 3.2 21.9 1.0
N C:ASN231 3.2 18.5 1.0
N C:THR192 3.3 16.4 1.0
CA C:THR191 3.6 16.4 1.0
OG1 C:THR191 3.6 16.4 1.0
NH2 C:ARG200 3.7 21.8 1.0
OG1 C:THR192 3.8 17.3 1.0
CB C:PHE230 3.8 20.0 1.0
CA C:ASN231 3.8 18.6 1.0
CZ C:ARG200 3.9 22.2 1.0
C C:THR191 3.9 16.8 1.0
CB C:THR191 4.1 16.5 1.0
CD C:ARG200 4.2 21.8 1.0
C C:PHE230 4.3 19.3 1.0
CA C:THR192 4.4 16.9 1.0
CA C:PHE230 4.4 19.4 1.0
CG C:PHE230 4.5 20.3 1.0
CB C:THR192 4.5 16.5 1.0
N C:MET193 4.6 17.7 1.0
O C:PRO190 4.7 15.9 1.0
CB C:ASN231 4.7 18.8 1.0
N C:THR191 4.7 16.1 1.0
CG2 C:THR192 4.8 16.3 1.0
CB C:ARG200 4.8 21.1 1.0
C C:THR192 5.0 17.2 1.0
CD1 C:PHE230 5.0 19.7 1.0
C C:ASN231 5.0 18.1 1.0
N C:TRP232 5.0 16.8 1.0

Chlorine binding site 4 out of 6 in 5a94

Go back to Chlorine Binding Sites List in 5a94
Chlorine binding site 4 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


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 Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl403

b:22.9
occ:1.00
O D:HOH2121 3.0 24.3 1.0
O D:HOH2108 3.0 17.0 1.0
NE D:ARG200 3.1 23.6 1.0
N D:ASN231 3.3 19.6 1.0
N D:THR192 3.4 16.4 1.0
NH2 D:ARG200 3.5 26.8 1.0
OG1 D:THR192 3.7 17.6 1.0
CA D:THR191 3.7 16.2 1.0
OG1 D:THR191 3.8 17.2 1.0
CZ D:ARG200 3.8 25.4 1.0
CB D:PHE230 3.8 20.9 1.0
CA D:ASN231 3.9 18.7 1.0
CD D:ARG200 4.0 23.6 1.0
C D:THR191 4.1 16.1 1.0
CB D:THR191 4.3 16.2 1.0
C D:PHE230 4.3 19.4 1.0
CA D:THR192 4.4 17.3 1.0
CA D:PHE230 4.5 20.1 1.0
CB D:THR192 4.5 17.0 1.0
CG D:PHE230 4.5 21.9 1.0
N D:MET193 4.7 19.1 1.0
CB D:ASN231 4.7 18.8 1.0
CB D:ARG200 4.7 22.5 1.0
CG2 D:THR192 4.8 17.2 1.0
O D:PRO190 4.8 17.7 1.0
N D:THR191 4.8 16.4 1.0
C D:THR192 4.9 17.8 1.0
CD1 D:PHE230 5.0 21.5 1.0
CG D:ARG200 5.0 22.9 1.0

Chlorine binding site 5 out of 6 in 5a94

Go back to Chlorine Binding Sites List in 5a94
Chlorine binding site 5 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


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 Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Cl403

b:23.8
occ:1.00
O E:HOH2172 3.1 26.0 1.0
NE E:ARG200 3.2 22.8 1.0
N E:ASN231 3.2 19.0 1.0
O E:HOH2162 3.3 25.1 1.0
N E:THR192 3.4 18.2 1.0
CA E:THR191 3.6 17.9 1.0
OG1 E:THR191 3.7 18.7 1.0
CB E:PHE230 3.7 19.6 1.0
NH2 E:ARG200 3.7 24.7 1.0
CA E:ASN231 3.8 18.5 1.0
OG1 E:THR192 3.8 19.2 1.0
CZ E:ARG200 3.9 24.2 1.0
C E:THR191 4.0 17.9 1.0
CD E:ARG200 4.1 22.9 1.0
CB E:THR191 4.1 17.7 1.0
C E:PHE230 4.2 19.0 1.0
CA E:PHE230 4.3 19.2 1.0
CG E:PHE230 4.4 20.2 1.0
CA E:THR192 4.5 18.4 1.0
CB E:THR192 4.6 18.5 1.0
O E:PRO190 4.6 18.1 1.0
CB E:ASN231 4.7 19.0 1.0
N E:THR191 4.7 17.8 1.0
N E:MET193 4.7 19.4 1.0
CB E:ARG200 4.8 21.5 1.0
CG2 E:THR192 4.8 18.2 1.0
CD1 E:PHE230 4.9 20.9 1.0
N E:TRP232 5.0 17.8 1.0
C E:ASN231 5.0 17.9 1.0

Chlorine binding site 6 out of 6 in 5a94

Go back to Chlorine Binding Sites List in 5a94
Chlorine binding site 6 out of 6 in the Crystal Structure of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1


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 Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans in Complex with Tetrasaccharide A, Form 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Cl403

b:24.9
occ:1.00
O F:HOH2118 3.0 27.1 1.0
O F:HOH2122 3.1 23.7 1.0
NE F:ARG200 3.2 23.9 1.0
N F:ASN231 3.2 19.3 1.0
N F:THR192 3.3 20.4 1.0
CA F:THR191 3.6 19.9 1.0
OG1 F:THR191 3.6 19.6 1.0
NH2 F:ARG200 3.7 25.2 1.0
OG1 F:THR192 3.7 20.3 1.0
CA F:ASN231 3.8 18.7 1.0
CB F:PHE230 3.8 19.7 1.0
CZ F:ARG200 3.9 24.7 1.0
C F:THR191 3.9 20.2 1.0
CB F:THR191 4.1 19.8 1.0
CD F:ARG200 4.2 23.8 1.0
C F:PHE230 4.3 19.7 1.0
CA F:THR192 4.4 20.7 1.0
CA F:PHE230 4.5 19.1 1.0
CB F:THR192 4.5 20.1 1.0
N F:MET193 4.6 21.5 1.0
CG F:PHE230 4.6 20.0 1.0
O F:PRO190 4.7 21.5 1.0
CB F:ASN231 4.7 19.1 1.0
N F:THR191 4.7 20.7 1.0
CG2 F:THR192 4.8 20.1 1.0
CB F:ARG200 4.8 22.8 1.0
C F:THR192 4.9 20.9 1.0
N F:TRP232 5.0 18.5 1.0
C F:ASN231 5.0 19.1 1.0

Reference:

M.Lafond, G.Sulzenbacher, T.Freyd, B.Henrissat, J.G.Berrin, M.L.Garron. The Quaternary Structure of A Glycoside Hydrolase Dictates Specificity Towards Beta-Glucans J.Biol.Chem. V. 291 7183 2016.
ISSN: ISSN 0021-9258
PubMed: 26755730
DOI: 10.1074/JBC.M115.695999
Page generated: Sat Dec 12 11:29:56 2020

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