Calcium in PDB 7zei: Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A
Protein crystallography data
The structure of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A, PDB code: 7zei
was solved by
M.Baudrexl,
T.Fida,
B.Berk,
W.Schwarz,
V.V.Zverlov,
M.Groll,
W.Liebl,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
30.00 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.09,
108.74,
251.27,
90,
90,
90
|
R / Rfree (%)
|
12.6 /
15.3
|
Other elements in 7zei:
The structure of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A
(pdb code 7zei). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 6 binding sites of Calcium where determined in the
Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A, PDB code: 7zei:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
Calcium binding site 1 out
of 6 in 7zei
Go back to
Calcium Binding Sites List in 7zei
Calcium binding site 1 out
of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca902
b:29.0
occ:1.00
|
O
|
A:HOH1220
|
2.2
|
26.6
|
1.0
|
NE2
|
A:HIS244
|
2.4
|
26.0
|
1.0
|
O
|
A:HOH1071
|
2.4
|
31.9
|
1.0
|
O
|
A:HOH1248
|
2.5
|
31.3
|
1.0
|
O
|
A:HOH1043
|
2.5
|
18.9
|
1.0
|
O
|
A:HOH1020
|
2.5
|
19.2
|
1.0
|
O
|
A:HOH1157
|
3.1
|
23.7
|
1.0
|
CD2
|
A:HIS244
|
3.2
|
25.8
|
1.0
|
CE1
|
A:HIS244
|
3.5
|
25.0
|
1.0
|
O
|
A:ALA143
|
3.9
|
18.2
|
1.0
|
O
|
A:PRO192
|
4.2
|
18.4
|
1.0
|
CG
|
A:HIS244
|
4.4
|
22.0
|
1.0
|
O
|
A:HOH1123
|
4.5
|
26.5
|
1.0
|
O
|
A:ALA245
|
4.5
|
19.1
|
1.0
|
ND1
|
A:HIS244
|
4.5
|
22.3
|
1.0
|
CA
|
A:GLY191
|
4.7
|
18.0
|
1.0
|
ND2
|
A:ASN193
|
4.7
|
24.6
|
1.0
|
O
|
A:ALA86
|
4.8
|
18.1
|
1.0
|
O
|
A:PRO87
|
4.8
|
19.7
|
1.0
|
C
|
A:GLY191
|
4.9
|
17.9
|
1.0
|
O
|
A:ASP142
|
4.9
|
19.1
|
1.0
|
C
|
A:ALA143
|
5.0
|
18.1
|
1.0
|
|
Calcium binding site 2 out
of 6 in 7zei
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Calcium Binding Sites List in 7zei
Calcium binding site 2 out
of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca902
b:22.7
occ:1.00
|
O
|
B:HOH1249
|
2.3
|
22.9
|
1.0
|
O
|
B:HOH1281
|
2.3
|
26.9
|
1.0
|
O
|
B:HOH1103
|
2.4
|
22.8
|
1.0
|
NE2
|
B:HIS244
|
2.4
|
23.0
|
1.0
|
O
|
B:HOH1146
|
2.4
|
17.7
|
1.0
|
O
|
B:HOH1053
|
2.4
|
18.2
|
1.0
|
O
|
B:HOH1211
|
3.0
|
25.1
|
1.0
|
CD2
|
B:HIS244
|
3.2
|
23.1
|
1.0
|
CE1
|
B:HIS244
|
3.5
|
22.1
|
1.0
|
O
|
B:ALA143
|
4.0
|
17.8
|
1.0
|
O
|
B:PRO192
|
4.2
|
17.2
|
1.0
|
CG
|
B:HIS244
|
4.4
|
20.3
|
1.0
|
O
|
B:HOH1142
|
4.4
|
27.0
|
1.0
|
O
|
B:ALA245
|
4.5
|
19.3
|
1.0
|
ND2
|
B:ASN193
|
4.5
|
21.2
|
1.0
|
ND1
|
B:HIS244
|
4.5
|
20.7
|
1.0
|
CA
|
B:GLY191
|
4.6
|
16.5
|
1.0
|
O
|
B:ALA86
|
4.8
|
16.8
|
1.0
|
C
|
B:GLY191
|
4.8
|
16.6
|
1.0
|
O
|
B:PRO87
|
4.8
|
18.8
|
1.0
|
O
|
B:GLY191
|
4.9
|
17.5
|
1.0
|
O
|
B:ASP142
|
4.9
|
17.8
|
1.0
|
CB
|
B:ALA86
|
4.9
|
17.5
|
1.0
|
C
|
B:ALA143
|
5.0
|
17.4
|
1.0
|
C
|
B:ASP142
|
5.0
|
17.2
|
1.0
|
|
Calcium binding site 3 out
of 6 in 7zei
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Calcium Binding Sites List in 7zei
Calcium binding site 3 out
of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca902
b:24.1
occ:1.00
|
O
|
C:HOH1223
|
2.3
|
23.5
|
1.0
|
O
|
C:HOH1228
|
2.4
|
29.2
|
1.0
|
NE2
|
C:HIS244
|
2.4
|
21.2
|
1.0
|
O
|
C:HOH1054
|
2.5
|
20.7
|
1.0
|
O
|
C:HOH1069
|
2.5
|
20.0
|
1.0
|
O
|
C:HOH1021
|
2.5
|
24.5
|
1.0
|
O
|
C:HOH1148
|
2.8
|
21.9
|
1.0
|
CD2
|
C:HIS244
|
3.2
|
22.1
|
1.0
|
CE1
|
C:HIS244
|
3.5
|
22.4
|
1.0
|
O
|
C:ALA143
|
4.0
|
18.0
|
1.0
|
O
|
C:PRO192
|
4.3
|
19.3
|
1.0
|
O
|
C:ALA245
|
4.4
|
19.7
|
1.0
|
CG
|
C:HIS244
|
4.4
|
21.0
|
1.0
|
ND1
|
C:HIS244
|
4.5
|
21.4
|
1.0
|
ND2
|
C:ASN193
|
4.6
|
22.6
|
1.0
|
O
|
C:PRO87
|
4.6
|
18.9
|
1.0
|
O
|
C:HOH1088
|
4.6
|
27.6
|
1.0
|
O
|
C:ALA86
|
4.7
|
17.9
|
1.0
|
CA
|
C:GLY191
|
4.8
|
18.6
|
1.0
|
CB
|
C:ALA86
|
4.9
|
17.1
|
1.0
|
C
|
C:GLY191
|
4.9
|
18.8
|
1.0
|
O
|
C:ASP142
|
5.0
|
18.3
|
1.0
|
|
Calcium binding site 4 out
of 6 in 7zei
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Calcium Binding Sites List in 7zei
Calcium binding site 4 out
of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca902
b:30.5
occ:1.00
|
O
|
D:HOH1252
|
2.3
|
27.7
|
1.0
|
O
|
D:HOH1056
|
2.4
|
20.7
|
1.0
|
NE2
|
D:HIS244
|
2.4
|
28.0
|
1.0
|
O
|
D:HOH1041
|
2.4
|
30.6
|
1.0
|
O
|
D:HOH1129
|
2.5
|
18.6
|
1.0
|
O
|
D:HOH1269
|
2.5
|
38.3
|
1.0
|
CD2
|
D:HIS244
|
3.2
|
27.2
|
1.0
|
O
|
D:HOH1179
|
3.4
|
28.3
|
1.0
|
CE1
|
D:HIS244
|
3.5
|
27.2
|
1.0
|
O
|
D:HOH1009
|
3.8
|
28.9
|
1.0
|
O
|
D:ALA143
|
4.0
|
16.9
|
1.0
|
O
|
D:PRO192
|
4.2
|
17.7
|
1.0
|
CG
|
D:HIS244
|
4.4
|
24.1
|
1.0
|
O
|
D:ALA245
|
4.5
|
19.8
|
1.0
|
ND1
|
D:HIS244
|
4.5
|
23.4
|
1.0
|
O
|
D:HOH1184
|
4.5
|
29.2
|
1.0
|
CA
|
D:GLY191
|
4.6
|
16.8
|
1.0
|
ND2
|
D:ASN193
|
4.6
|
24.4
|
1.0
|
C
|
D:GLY191
|
4.8
|
16.1
|
1.0
|
O
|
D:ALA86
|
4.8
|
18.4
|
1.0
|
O
|
D:GLY191
|
4.9
|
16.1
|
1.0
|
O
|
D:ASP142
|
4.9
|
17.5
|
1.0
|
C
|
D:ALA143
|
5.0
|
16.8
|
1.0
|
O
|
D:PRO87
|
5.0
|
20.5
|
1.0
|
|
Calcium binding site 5 out
of 6 in 7zei
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Calcium Binding Sites List in 7zei
Calcium binding site 5 out
of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca902
b:28.9
occ:1.00
|
O
|
E:HOH1511
|
2.2
|
28.1
|
1.0
|
O
|
E:HOH1328
|
2.4
|
30.7
|
1.0
|
NE2
|
E:HIS244
|
2.4
|
27.5
|
1.0
|
O
|
E:HOH1341
|
2.4
|
20.5
|
1.0
|
O
|
E:HOH1416
|
2.4
|
18.7
|
1.0
|
O
|
E:HOH1573
|
2.5
|
34.6
|
1.0
|
CD2
|
E:HIS244
|
3.2
|
27.1
|
1.0
|
O
|
E:HOH1451
|
3.4
|
25.1
|
1.0
|
CE1
|
E:HIS244
|
3.5
|
26.2
|
1.0
|
O
|
E:ALA143
|
3.9
|
18.6
|
1.0
|
O
|
E:HOH1304
|
4.0
|
30.0
|
1.0
|
O
|
E:PRO192
|
4.2
|
19.6
|
1.0
|
CG
|
E:HIS244
|
4.4
|
23.6
|
1.0
|
O
|
E:HOH1422
|
4.5
|
30.4
|
1.0
|
ND1
|
E:HIS244
|
4.5
|
22.8
|
1.0
|
O
|
E:ALA245
|
4.5
|
19.8
|
1.0
|
CA
|
E:GLY191
|
4.6
|
19.3
|
1.0
|
ND2
|
E:ASN193
|
4.6
|
25.1
|
1.0
|
C
|
E:GLY191
|
4.8
|
19.2
|
1.0
|
O
|
E:ALA86
|
4.8
|
16.6
|
1.0
|
O
|
E:ASP142
|
4.9
|
18.8
|
1.0
|
O
|
E:GLY191
|
4.9
|
18.9
|
1.0
|
C
|
E:ALA143
|
4.9
|
18.4
|
1.0
|
O
|
E:PRO87
|
4.9
|
19.0
|
1.0
|
C
|
E:ASP142
|
5.0
|
18.1
|
1.0
|
CB
|
E:ALA86
|
5.0
|
17.4
|
1.0
|
|
Calcium binding site 6 out
of 6 in 7zei
Go back to
Calcium Binding Sites List in 7zei
Calcium binding site 6 out
of 6 in the Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca902
b:25.8
occ:1.00
|
O
|
F:HOH1180
|
2.3
|
25.1
|
1.0
|
O
|
F:HOH1218
|
2.4
|
31.0
|
1.0
|
O
|
F:HOH1027
|
2.4
|
27.2
|
1.0
|
O
|
F:HOH1112
|
2.4
|
19.2
|
1.0
|
O
|
F:HOH1035
|
2.4
|
19.8
|
1.0
|
NE2
|
F:HIS244
|
2.4
|
22.6
|
1.0
|
O
|
F:HOH1151
|
3.0
|
27.6
|
1.0
|
CD2
|
F:HIS244
|
3.3
|
24.2
|
1.0
|
CE1
|
F:HIS244
|
3.5
|
22.7
|
1.0
|
O
|
F:ALA143
|
4.0
|
19.2
|
1.0
|
O
|
F:PRO192
|
4.3
|
19.1
|
1.0
|
CG
|
F:HIS244
|
4.5
|
22.3
|
1.0
|
O
|
F:ALA245
|
4.5
|
23.1
|
1.0
|
O
|
F:HOH1109
|
4.5
|
32.7
|
1.0
|
ND2
|
F:ASN193
|
4.6
|
24.4
|
1.0
|
ND1
|
F:HIS244
|
4.6
|
22.1
|
1.0
|
CA
|
F:GLY191
|
4.7
|
19.8
|
1.0
|
O
|
F:ALA86
|
4.8
|
17.7
|
1.0
|
O
|
F:PRO87
|
4.8
|
21.8
|
1.0
|
C
|
F:GLY191
|
4.9
|
19.2
|
1.0
|
O
|
F:ASP142
|
4.9
|
19.0
|
1.0
|
O
|
F:GLY191
|
4.9
|
20.1
|
1.0
|
C
|
F:ALA143
|
4.9
|
19.3
|
1.0
|
C
|
F:ASP142
|
5.0
|
18.4
|
1.0
|
CB
|
F:ALA86
|
5.0
|
17.8
|
1.0
|
|
Reference:
M.Baudrexl,
T.Fida,
B.Berk,
W.H.Schwarz,
V.V.Zverlov,
M.Groll,
W.Liebl.
Biochemical and Structural Characterization of Thermostable GH159 Glycoside Hydrolases Exhibiting Alpha-L-Arabinofuranosidase Activity. Front Mol Biosci V. 9 07439 2022.
ISSN: ESSN 2296-889X
PubMed: 35847984
DOI: 10.3389/FMOLB.2022.907439
Page generated: Fri Jul 19 06:31:32 2024
|