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Zinc in PDB 1r85: Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution

Enzymatic activity of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution

All present enzymatic activity of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution, PDB code: 1r85 was solved by M.Bar, G.Golan, M.Nechama, G.Zolotnitsky, Y.Shoham, G.Shoham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 40.00 / 1.45
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 121.510, 61.710, 89.090, 90.00, 119.07, 90.00
R / Rfree (%) 12.6 / 18.1

Other elements in 1r85:

The structure of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution (pdb code 1r85). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 7 binding sites of Zinc where determined in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution, PDB code: 1r85:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 1r85

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Zinc binding site 1 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:15.7
occ:1.00
 OD2 A:ASP365 1.9 16.3 1.0
NE2 A:HIS11 2.0 16.0 1.0
CL A:CL701 2.3 21.1 1.0
CG A:ASP365 2.8 16.1 1.0
CD2 A:HIS11 3.0 16.8 1.0
CE1 A:HIS11 3.1 14.0 1.0
OD1 A:ASP365 3.1 15.8 1.0
O2 A:GOL518 3.9 44.0 0.5
O A:HOH1039 4.0 24.8 1.0
CD A:LYS367 4.1 20.0 1.0
CG A:HIS11 4.2 17.6 1.0
C2 A:GOL518 4.2 36.2 0.5
ND1 A:HIS11 4.2 16.2 1.0
CB A:ASP365 4.2 14.5 1.0
C1 A:GOL518 4.3 36.0 0.5
CB A:LYS367 4.6 16.0 1.0
O A:HOH1081 4.6 24.2 1.0
CG A:LYS367 4.8 17.0 1.0
NZ A:LYS367 4.8 18.6 1.0
CE A:LYS367 5.0 21.2 1.0

Zinc binding site 2 out of 7 in 1r85

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Zinc binding site 2 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:17.0
occ:1.00
 OD2 A:ASP21 2.0 16.9 1.0
O A:HOH1214 2.0 19.7 1.0
O A:HOH1213 2.1 17.7 1.0
O A:HOH1216 2.1 24.0 1.0
O A:HOH1212 2.1 15.4 1.0
O A:HOH1215 2.2 19.0 1.0
CG A:ASP21 3.0 16.8 1.0
OD1 A:ASP21 3.2 16.6 1.0
C1 A:GOL515 3.9 38.4 0.5
O A:HOH1433 4.1 49.5 1.0
O3 A:GOL501 4.1 44.2 0.8
O A:HOH1063 4.1 21.2 1.0
O A:HOH1435 4.2 45.3 1.0
O A:PHE52 4.2 16.1 1.0
O A:LYS49 4.2 18.3 1.0
O1 A:GOL501 4.3 30.1 0.8
C2 A:GOL515 4.3 39.4 0.5
CB A:ASP21 4.3 14.8 1.0
C3 A:GOL515 4.4 39.6 0.5
O A:ARG50 4.4 18.7 1.0
OE1 A:GLN22 4.5 28.9 1.0
C3 A:GOL501 4.5 47.4 0.8
O1 A:GOL515 4.5 33.3 0.5
CB A:ASN53 4.6 13.4 1.0
C A:PHE52 4.8 13.1 1.0
CG A:GLN22 4.8 19.9 1.0
C1 A:GOL501 4.9 47.6 0.8
C A:ARG50 4.9 15.3 1.0

Zinc binding site 3 out of 7 in 1r85

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Zinc binding site 3 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:23.2
occ:0.56
 OD2 A:ASP282 2.0 22.5 0.6
O A:HOH1291 2.1 30.3 1.0
OD1 A:ASP282 2.2 21.8 0.4
OD2 A:ASP282 2.8 25.6 0.4
CG A:ASP282 2.9 21.9 0.4
CG A:ASP282 3.1 22.3 0.6
O A:HOH1337 3.6 47.1 1.0
O A:HOH1465 3.7 58.2 1.0
ZN A:ZN907 3.8 40.3 0.4
OD1 A:ASP282 3.8 23.8 0.6
CB A:ASP282 4.2 19.5 0.6
CB A:ASP282 4.3 19.6 0.4
O A:HOH1101 4.3 24.3 1.0
CB A:THR280 4.6 17.9 1.0
N A:ASP282 4.7 17.6 0.4
N A:ASP282 4.7 17.5 0.6
O A:HOH1056 4.8 40.8 1.0
O1 A:SO4802 4.9 42.6 0.7
CG2 A:THR280 5.0 21.8 1.0
OG1 A:THR280 5.0 20.4 1.0

Zinc binding site 4 out of 7 in 1r85

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Zinc binding site 4 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:19.3
occ:1.00
 OE1 A:GLU58 1.9 18.7 0.6
NE2 A:HIS322 2.0 22.9 1.0
O A:HOH1020 2.0 17.1 1.0
CL A:CL702 2.1 24.5 1.0
OE2 A:GLU58 2.3 18.2 0.4
OE1 A:GLU58 2.4 19.5 0.4
CD A:GLU58 2.6 18.7 0.4
CD A:GLU58 2.7 19.1 0.6
CE1 A:HIS322 2.8 26.9 1.0
OE2 A:GLU58 2.9 18.9 0.6
CD2 A:HIS322 3.1 19.4 1.0
OE2 A:GLU35 3.9 22.5 1.0
ND1 A:HIS322 4.0 28.4 1.0
O A:HOH1072 4.0 25.7 1.0
O A:HOH1440 4.0 62.3 1.0
CG A:GLU58 4.0 17.7 0.4
CG A:GLU35 4.0 17.4 1.0
CG A:HIS322 4.1 19.6 1.0
CG A:GLU58 4.1 17.5 0.6
O A:HOH1007 4.3 13.9 1.0
O2 A:GOL513 4.4 38.6 0.7
CD A:GLU35 4.5 16.0 1.0
ND2 A:ASN59 4.5 17.0 1.0
C2 A:GOL513 4.6 34.2 0.7
O1 A:GOL513 4.7 47.2 0.7
CB A:GLU58 4.7 17.3 0.6
CB A:GLU58 4.7 16.6 0.4
C1 A:GOL513 4.8 36.5 0.7
O A:HOH1037 4.9 20.8 1.0

Zinc binding site 5 out of 7 in 1r85

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Zinc binding site 5 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:23.0
occ:0.44
 O A:SER307 2.2 19.6 1.0
O A:GLU27 2.3 18.8 1.0
O A:ILE310 2.3 18.3 1.0
O2 A:GOL510 2.5 16.3 0.5
O1 A:GOL510 2.5 18.1 0.5
C1 A:GOL510 2.6 23.8 0.5
O A:HOH1108 2.7 28.7 1.0
C2 A:GOL510 2.7 23.1 0.5
C A:ILE310 3.4 15.6 1.0
C A:SER307 3.4 18.6 1.0
C A:GLU27 3.5 17.8 1.0
O A:HOH1158 4.0 35.9 1.0
CA A:SER311 4.1 14.6 1.0
CA A:SER307 4.2 16.5 1.0
N A:SER311 4.2 15.2 1.0
C3 A:GOL510 4.2 25.7 0.5
CB A:SER307 4.3 19.4 1.0
CB A:PHE28 4.3 13.5 1.0
CA A:PHE28 4.3 14.4 1.0
N A:PHE28 4.3 15.6 1.0
N A:ILE310 4.3 18.7 1.0
CA A:ILE310 4.4 15.3 1.0
N A:ASP308 4.5 22.1 1.0
CA A:GLU27 4.5 17.3 1.0
CA A:ASP308 4.6 24.0 1.0
O A:HOH1259 4.6 43.2 1.0
CD2 A:PHE28 4.7 17.6 1.0
O A:HOH1131 4.8 32.5 1.0
O3 A:GOL510 4.8 33.6 0.5
C A:ASP308 4.8 22.7 1.0
C A:SER311 4.8 14.9 1.0
OG A:SER307 4.9 23.4 1.0
CB A:ILE310 5.0 16.7 1.0
O A:ASN26 5.0 20.4 1.0

Zinc binding site 6 out of 7 in 1r85

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Zinc binding site 6 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn906

b:21.0
occ:0.69
 O A:ALA374 2.2 18.2 1.0
O A:LYS379 2.3 27.8 1.0
OD1 A:ASP297 2.4 21.2 1.0
O A:HOH1111 2.4 23.8 1.0
OD1 A:ASP377 2.4 19.9 1.0
O A:HOH1021 2.4 17.1 1.0
O A:HOH1049 2.4 25.0 1.0
C A:ALA374 3.4 16.7 1.0
CG A:ASP377 3.5 22.1 1.0
CG A:ASP297 3.5 20.1 1.0
C A:LYS379 3.5 27.2 1.0
OD2 A:ASP377 3.8 22.8 1.0
CE A:LYS301 4.0 16.1 0.4
OXT A:LYS379 4.3 35.0 1.0
CA A:ALA374 4.3 17.5 1.0
CB A:ASP297 4.3 17.5 1.0
N A:LYS379 4.3 25.6 1.0
CA A:ASP297 4.4 18.2 1.0
OD2 A:ASP297 4.4 28.6 1.0
N A:ILE375 4.4 15.3 1.0
CA A:ILE375 4.4 15.5 1.0
CA A:LYS379 4.5 27.7 1.0
O A:HOH1057 4.5 19.7 1.0
O A:HOH1356 4.5 41.7 1.0
O A:HOH1264 4.5 45.7 1.0
NZ A:LYS301 4.6 16.2 0.4
O A:ASP377 4.6 20.3 1.0
O A:ASP297 4.6 18.4 1.0
C A:ASP377 4.8 19.5 1.0
CG A:LYS301 4.8 21.3 0.4
CB A:ASP377 4.8 20.2 1.0
CB A:ALA374 4.9 19.0 1.0
C A:ASP297 4.9 18.1 1.0
CD A:LYS301 5.0 17.9 0.4

Zinc binding site 7 out of 7 in 1r85

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Zinc binding site 7 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6): the Wt Enzyme (Monoclinic Form) at 1.45A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn907

b:40.3
occ:0.44
 O A:HOH1506 1.6 39.4 0.4
O1 A:GOL518 1.9 35.9 0.5
OD1 A:ASP282 2.0 23.8 0.6
CG A:ASP282 2.9 22.3 0.6
C1 A:GOL518 3.0 36.0 0.5
OD2 A:ASP282 3.1 22.5 0.6
O A:HOH1056 3.1 40.8 1.0
C2 A:GOL518 3.5 36.2 0.5
O2 A:GOL518 3.6 44.0 0.5
ZN A:ZN903 3.8 23.2 0.6
C3 A:GOL518 3.9 37.0 0.5
O A:HOH1187 4.1 37.0 1.0
OD2 A:ASP282 4.1 25.6 0.4
CG A:ASP282 4.1 21.9 0.4
CB A:ASP282 4.3 19.5 0.6
OD1 A:ASP282 4.3 21.8 0.4
N A:ASP282 4.5 17.5 0.6
N A:ASP282 4.5 17.6 0.4
CB A:TYR281 4.5 18.3 1.0
CD2 A:TYR281 4.6 19.7 1.0
CB A:ASP282 4.7 19.6 0.4
CA A:ASP282 4.7 18.9 0.4
CA A:ASP282 4.7 18.7 0.6
CG A:TYR281 5.0 17.9 1.0

Reference:

G.Zolotnitsky, U.Cogan, N.Adir, V.Solomon, G.Shoham, Y.Shoham. Mapping Glycoside Hydrolase Substrate Subsites By Isothermal Titration Calorimetry. Proc.Natl.Acad.Sci.Usa V. 101 11275 2004.
ISSN: ISSN 0027-8424
PubMed: 15277671
DOI: 10.1073/PNAS.0404311101
Page generated: Wed Oct 16 18:27:31 2024

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