Chlorine in PDB 7dfn: Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose

Enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose

All present enzymatic activity of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose, PDB code: 7dfn 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) 49.22 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 134.233, 134.233, 72.235, 90, 90, 120
R / Rfree (%) 16.5 / 20.9

Other elements in 7dfn:

The structure of Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose also contains other interesting chemical elements:

Sodium (Na) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 30; Page 4, Binding sites: 31 - 40; Page 5, Binding sites: 41 - 50; Page 6, Binding sites: 51 - 59;

Binding sites:

The binding sites of Chlorine atom in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose (pdb code 7dfn). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 59 binding sites of Chlorine where determined in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose, PDB code: 7dfn:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 59 in 7dfn

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Chlorine binding site 1 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:28.9
occ:1.00
 N A:LYS143 3.0 17.8 1.0
ND2 D:ASN123 3.2 19.8 1.0
CA A:SER142 3.6 19.9 1.0
CB A:SER142 3.7 20.8 1.0
CB A:LYS143 3.8 17.4 1.0
C A:SER142 3.8 19.3 1.0
CA A:LYS143 4.0 17.4 1.0
CG A:LYS143 4.1 17.9 1.0
O A:LYS143 4.2 14.8 1.0
O A:HOH502 4.3 28.1 1.0
CD2 D:TYR122 4.3 16.8 1.0
CG D:ASN123 4.4 19.9 1.0
C A:LYS143 4.6 16.4 1.0
CD A:LYS143 4.6 16.4 1.0
OD1 D:ASN123 4.7 21.6 1.0
CB D:TYR122 4.8 16.6 1.0
OG1 D:THR132 4.9 23.8 1.0
OG A:SER142 4.9 21.0 1.0
N A:SER142 5.0 18.5 1.0
O A:GLN141 5.0 21.8 1.0
CG D:TYR122 5.0 16.3 1.0

Chlorine binding site 2 out of 59 in 7dfn

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Chlorine binding site 2 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl402

b:22.6
occ:1.00
 N A:THR148 3.2 18.2 1.0
NH1 A:ARG144 3.2 17.7 1.0
O A:ASP110 3.6 19.7 1.0
CA A:GLY147 3.8 18.1 1.0
CB A:ASP110 3.9 19.6 1.0
C A:GLY147 4.0 18.5 1.0
O A:THR148 4.0 14.4 1.0
O A:HOH557 4.0 31.4 1.0
CB A:THR148 4.0 18.6 1.0
CA A:THR148 4.1 17.6 1.0
C A:ASP110 4.1 18.6 1.0
CA A:ASP110 4.2 19.8 1.0
OG1 A:THR148 4.2 19.4 1.0
CZ A:ARG144 4.2 17.8 1.0
NH2 A:ARG144 4.4 17.1 1.0
C A:THR148 4.5 16.5 1.0
O A:HOH607 4.6 26.8 1.0
O A:HOH580 4.8 25.7 1.0
OD1 A:ASP110 4.8 21.5 1.0
CG A:ASP110 4.8 19.8 1.0

Chlorine binding site 3 out of 59 in 7dfn

Go back to Chlorine Binding Sites List in 7dfn
Chlorine binding site 3 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl403

b:24.3
occ:1.00
 CL A:CL419 3.0 44.2 1.0
OG1 A:THR145 3.0 14.9 1.0
O D:HOH483 3.1 33.4 1.0
N D:TYR122 3.3 18.7 1.0
ND2 A:ASN93 3.4 13.1 1.0
O A:HOH512 3.5 13.8 1.0
CA D:ARG121 3.7 19.3 1.0
CB A:THR145 3.8 15.9 1.0
CD1 D:TYR122 3.9 16.9 1.0
O D:THR120 3.9 16.7 1.0
C D:ARG121 3.9 18.7 1.0
N A:THR145 4.0 16.6 1.0
CB D:TYR122 4.2 16.6 1.0
O D:TYR122 4.2 19.4 1.0
CA D:TYR122 4.2 18.5 1.0
CD D:ARG121 4.2 26.1 1.0
O A:PHE67 4.2 14.1 1.0
O D:HOH416 4.4 18.2 1.0
CB D:ARG121 4.5 21.0 1.0
CG D:TYR122 4.5 16.3 1.0
CA A:THR145 4.5 16.3 1.0
C A:ARG144 4.6 16.0 1.0
N D:ARG121 4.6 17.6 1.0
C D:THR120 4.6 17.4 1.0
CG A:ASN93 4.6 14.2 1.0
C D:TYR122 4.7 18.1 1.0
CG D:ARG121 4.8 22.4 1.0
CE1 D:TYR122 4.9 16.0 1.0
CA A:ARG144 5.0 16.4 1.0
CG2 A:THR145 5.0 16.1 1.0

Chlorine binding site 4 out of 59 in 7dfn

Go back to Chlorine Binding Sites List in 7dfn
Chlorine binding site 4 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl404

b:33.6
occ:1.00
 NE2 A:GLN118 3.2 28.2 1.0
ND2 A:ASN134 3.3 17.2 1.0
OD1 A:ASN134 4.0 18.7 1.0
CG A:ASN134 4.0 18.0 1.0
O A:HOH574 4.3 28.0 1.0
O A:HOH587 4.3 26.6 1.0
NA A:NA418 4.3 32.2 1.0
CD A:GLN118 4.3 24.3 1.0
OE1 A:GLN118 4.6 24.7 1.0
O A:HOH623 5.0 34.9 1.0

Chlorine binding site 5 out of 59 in 7dfn

Go back to Chlorine Binding Sites List in 7dfn
Chlorine binding site 5 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl405

b:20.5
occ:1.00
 OG A:SER142 3.2 21.0 1.0
N A:THR113 3.3 18.2 1.0
N A:SER142 3.6 18.5 1.0
CA A:GLY112 3.6 20.3 1.0
O A:THR113 3.8 16.9 1.0
CB A:GLN141 3.9 19.9 1.0
O A:HOH526 3.9 26.7 1.0
C A:GLY112 4.0 19.1 1.0
N A:GLN141 4.0 17.9 1.0
CB A:SER142 4.0 20.8 1.0
C A:GLN141 4.1 20.1 1.0
CA A:GLN141 4.2 19.6 1.0
CA A:THR113 4.3 19.1 1.0
CG A:ARG140 4.3 16.5 1.0
CA A:SER142 4.4 19.9 1.0
C A:THR113 4.5 18.1 1.0
CB A:THR113 4.5 20.4 1.0
NE A:ARG140 4.5 15.8 1.0
OG1 A:THR113 4.8 20.9 1.0
O A:HOH569 4.8 25.2 1.0
O A:SER142 4.9 19.7 1.0
OE1 A:GLN141 4.9 18.9 1.0
N A:GLY112 5.0 19.8 1.0
CG A:GLN141 5.0 20.7 1.0
CZ A:ARG140 5.0 18.0 1.0
O A:HOH599 5.0 21.9 1.0

Chlorine binding site 6 out of 59 in 7dfn

Go back to Chlorine Binding Sites List in 7dfn
Chlorine binding site 6 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl406

b:45.5
occ:1.00
 O A:HOH558 3.1 31.6 1.0
N A:SER54 3.2 22.5 1.0
O A:HOH551 3.3 45.5 1.0
OG A:SER54 3.4 26.8 1.0
O A:HOH619 3.4 25.9 1.0
CA A:TRP53 3.6 20.4 1.0
C A:TRP53 3.9 22.0 1.0
CB A:SER54 4.0 24.9 1.0
CD1 A:TRP53 4.0 25.5 1.0
CB A:TRP53 4.1 21.2 1.0
CA A:SER54 4.2 23.6 1.0
CB A:TYR16 4.3 26.8 1.0
CG A:TRP53 4.4 23.8 1.0
O A:GLY52 4.5 17.9 1.0
O A:HOH501 4.5 34.1 1.0
N A:TYR16 4.6 24.6 1.0
N A:TRP53 4.8 18.6 1.0

Chlorine binding site 7 out of 59 in 7dfn

Go back to Chlorine Binding Sites List in 7dfn
Chlorine binding site 7 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl407

b:38.7
occ:1.00
 N A:TYR103 3.0 17.6 1.0
O A:GLY101 3.5 17.1 1.0
CA A:THR102 3.6 18.8 1.0
CB A:TYR103 3.6 18.0 1.0
C A:THR102 3.8 18.0 1.0
CA A:TYR103 3.9 18.3 1.0
O A:HOH525 4.3 42.0 1.0
C A:GLY101 4.3 19.2 1.0
N A:THR102 4.4 18.2 1.0
CG2 A:THR102 4.5 20.4 1.0
O A:TYR103 4.5 17.4 1.0
CB A:THR102 4.6 19.3 1.0
C A:TYR103 4.8 17.8 1.0

Chlorine binding site 8 out of 59 in 7dfn

Go back to Chlorine Binding Sites List in 7dfn
Chlorine binding site 8 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl408

b:29.7
occ:1.00
 O A:HOH620 3.0 33.5 1.0
N A:THR120 3.2 18.1 1.0
CA A:THR119 3.5 18.4 1.0
CB A:THR119 3.6 18.8 1.0
O A:THR120 3.8 19.1 1.0
C A:THR119 3.8 18.8 1.0
CG2 A:THR119 4.0 19.0 1.0
CA A:THR120 4.2 18.2 1.0
O A:HOH514 4.3 35.9 1.0
CB A:THR120 4.4 17.2 1.0
C A:THR120 4.5 18.0 1.0
OG1 A:THR120 4.6 16.0 1.0
O A:HOH503 4.7 29.0 1.0
O A:HOH555 4.7 17.7 1.0
O A:HOH631 4.8 39.8 1.0
OG1 A:THR119 4.9 18.3 1.0
N A:THR119 4.9 18.1 1.0
O A:HOH624 5.0 28.5 1.0
O A:GLN118 5.0 16.7 1.0

Chlorine binding site 9 out of 59 in 7dfn

Go back to Chlorine Binding Sites List in 7dfn
Chlorine binding site 9 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl409

b:36.4
occ:1.00
 O A:HOH584 3.0 17.5 1.0
N A:PHE168 3.1 21.1 1.0
CA A:SER167 3.6 20.1 1.0
CD2 A:PHE168 3.8 21.1 1.0
C A:SER167 3.9 21.0 1.0
CB A:SER167 4.0 20.6 1.0
CB A:PHE168 4.0 21.8 1.0
CA A:PHE168 4.1 21.5 1.0
CG A:PHE168 4.3 21.8 1.0
OG A:SER167 4.5 23.1 1.0
C A:PHE168 4.7 21.6 1.0
CE2 A:PHE168 4.8 21.3 1.0
O A:HOH530 4.9 29.9 1.0
N A:SER167 4.9 19.3 1.0
O A:PHE168 4.9 21.0 1.0
O A:GLY166 5.0 18.7 1.0

Chlorine binding site 10 out of 59 in 7dfn

Go back to Chlorine Binding Sites List in 7dfn
Chlorine binding site 10 out of 59 in the Crystal Structure of Glycoside Hydrolase Family 11 Beta-Xylanase From Streptomyces Olivaceoviridis E-86 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose


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 in Complex with Alpha-L- Arabinofuranosyl Xylotetraose within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl410

b:42.0
occ:1.00
 NE2 A:GLN8 3.1 34.4 1.0
OG1 A:THR6 3.1 35.3 1.0
N A:THR5 3.3 27.4 1.0
CB A:THR6 3.5 32.2 1.0
N A:THR6 3.6 28.5 1.0
CA A:ILE4 3.7 27.7 1.0
C A:ILE4 4.0 28.3 1.0
OG1 A:THR5 4.0 32.9 1.0
CA A:THR6 4.2 29.0 1.0
CD1 A:ILE4 4.2 30.6 1.0
O A:VAL3 4.2 32.9 1.0
CG2 A:ILE4 4.2 30.9 1.0
CD A:GLN8 4.3 32.4 1.0
CA A:THR5 4.3 27.9 1.0
C A:THR5 4.4 27.5 1.0
O A:THR6 4.5 27.5 1.0
CB A:ILE4 4.5 28.2 1.0
OE1 A:GLN8 4.7 32.4 1.0
N A:ILE4 4.7 26.8 1.0
CG2 A:THR6 4.8 31.2 1.0
C A:THR6 4.8 25.9 1.0
CB A:THR5 4.9 28.7 1.0
C A:VAL3 4.9 29.9 1.0
CG1 A:ILE4 5.0 30.5 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: Sun Jan 24 14:39:32 2021

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