Atomistry » Zinc » PDB 1r2y-1raf » 1r87
Atomistry »
  Zinc »
    PDB 1r2y-1raf »
      1r87 »

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

Go back to Zinc Binding Sites List in 1r87
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

Go back to Zinc Binding Sites List in 1r87
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

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy