Magnesium 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:
Magnesium Binding Sites:
The binding sites of Magnesium 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 Magnesium atom.
In total 6 binding sites of Magnesium where determined in the
Thermostable GH159 Glycoside Hydrolase From Caldicellulosiruptor at 1.7 A, PDB code: 7zei:
Jump to Magnesium binding site number:
1;
2;
3;
4;
5;
6;
Magnesium binding site 1 out
of 6 in 7zei
Go back to
Magnesium Binding Sites List in 7zei
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901
b:25.8
occ:1.00
|
O
|
A:HOH1001
|
2.2
|
42.2
|
1.0
|
O
|
A:HOH1050
|
2.3
|
43.0
|
1.0
|
OD1
|
A:ASP246
|
2.3
|
22.3
|
1.0
|
O
|
A:HOH1107
|
2.3
|
24.9
|
1.0
|
O
|
A:HOH1349
|
2.4
|
43.1
|
1.0
|
O
|
A:HOH1263
|
2.6
|
36.7
|
1.0
|
O
|
A:HOH1055
|
2.6
|
23.6
|
1.0
|
O
|
A:HOH1123
|
3.0
|
26.5
|
1.0
|
CG
|
A:ASP246
|
3.1
|
20.8
|
1.0
|
OD2
|
A:ASP246
|
3.3
|
23.3
|
1.0
|
ND2
|
A:ASN193
|
3.9
|
24.6
|
1.0
|
OE2
|
A:GLU88
|
4.0
|
27.0
|
1.0
|
O
|
A:VAL247
|
4.1
|
19.5
|
1.0
|
OE1
|
A:GLU88
|
4.3
|
22.8
|
1.0
|
O
|
A:HOH1151
|
4.3
|
34.5
|
1.0
|
OG1
|
A:THR21
|
4.4
|
25.5
|
1.0
|
O
|
A:HOH1112
|
4.4
|
25.3
|
1.0
|
O
|
A:HOH1256
|
4.4
|
29.3
|
1.0
|
OD1
|
A:ASN193
|
4.5
|
25.9
|
1.0
|
CB
|
A:ASP246
|
4.6
|
20.0
|
1.0
|
CD
|
A:GLU88
|
4.6
|
24.8
|
1.0
|
CG
|
A:ASN193
|
4.7
|
21.8
|
1.0
|
O
|
A:HOH1022
|
4.7
|
35.3
|
1.0
|
O
|
A:HOH1074
|
4.8
|
26.1
|
1.0
|
N
|
A:VAL247
|
4.9
|
18.6
|
1.0
|
O
|
A:HOH1070
|
4.9
|
22.4
|
1.0
|
O
|
A:ILE22
|
5.0
|
18.1
|
1.0
|
|
Magnesium binding site 2 out
of 6 in 7zei
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Magnesium Binding Sites List in 7zei
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901
b:25.9
occ:1.00
|
O
|
B:HOH1147
|
2.3
|
26.6
|
1.0
|
O
|
B:HOH1038
|
2.3
|
41.7
|
1.0
|
O
|
B:HOH1247
|
2.4
|
37.8
|
1.0
|
OD1
|
B:ASP246
|
2.4
|
21.2
|
1.0
|
O
|
B:HOH1042
|
2.4
|
24.4
|
1.0
|
O
|
B:HOH1142
|
3.1
|
27.0
|
1.0
|
CG
|
B:ASP246
|
3.2
|
19.7
|
1.0
|
OD2
|
B:ASP246
|
3.4
|
20.6
|
1.0
|
ND2
|
B:ASN193
|
4.0
|
21.2
|
1.0
|
OE2
|
B:GLU88
|
4.0
|
21.5
|
1.0
|
O
|
B:VAL247
|
4.0
|
19.1
|
1.0
|
O
|
B:HOH1120
|
4.2
|
24.1
|
1.0
|
O
|
B:HOH1214
|
4.2
|
68.1
|
1.0
|
OD1
|
B:ASN193
|
4.3
|
21.6
|
1.0
|
OE1
|
B:GLU88
|
4.4
|
19.6
|
1.0
|
OG1
|
B:THR21
|
4.4
|
26.5
|
1.0
|
O
|
B:HOH1229
|
4.5
|
31.9
|
1.0
|
CG
|
B:ASN193
|
4.6
|
19.4
|
1.0
|
CD
|
B:GLU88
|
4.6
|
20.0
|
1.0
|
CB
|
B:ASP246
|
4.7
|
19.1
|
1.0
|
O
|
B:HOH1016
|
4.8
|
33.1
|
1.0
|
O
|
B:HOH1043
|
4.8
|
21.1
|
1.0
|
O
|
B:HOH1125
|
4.8
|
28.2
|
1.0
|
N
|
B:VAL247
|
4.8
|
18.1
|
1.0
|
|
Magnesium binding site 3 out
of 6 in 7zei
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Magnesium Binding Sites List in 7zei
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901
b:26.6
occ:1.00
|
O
|
C:HOH1304
|
2.2
|
48.9
|
1.0
|
O
|
C:HOH1128
|
2.3
|
28.7
|
1.0
|
O
|
C:HOH1016
|
2.3
|
41.3
|
1.0
|
OD1
|
C:ASP246
|
2.3
|
22.7
|
1.0
|
O
|
C:HOH1008
|
2.4
|
39.3
|
1.0
|
O
|
C:HOH1099
|
2.5
|
24.1
|
1.0
|
O
|
C:HOH1088
|
2.9
|
27.6
|
1.0
|
CG
|
C:ASP246
|
3.2
|
20.9
|
1.0
|
OD2
|
C:ASP246
|
3.4
|
21.1
|
1.0
|
ND2
|
C:ASN193
|
3.9
|
22.6
|
1.0
|
O
|
C:HOH1275
|
3.9
|
56.6
|
1.0
|
OE2
|
C:GLU88
|
4.0
|
24.0
|
1.0
|
O
|
C:VAL247
|
4.1
|
18.6
|
1.0
|
O
|
C:HOH1106
|
4.2
|
34.4
|
1.0
|
O
|
C:HOH1066
|
4.2
|
26.6
|
1.0
|
OD1
|
C:ASN193
|
4.3
|
25.0
|
1.0
|
OE1
|
C:GLU88
|
4.3
|
21.0
|
1.0
|
OG1
|
C:THR21
|
4.4
|
24.9
|
1.0
|
CG
|
C:ASN193
|
4.5
|
21.6
|
1.0
|
CD
|
C:GLU88
|
4.6
|
21.4
|
1.0
|
CB
|
C:ASP246
|
4.6
|
19.5
|
1.0
|
O
|
C:HOH1216
|
4.7
|
32.7
|
1.0
|
O
|
C:HOH1030
|
4.7
|
33.5
|
1.0
|
O
|
C:HOH1036
|
4.8
|
22.4
|
1.0
|
N
|
C:VAL247
|
4.8
|
18.5
|
1.0
|
|
Magnesium binding site 4 out
of 6 in 7zei
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Magnesium Binding Sites List in 7zei
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901
b:25.7
occ:1.00
|
O
|
D:HOH1343
|
2.1
|
50.1
|
1.0
|
O
|
D:HOH1178
|
2.3
|
27.1
|
1.0
|
O
|
D:HOH1010
|
2.3
|
43.1
|
1.0
|
OD1
|
D:ASP246
|
2.3
|
22.7
|
1.0
|
O
|
D:HOH1007
|
2.3
|
34.0
|
1.0
|
O
|
D:HOH1050
|
2.5
|
25.0
|
1.0
|
O
|
D:HOH1219
|
2.6
|
46.9
|
1.0
|
O
|
D:HOH1184
|
3.1
|
29.2
|
1.0
|
CG
|
D:ASP246
|
3.2
|
22.1
|
1.0
|
OD2
|
D:ASP246
|
3.3
|
25.0
|
1.0
|
ND2
|
D:ASN193
|
3.9
|
24.4
|
1.0
|
OE2
|
D:GLU88
|
4.0
|
23.0
|
1.0
|
O
|
D:VAL247
|
4.1
|
20.9
|
1.0
|
O
|
D:HOH1088
|
4.2
|
36.0
|
1.0
|
O
|
D:HOH1125
|
4.2
|
25.0
|
1.0
|
OE1
|
D:GLU88
|
4.4
|
19.6
|
1.0
|
OD1
|
D:ASN193
|
4.4
|
25.1
|
1.0
|
O
|
D:HOH1226
|
4.5
|
31.5
|
1.0
|
OG1
|
D:THR21
|
4.5
|
27.2
|
1.0
|
CB
|
D:ASP246
|
4.6
|
20.6
|
1.0
|
CD
|
D:GLU88
|
4.6
|
21.0
|
1.0
|
CG
|
D:ASN193
|
4.6
|
20.9
|
1.0
|
O
|
D:HOH1085
|
4.9
|
32.4
|
1.0
|
O
|
D:HOH1053
|
4.9
|
21.5
|
1.0
|
N
|
D:VAL247
|
4.9
|
18.1
|
1.0
|
|
Magnesium binding site 5 out
of 6 in 7zei
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Magnesium Binding Sites List in 7zei
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901
b:27.4
occ:1.00
|
O
|
E:HOH1301
|
2.1
|
47.1
|
1.0
|
OD1
|
E:ASP246
|
2.3
|
23.7
|
1.0
|
O
|
E:HOH1406
|
2.3
|
25.0
|
1.0
|
O
|
E:HOH1534
|
2.3
|
34.9
|
1.0
|
O
|
E:HOH1644
|
2.4
|
39.0
|
1.0
|
O
|
E:HOH1347
|
2.6
|
26.2
|
1.0
|
CG
|
E:ASP246
|
3.1
|
22.0
|
1.0
|
O
|
E:HOH1422
|
3.1
|
30.4
|
1.0
|
OD2
|
E:ASP246
|
3.2
|
24.0
|
1.0
|
OE2
|
E:GLU88
|
4.0
|
25.4
|
1.0
|
ND2
|
E:ASN193
|
4.1
|
25.1
|
1.0
|
O
|
E:VAL247
|
4.1
|
20.4
|
1.0
|
O
|
E:HOH1429
|
4.2
|
26.3
|
1.0
|
O
|
E:HOH1433
|
4.3
|
37.1
|
1.0
|
O
|
E:HOH1544
|
4.3
|
29.5
|
1.0
|
OE1
|
E:GLU88
|
4.4
|
21.3
|
1.0
|
OG1
|
E:THR21
|
4.5
|
25.5
|
1.0
|
OD1
|
E:ASN193
|
4.5
|
27.2
|
1.0
|
CB
|
E:ASP246
|
4.6
|
20.5
|
1.0
|
O
|
E:HOH1316
|
4.6
|
39.2
|
1.0
|
CD
|
E:GLU88
|
4.6
|
22.8
|
1.0
|
O
|
E:HOH1413
|
4.7
|
26.5
|
1.0
|
CG
|
E:ASN193
|
4.7
|
23.2
|
1.0
|
N
|
E:VAL247
|
4.9
|
19.1
|
1.0
|
O
|
E:ILE22
|
5.0
|
18.4
|
1.0
|
O
|
E:HOH1386
|
5.0
|
22.8
|
1.0
|
|
Magnesium binding site 6 out
of 6 in 7zei
Go back to
Magnesium Binding Sites List in 7zei
Magnesium 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 Magnesium with other atoms in the Mg 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:Mg901
b:34.4
occ:1.00
|
O
|
F:HOH1153
|
2.2
|
26.3
|
1.0
|
O
|
F:HOH1166
|
2.3
|
44.1
|
1.0
|
O
|
F:HOH1001
|
2.3
|
42.3
|
1.0
|
OD1
|
F:ASP246
|
2.4
|
25.2
|
1.0
|
O
|
F:HOH1295
|
2.5
|
41.8
|
1.0
|
O
|
F:HOH1022
|
2.5
|
29.6
|
1.0
|
O
|
F:HOH1109
|
3.1
|
32.7
|
1.0
|
CG
|
F:ASP246
|
3.2
|
24.1
|
1.0
|
OD2
|
F:ASP246
|
3.3
|
25.0
|
1.0
|
O
|
F:VAL247
|
3.9
|
23.2
|
1.0
|
ND2
|
F:ASN193
|
4.0
|
24.4
|
1.0
|
OE2
|
F:GLU88
|
4.1
|
24.6
|
1.0
|
O
|
F:HOH1130
|
4.1
|
29.7
|
1.0
|
O
|
F:HOH1058
|
4.2
|
44.3
|
1.0
|
OD1
|
F:ASN193
|
4.3
|
27.2
|
1.0
|
OE1
|
F:GLU88
|
4.3
|
22.5
|
1.0
|
O
|
F:HOH1203
|
4.4
|
40.6
|
1.0
|
OG1
|
F:THR21
|
4.6
|
28.2
|
1.0
|
CG
|
F:ASN193
|
4.6
|
24.2
|
1.0
|
CB
|
F:ASP246
|
4.6
|
22.7
|
1.0
|
CD
|
F:GLU88
|
4.7
|
22.5
|
1.0
|
O
|
F:HOH1063
|
4.8
|
23.3
|
1.0
|
O
|
F:HOH1002
|
4.8
|
36.5
|
1.0
|
O
|
F:HOH1076
|
4.8
|
31.9
|
1.0
|
N
|
F:VAL247
|
4.9
|
22.7
|
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: Thu Oct 3 16:45:07 2024
|