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:
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 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
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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 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
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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
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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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