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Chlorine in PDB 7dfm: Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86

Enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86

All present enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86, PDB code: 7dfm was solved by Z.Fujimoto, N.Kishine, S.Kaneko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.41 / 2.40
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 135.039, 135.039, 72.343, 90, 90, 120
R / Rfree (%) 16.8 / 24.5

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 22;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 (pdb code 7dfm). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 22 binding sites of Chlorine where determined in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86, PDB code: 7dfm:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 22 in 7dfm

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Chlorine binding site 1 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:26.6
occ:1.00
 OG A:SER142 3.0 25.7 1.0
N A:THR113 3.2 24.0 1.0
CA A:GLY112 3.6 25.5 1.0
N A:SER142 3.7 21.6 1.0
CB A:GLN141 3.8 24.5 1.0
O A:HOH509 3.9 22.0 1.0
O A:THR113 3.9 27.9 1.0
C A:GLY112 3.9 25.3 1.0
N A:GLN141 4.0 19.8 1.0
CB A:SER142 4.1 25.9 1.0
C A:GLN141 4.1 22.6 1.0
CG A:ARG140 4.2 23.6 1.0
CA A:GLN141 4.2 23.1 1.0
CA A:THR113 4.3 26.4 1.0
NE A:ARG140 4.5 25.0 1.0
CA A:SER142 4.5 24.1 1.0
C A:THR113 4.5 26.8 1.0
CB A:THR113 4.5 28.0 1.0
CG A:GLN141 4.9 25.8 1.0
CZ A:ARG140 4.9 26.7 1.0
CD A:ARG140 4.9 23.7 1.0
O A:GLN141 4.9 28.2 1.0
N A:GLY112 5.0 23.0 1.0

Chlorine binding site 2 out of 22 in 7dfm

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Chlorine binding site 2 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:25.5
occ:1.00
 OG1 A:THR145 2.8 20.1 1.0
O A:HOH531 2.9 21.5 1.0
O A:HOH507 3.2 27.6 1.0
ND2 A:ASN93 3.3 16.8 1.0
N D:TYR122 3.4 29.5 1.0
CA D:ARG121 3.7 29.2 1.0
CB A:THR145 3.8 24.0 1.0
O D:THR120 3.8 28.1 1.0
CD1 D:TYR122 3.9 21.6 1.0
O A:PHE67 4.1 15.9 1.0
C D:ARG121 4.1 29.6 1.0
N A:THR145 4.2 22.6 1.0
O D:TYR122 4.3 19.2 1.0
CB D:TYR122 4.4 22.6 1.0
CA D:TYR122 4.4 25.1 1.0
CG A:ASN93 4.5 20.8 1.0
NE D:ARG121 4.5 52.2 1.0
O A:HOH521 4.5 15.3 1.0
CB D:ARG121 4.6 33.5 1.0
NH2 D:ARG121 4.6 59.2 1.0
C D:THR120 4.6 25.2 1.0
CA A:THR145 4.6 22.8 1.0
CG D:TYR122 4.7 22.1 1.0
N D:ARG121 4.7 28.0 1.0
O D:HOH414 4.7 17.3 1.0
C A:ARG144 4.7 22.9 1.0
CZ D:ARG121 4.8 55.9 1.0
CE1 D:TYR122 4.9 21.5 1.0
CG2 A:THR145 4.9 24.2 1.0
C D:TYR122 4.9 23.0 1.0
OD1 A:ASN93 4.9 20.2 1.0

Chlorine binding site 3 out of 22 in 7dfm

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Chlorine binding site 3 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:35.3
occ:1.00
 N A:LYS143 3.1 21.6 1.0
ND2 D:ASN123 3.3 22.5 1.0
CB A:SER142 3.7 25.9 1.0
CA A:SER142 3.7 24.1 1.0
CB A:LYS143 3.9 21.8 1.0
C A:SER142 3.9 23.2 1.0
CA A:LYS143 4.1 21.7 1.0
O A:LYS143 4.3 19.0 1.0
CG A:LYS143 4.3 22.9 1.0
CD2 D:TYR122 4.3 21.2 1.0
CD A:LYS143 4.4 21.0 1.0
CG D:ASN123 4.4 25.2 1.0
C A:LYS143 4.7 21.8 1.0
CB D:TYR122 4.7 22.6 1.0
OD1 D:ASN123 4.8 26.7 1.0
CG D:TYR122 4.9 22.1 1.0
OG1 D:THR132 5.0 28.4 1.0
OG A:SER142 5.0 25.7 1.0

Chlorine binding site 4 out of 22 in 7dfm

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Chlorine binding site 4 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:39.7
occ:1.00
 OG A:SER182 3.0 15.5 1.0
C A:SER181 3.4 18.1 1.0
CA A:SER181 3.7 21.0 1.0
N A:SER182 3.7 18.0 1.0
O A:SER181 3.7 18.2 1.0
CA A:ASN43 3.9 24.3 1.0
CB A:SER182 4.0 17.4 1.0
N A:ASN43 4.1 24.5 1.0
OD1 A:ASN43 4.2 23.6 1.0
CB A:ASN43 4.3 26.7 1.0
N A:SER181 4.3 24.3 1.0
O A:GLN180 4.3 23.7 1.0
CA A:SER182 4.4 18.9 1.0
C A:GLN180 4.6 25.2 1.0
CG A:ASN43 4.7 28.6 1.0
O A:SER70 4.7 25.2 1.0
CB A:SER181 4.9 23.8 1.0

Chlorine binding site 5 out of 22 in 7dfm

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Chlorine binding site 5 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:45.0
occ:1.00
 N A:TYR103 3.2 22.1 1.0
CA A:THR102 3.7 22.3 1.0
CB A:TYR103 3.7 22.9 1.0
O A:GLY101 3.8 20.9 1.0
C A:THR102 3.9 21.5 1.0
CA A:TYR103 4.1 24.4 1.0
CG2 A:THR102 4.5 22.8 1.0
C A:GLY101 4.6 24.2 1.0
N A:THR102 4.6 22.5 1.0
O A:TYR103 4.6 25.5 1.0
CB A:THR102 4.7 23.1 1.0
C A:TYR103 4.9 25.3 1.0

Chlorine binding site 6 out of 22 in 7dfm

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Chlorine binding site 6 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:28.4
occ:1.00
 NH1 A:ARG144 3.2 22.0 1.0
N A:THR148 3.3 22.7 1.0
O A:ASP110 3.7 20.9 1.0
CB A:ASP110 3.9 21.7 1.0
O A:THR148 3.9 22.4 1.0
CA A:GLY147 3.9 23.3 1.0
CB A:THR148 4.0 28.3 1.0
C A:ASP110 4.1 21.3 1.0
C A:GLY147 4.1 24.0 1.0
CA A:THR148 4.1 25.3 1.0
OG1 A:THR148 4.2 36.7 1.0
CA A:ASP110 4.2 22.0 1.0
CZ A:ARG144 4.3 24.1 1.0
NH2 A:ARG144 4.5 25.7 1.0
C A:THR148 4.5 23.7 1.0
OD1 A:ASP110 4.8 22.4 1.0
CG A:ASP110 4.8 22.6 1.0

Chlorine binding site 7 out of 22 in 7dfm

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Chlorine binding site 7 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:29.8
occ:1.00
 OH D:TYR122 3.1 18.8 1.0
O A:HOH521 3.3 15.3 1.0
NZ A:LYS143 3.4 25.3 1.0
CA A:GLY95 3.6 20.6 1.0
CE1 D:TYR122 3.7 21.5 1.0
CZ D:TYR122 3.7 21.1 1.0
CG A:PRO69 3.8 26.9 1.0
O A:TRP94 3.8 16.5 1.0
O A:PRO69 4.0 27.6 1.0
C A:GLY95 4.2 21.5 1.0
O A:GLY95 4.4 23.4 1.0
CD A:PRO69 4.4 27.3 1.0
O A:HOH529 4.6 30.6 1.0
O D:HOH433 4.6 15.1 1.0
N A:GLY95 4.6 21.1 1.0
C A:TRP94 4.6 19.6 1.0
O A:HOH507 4.8 27.6 1.0
CE A:LYS143 4.9 22.1 1.0
CD1 D:TYR122 4.9 21.6 1.0
CE2 D:TYR122 4.9 20.0 1.0
CB A:PRO69 5.0 28.2 1.0
C A:PRO69 5.0 26.1 1.0

Chlorine binding site 8 out of 22 in 7dfm

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Chlorine binding site 8 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:34.2
occ:1.00
 OG1 B:THR130 3.1 24.5 1.0
N A:GLY111 3.3 21.4 1.0
N B:THR130 3.3 23.9 1.0
CB B:THR130 3.5 25.7 1.0
CA A:GLY111 3.8 22.8 1.0
N A:ASP110 3.9 22.6 1.0
CA B:THR130 4.0 24.8 1.0
C B:GLY129 4.3 26.4 1.0
CG2 A:THR108 4.3 25.0 1.0
CA B:GLY129 4.3 23.4 1.0
C A:SER109 4.3 24.6 1.0
C A:ASP110 4.3 21.3 1.0
CA A:ASP110 4.4 22.0 1.0
C A:GLY111 4.7 23.8 1.0
CA A:SER109 4.7 24.1 1.0
O B:THR130 4.8 28.0 1.0
N A:GLY112 4.9 23.0 1.0
N A:SER109 4.9 27.5 1.0
CG2 B:THR130 4.9 25.1 1.0
O A:SER109 4.9 22.1 1.0
C B:THR130 5.0 27.7 1.0

Chlorine binding site 9 out of 22 in 7dfm

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Chlorine binding site 9 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl402

b:32.2
occ:1.00
 NE B:ARG121 3.1 39.0 1.0
NH2 B:ARG121 3.2 41.0 1.0
N B:TYR122 3.4 29.4 1.0
CZ B:ARG121 3.6 38.6 1.0
CA B:ARG121 3.8 28.8 1.0
O B:TYR122 3.9 23.5 1.0
C B:ARG121 4.0 28.7 1.0
CD B:ARG121 4.2 35.1 1.0
CB B:ARG121 4.2 28.9 1.0
CA B:TYR122 4.4 36.4 1.0
C B:TYR122 4.5 31.3 1.0
CB B:TYR122 4.7 44.2 1.0
O B:THR120 4.7 25.7 1.0
CG B:ARG121 4.9 31.5 1.0
CB B:ALA124 4.9 26.5 1.0
NH1 B:ARG121 4.9 38.0 1.0
N B:ARG121 5.0 25.8 1.0

Chlorine binding site 10 out of 22 in 7dfm

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Chlorine binding site 10 out of 22 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86


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 Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl403

b:33.2
occ:1.00
 OG B:SER142 2.9 49.4 1.0
N B:SER142 3.5 35.6 1.0
N B:THR113 3.6 25.8 1.0
CA B:GLY112 3.8 30.0 1.0
O B:THR113 3.9 28.0 1.0
C B:GLN141 4.1 30.8 1.0
CB B:SER142 4.1 42.5 1.0
CB B:GLN141 4.1 28.8 1.0
N B:GLN141 4.1 29.4 1.0
C B:GLY112 4.2 27.8 1.0
CG B:ARG140 4.2 25.4 1.0
CA B:GLN141 4.3 30.3 1.0
CA B:SER142 4.3 41.3 1.0
NE B:ARG140 4.5 28.4 1.0
CA B:THR113 4.6 26.5 1.0
C B:THR113 4.7 25.6 1.0
O B:SER142 4.8 38.0 1.0
CB B:THR113 4.8 26.4 1.0
O B:GLN141 4.9 30.6 1.0
CZ B:ARG140 4.9 29.3 1.0
NH2 B:ARG140 5.0 33.1 1.0
CD B:ARG140 5.0 26.2 1.0
OE1 B:GLN141 5.0 30.9 1.0

Reference:

Z.Fujimoto, K.Naomi, K.Teramoto, S.Tsutsui, S.Kaneko. Structure-Based Substrate Specificity of GH11 Xylanase From Streptomyces Olivaceoviridis E-86 To Be Published.
Page generated: Mon Jul 29 20:03:59 2024

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