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Zinc in PDB 1r87: Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution

Enzymatic activity of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution

All present enzymatic activity of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution:
3.2.1.8;

Protein crystallography data

The structure of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution, PDB code: 1r87 was solved by M.Bar, G.Golan, 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) 25.00 / 1.67
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 120.422, 61.221, 89.583, 90.00, 119.50, 90.00
R / Rfree (%) 16.9 / 18.6

Other elements in 1r87:

The structure of Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution (pdb code 1r87). 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution, PDB code: 1r87:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7;

Zinc binding site 1 out of 7 in 1r87

Go back to Zinc Binding Sites List in 1r87
Zinc binding site 1 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn901

b:18.9
occ:1.00
 OD2 A:ASP365 1.8 19.8 1.0
NE2 A:HIS11 2.0 16.9 1.0
CL A:CL701 2.2 20.9 1.0
CG A:ASP365 2.8 19.7 1.0
CD2 A:HIS11 3.0 17.6 1.0
CE1 A:HIS11 3.0 17.6 1.0
OD1 A:ASP365 3.1 17.1 1.0
CD A:LYS367 4.0 15.2 1.0
ND1 A:HIS11 4.1 18.2 1.0
CG A:HIS11 4.2 18.5 1.0
CB A:ASP365 4.2 17.8 1.0
CB A:LYS367 4.5 15.2 1.0
O A:HOH1064 4.6 24.8 1.0
NZ A:LYS367 4.8 20.1 1.0
CG A:LYS367 4.8 16.2 1.0

Zinc binding site 2 out of 7 in 1r87

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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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn902

b:20.9
occ:1.00
 OD2 A:ASP21 2.0 17.9 1.0
O A:HOH1153 2.0 22.0 1.0
O A:HOH1155 2.1 21.7 1.0
O A:HOH1154 2.1 23.4 1.0
O A:HOH1156 2.2 22.8 1.0
O A:HOH1152 2.2 20.3 1.0
CG A:ASP21 3.0 19.9 1.0
OD1 A:ASP21 3.2 19.5 1.0
O A:HOH1097 4.1 28.0 1.0
O A:PHE52 4.1 17.0 1.0
O A:LYS49 4.1 21.9 1.0
O A:HOH1187 4.2 40.5 1.0
O A:HOH1099 4.4 40.6 1.0
CB A:ASP21 4.4 17.9 1.0
O A:ARG50 4.4 20.2 1.0
OE1 A:GLN22 4.5 31.0 1.0
CB A:ASN53 4.7 15.5 1.0
C A:PHE52 4.7 15.4 1.0
CG A:GLN22 4.7 20.9 1.0

Zinc binding site 3 out of 7 in 1r87

Go back to Zinc Binding Sites List in 1r87
Zinc binding site 3 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:19.1
occ:0.50
 OD2 A:ASP282 1.7 34.9 1.0
O A:HOH1234 2.2 35.0 1.0
CG A:ASP282 2.7 27.8 1.0
OD1 A:ASP282 3.0 29.3 1.0
ZN A:ZN904 3.5 37.6 0.4
O A:HOH1205 3.9 38.3 1.0
CB A:ASP282 4.2 22.7 1.0
O A:HOH1062 4.3 30.6 1.0
CB A:THR280 4.5 22.6 1.0
N A:ASP282 4.6 19.9 1.0
O A:HOH1180 4.8 38.9 1.0
CG2 A:THR280 4.9 25.9 1.0

Zinc binding site 4 out of 7 in 1r87

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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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn904

b:37.6
occ:0.40
 O A:HOH1180 2.0 38.9 1.0
OD1 A:ASP282 2.3 29.3 1.0
CG A:ASP282 3.3 27.8 1.0
ZN A:ZN903 3.5 19.1 0.5
OD2 A:ASP282 3.7 34.9 1.0
N A:ASP282 4.5 19.9 1.0
CB A:TYR281 4.5 18.2 1.0
CB A:ASP282 4.5 22.7 1.0
CA A:ASP282 4.7 20.6 1.0
CD2 A:TYR281 4.7 18.7 1.0

Zinc binding site 5 out of 7 in 1r87

Go back to Zinc Binding Sites List in 1r87
Zinc binding site 5 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn905

b:22.6
occ:0.95
 CL A:CL702 2.0 32.2 1.0
NE2 A:HIS322 2.0 25.9 0.8
O A:HOH1024 2.1 23.0 1.0
OE2 A:GLU58 2.3 25.9 1.0
CE1 A:HIS322 2.3 25.7 0.2
NE2 A:HIS322 2.3 26.8 0.2
OE1 A:GLU58 2.4 24.9 1.0
CD A:GLU58 2.6 23.3 1.0
CE1 A:HIS322 2.9 29.0 0.8
CD2 A:HIS322 3.0 26.0 0.8
ND1 A:HIS322 3.5 26.8 0.2
CD2 A:HIS322 3.6 27.3 0.2
O3B A:XYP451 3.7 22.2 1.0
OE2 A:GLU35 4.0 25.8 1.0
O A:HOH1020 4.0 18.1 1.0
CG A:GLU58 4.1 22.6 1.0
ND1 A:HIS322 4.1 28.9 0.8
CG A:HIS322 4.2 23.9 0.8
CG A:HIS322 4.2 24.6 0.2
O A:HOH1162 4.4 33.7 1.0
CG A:GLU35 4.4 22.0 1.0
O2B A:XYP451 4.5 23.3 1.0
ND2 A:ASN59 4.5 21.6 1.0
CD A:GLU35 4.7 22.9 1.0
N A:TRP324 4.7 17.2 1.0
C3B A:XYP451 4.8 23.2 1.0
CB A:GLU58 4.9 18.9 1.0
CB A:TRP324 5.0 17.3 1.0

Zinc binding site 6 out of 7 in 1r87

Go back to Zinc Binding Sites List in 1r87
Zinc binding site 6 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn906

b:20.3
occ:0.35
 O A:GLU27 2.2 20.7 1.0
O A:SER307 2.3 21.8 1.0
O A:ILE310 2.4 19.2 1.0
O A:HOH1159 2.4 33.1 1.0
O A:HOH1221 2.5 44.1 1.0
O2 A:SO4801 2.6 44.7 0.6
C A:GLU27 3.4 20.1 1.0
C A:SER307 3.4 21.1 1.0
C A:ILE310 3.5 19.3 1.0
S A:SO4801 3.7 45.3 0.6
O1 A:SO4801 3.9 47.6 0.6
O A:HOH1182 4.0 44.5 1.0
O3 A:SO4801 4.0 47.7 0.6
CA A:SER311 4.0 17.7 1.0
CA A:SER307 4.2 19.2 1.0
N A:SER311 4.2 17.1 1.0
CB A:PHE28 4.2 16.1 1.0
CA A:PHE28 4.2 17.5 1.0
CB A:SER307 4.2 21.1 1.0
N A:PHE28 4.3 18.3 1.0
N A:ILE310 4.3 20.3 1.0
N A:ASP308 4.4 21.9 1.0
CA A:GLU27 4.5 18.8 1.0
CA A:ASP308 4.5 26.7 1.0
CA A:ILE310 4.5 17.2 1.0
CD2 A:PHE28 4.6 17.4 1.0
O A:HOH1197 4.6 35.0 1.0
C A:ASP308 4.8 26.6 1.0
C A:SER311 4.8 18.1 1.0
OG A:SER307 4.9 23.4 1.0
O A:HOH1140 4.9 49.3 1.0
O4 A:SO4801 4.9 44.0 0.6
CG A:PHE28 4.9 16.5 1.0

Zinc binding site 7 out of 7 in 1r87

Go back to Zinc Binding Sites List in 1r87
Zinc binding site 7 out of 7 in the Crystal Structure of the Extracellular Xylanase From Geobacillus Stearothermophilus T-6 (XT6, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A 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, Monoclinic Form): the Complex of the Wt Enzyme with Xylopentaose at 1.67A Resolution within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn907

b:26.0
occ:0.80
 OD1 A:ASP297 2.3 21.4 1.0
O A:ALA374 2.3 19.8 1.0
OXT A:LYS379 2.3 31.7 1.0
O A:HOH1017 2.4 26.9 1.0
O A:HOH1052 2.4 24.2 1.0
OD1 A:ASP377 2.4 22.6 1.0
O A:HOH1012 2.6 21.1 1.0
CG A:ASP297 3.4 23.6 1.0
C A:ALA374 3.5 18.3 1.0
CG A:ASP377 3.5 24.5 1.0
C A:LYS379 3.5 35.6 1.0
OD2 A:ASP377 3.8 24.6 1.0
CB A:ASP297 4.2 19.3 1.0
N A:LYS379 4.2 31.4 1.0
OD2 A:ASP297 4.3 29.2 1.0
O A:LYS379 4.3 37.0 1.0
CA A:ALA374 4.3 18.1 1.0
O A:HOH1143 4.3 43.5 1.0
CE A:LYS301 4.3 33.0 1.0
CA A:ASP297 4.4 17.4 1.0
N A:ILE375 4.4 16.0 1.0
CA A:ILE375 4.4 17.1 1.0
CA A:LYS379 4.4 34.7 1.0
O A:HOH1235 4.5 37.9 1.0
O A:ASP377 4.5 19.3 1.0
O A:HOH1022 4.5 19.4 1.0
NZ A:LYS301 4.5 34.6 1.0
O A:ASP297 4.6 18.0 1.0
C A:ASP377 4.7 22.9 1.0
CB A:ASP377 4.9 24.0 1.0
CB A:LYS379 4.9 36.2 1.0
CB A:ALA374 4.9 18.6 1.0
C A:ASP297 4.9 17.5 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 18:28:29 2024

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