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Chlorine in PDB 5a8m: Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans

Enzymatic activity of Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans

All present enzymatic activity of Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans:
3.2.1.73;

Protein crystallography data

The structure of Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans, PDB code: 5a8m 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) 47.33 / 1.86
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 142.605, 142.605, 136.277, 90.00, 90.00, 90.00
R / Rfree (%) 14.3 / 16.5

Other elements in 5a8m:

The structure of Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans (pdb code 5a8m). 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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans, PDB code: 5a8m:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 5a8m

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Chlorine binding site 1 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1365

b:15.3
occ:1.00
 O A:HOH2288 3.1 26.1 1.0
O A:HOH2272 3.2 15.8 1.0
N A:ASN231 3.2 11.7 1.0
NE A:ARG200 3.2 14.7 1.0
N A:THR192 3.3 11.2 1.0
CA A:THR191 3.6 11.2 1.0
CB A:PHE230 3.7 12.6 1.0
OG1 A:THR191 3.8 12.0 1.0
CA A:ASN231 3.8 12.0 1.0
OG1 A:THR192 3.9 11.3 1.0
NH2 A:ARG200 3.9 16.1 1.0
C A:THR191 4.0 11.3 1.0
CD A:ARG200 4.0 14.2 1.0
CZ A:ARG200 4.1 15.1 1.0
CB A:THR191 4.2 11.7 1.0
C A:PHE230 4.3 11.9 1.0
CA A:PHE230 4.4 12.1 1.0
CA A:THR192 4.4 11.2 1.0
CG A:PHE230 4.4 12.9 1.0
CB A:THR192 4.6 11.4 1.0
O A:PRO190 4.7 9.5 1.0
N A:THR191 4.7 10.6 1.0
N A:MSE193 4.7 12.1 1.0
CB A:ASN231 4.7 12.1 1.0
CB A:ARG200 4.8 13.3 1.0
CG2 A:THR192 4.8 11.5 1.0
CD1 A:PHE230 4.9 13.8 1.0

Chlorine binding site 2 out of 9 in 5a8m

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Chlorine binding site 2 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1366

b:47.1
occ:1.00
 N A:ILE304 3.4 16.3 1.0
CA A:HIS303 3.8 17.2 1.0
CG1 A:ILE304 4.0 19.9 1.0
CB A:HIS303 4.1 17.4 1.0
C A:HIS303 4.1 15.6 1.0
CB A:ILE304 4.2 19.0 1.0
CD1 A:ILE304 4.3 22.3 1.0
CE A:LYS307 4.3 23.7 1.0
NZ A:LYS307 4.4 25.6 1.0
CA A:ILE304 4.5 16.9 1.0
O A:ALA302 4.9 16.5 1.0
N A:HIS303 5.0 16.3 1.0

Chlorine binding site 3 out of 9 in 5a8m

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Chlorine binding site 3 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl1367

b:55.2
occ:1.00
 ND2 A:ASN100 3.2 15.7 1.0
NH2 A:ARG69 3.3 25.4 0.5
O A:HOH2103 3.5 25.6 1.0
NH2 A:ARG69 3.9 24.2 0.5
CB A:ASN100 4.1 14.7 1.0
CG A:ASN100 4.1 14.7 1.0
CZ A:ARG69 4.3 23.1 0.5
CE1 A:PHE66 4.5 17.4 1.0
NH1 A:ARG69 4.7 24.2 0.5
CZ A:ARG69 5.0 24.1 0.5

Chlorine binding site 4 out of 9 in 5a8m

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Chlorine binding site 4 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1366

b:15.1
occ:1.00
 O B:HOH2248 3.1 13.3 1.0
O B:HOH2263 3.1 28.0 1.0
NE B:ARG200 3.2 15.5 1.0
N B:ASN231 3.2 11.9 1.0
N B:THR192 3.3 11.5 1.0
CA B:THR191 3.6 11.1 1.0
CB B:PHE230 3.8 12.9 1.0
OG1 B:THR191 3.8 11.2 1.0
CA B:ASN231 3.8 12.1 1.0
OG1 B:THR192 3.8 12.1 1.0
NH2 B:ARG200 3.9 15.7 1.0
CZ B:ARG200 4.0 15.7 1.0
CD B:ARG200 4.0 15.5 1.0
C B:THR191 4.0 11.0 1.0
CB B:THR191 4.2 11.4 1.0
C B:PHE230 4.3 12.1 1.0
CA B:PHE230 4.4 12.2 1.0
CA B:THR192 4.4 11.2 1.0
CG B:PHE230 4.5 13.0 1.0
CB B:THR192 4.6 11.6 1.0
CB B:ASN231 4.7 12.8 1.0
N B:MSE193 4.7 11.7 1.0
O B:PRO190 4.7 10.1 1.0
N B:THR191 4.8 11.0 1.0
CB B:ARG200 4.8 14.7 1.0
CG2 B:THR192 4.8 11.7 1.0
O B:HOH2134 4.9 40.6 1.0
CD1 B:PHE230 5.0 13.2 1.0
C B:THR192 5.0 11.4 1.0
N B:TRP232 5.0 10.6 1.0
C B:ASN231 5.0 11.2 1.0

Chlorine binding site 5 out of 9 in 5a8m

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Chlorine binding site 5 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1367

b:43.0
occ:1.00
 N B:ILE304 3.3 16.2 1.0
CA B:HIS303 3.6 17.4 1.0
CB B:HIS303 3.9 18.3 1.0
C B:HIS303 3.9 16.2 1.0
CG1 B:ILE304 4.0 21.9 1.0
CB B:ILE304 4.1 20.4 1.0
CA B:ILE304 4.3 17.2 1.0
CD1 B:ILE304 4.3 23.8 1.0
O B:HOH2350 4.3 42.6 1.0
CE B:LYS307 4.5 25.1 1.0
NZ B:LYS307 4.6 26.3 1.0
O B:ILE304 4.9 14.8 1.0
N B:HIS303 4.9 17.6 1.0
O B:ALA302 4.9 16.1 1.0

Chlorine binding site 6 out of 9 in 5a8m

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Chlorine binding site 6 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl1368

b:49.9
occ:1.00
 NH2 B:ARG69 3.0 28.9 0.5
ND2 B:ASN100 3.3 20.0 1.0
O B:HOH2088 3.6 23.9 1.0
NH2 B:ARG69 3.6 27.8 0.5
CZ B:ARG69 4.1 27.2 0.5
CB B:ASN100 4.2 17.1 1.0
CG B:ASN100 4.2 18.1 1.0
NH1 B:ARG69 4.5 27.9 0.5
O B:HOH2194 4.7 35.0 1.0
CZ B:ARG69 4.7 27.0 0.5
CE1 B:PHE66 4.9 19.4 1.0

Chlorine binding site 7 out of 9 in 5a8m

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Chlorine binding site 7 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1365

b:13.4
occ:1.00
 O C:HOH2236 3.1 14.8 1.0
O C:HOH2246 3.1 27.0 1.0
NE C:ARG200 3.2 13.9 1.0
N C:ASN231 3.2 12.2 1.0
N C:THR192 3.4 11.0 1.0
CA C:THR191 3.7 10.7 1.0
CB C:PHE230 3.8 12.8 1.0
OG1 C:THR191 3.8 10.2 1.0
CA C:ASN231 3.8 12.3 1.0
OG1 C:THR192 3.9 11.1 1.0
NH2 C:ARG200 3.9 15.5 1.0
CZ C:ARG200 4.0 15.4 1.0
CD C:ARG200 4.0 13.9 1.0
C C:THR191 4.0 11.4 1.0
CB C:THR191 4.2 10.9 1.0
C C:PHE230 4.3 11.9 1.0
CA C:PHE230 4.4 12.3 1.0
CA C:THR192 4.5 11.3 1.0
CG C:PHE230 4.5 13.4 1.0
CB C:THR192 4.6 11.0 1.0
CB C:ASN231 4.6 13.1 1.0
O C:PRO190 4.7 9.8 1.0
N C:MSE193 4.7 11.6 1.0
N C:THR191 4.7 10.6 1.0
CB C:ARG200 4.8 12.8 1.0
CG2 C:THR192 4.9 11.2 1.0
CD1 C:PHE230 5.0 13.4 1.0
C C:ASN231 5.0 11.8 1.0

Chlorine binding site 8 out of 9 in 5a8m

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Chlorine binding site 8 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1366

b:47.5
occ:1.00
 N C:ILE304 3.3 17.3 1.0
CA C:HIS303 3.7 17.5 1.0
CG1 C:ILE304 4.0 20.3 1.0
CB C:HIS303 4.0 16.9 1.0
C C:HIS303 4.1 16.4 1.0
CB C:ILE304 4.1 18.8 1.0
CD1 C:ILE304 4.3 20.6 1.0
CA C:ILE304 4.4 16.9 1.0
CE C:LYS307 4.5 24.9 1.0
NZ C:LYS307 4.5 27.6 1.0
O C:ALA302 5.0 18.1 1.0

Chlorine binding site 9 out of 9 in 5a8m

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Chlorine binding site 9 out of 9 in the Crystal Structure of the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans


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 the Selenomethionine Derivative of Beta-Glucanase SDGLUC5_26A From Saccharophagus Degradans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl1367

b:53.7
occ:1.00
 ND2 C:ASN100 3.1 15.0 1.0
NH2 C:ARG69 3.5 21.9 0.5
O C:HOH2093 3.6 21.9 1.0
O C:HOH2095 3.8 28.0 1.0
NH2 C:ARG69 4.0 25.6 0.5
CB C:ASN100 4.0 14.9 1.0
CG C:ASN100 4.1 14.6 1.0
O C:HOH2186 4.3 35.5 1.0
CE1 C:PHE66 4.3 18.2 1.0
CZ C:ARG69 4.4 20.9 0.5
NH1 C:ARG69 4.7 22.7 0.5
O C:HOH2096 4.8 38.8 1.0
CD1 C:PHE66 4.9 18.3 1.0
O C:THR67 5.0 13.2 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 11:29:47 2020

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