Calcium in PDB 9fyz: Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Enzymatic activity of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
All present enzymatic activity of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe:
3.2.1.135;
Protein crystallography data
The structure of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe, PDB code: 9fyz
was solved by
I.B.Pickles,
O.Moroz,
G.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
58.25 /
2.43
|
Space group
|
P 32 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
105.978,
105.978,
753.691,
90,
90,
120
|
R / Rfree (%)
|
23 /
28.1
|
Calcium Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Calcium atom in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
(pdb code 9fyz). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 12 binding sites of Calcium where determined in the
Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe, PDB code: 9fyz:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Calcium binding site 1 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 1 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca706
b:58.8
occ:1.00
|
OD2
|
A:ASP166
|
2.3
|
40.9
|
1.0
|
OD1
|
A:ASN138
|
2.3
|
47.8
|
1.0
|
OD1
|
A:ASP144
|
2.3
|
43.5
|
1.0
|
O
|
A:HOH855
|
2.4
|
39.1
|
1.0
|
O
|
A:GLY164
|
2.5
|
43.2
|
1.0
|
O
|
A:ASN140
|
2.6
|
53.5
|
1.0
|
OD1
|
A:ASN143
|
2.6
|
70.8
|
1.0
|
CG
|
A:ASN138
|
3.1
|
49.0
|
1.0
|
CG
|
A:ASP166
|
3.4
|
41.8
|
1.0
|
C
|
A:ASN140
|
3.4
|
56.7
|
1.0
|
ND2
|
A:ASN138
|
3.5
|
46.0
|
1.0
|
CG
|
A:ASP144
|
3.5
|
41.8
|
1.0
|
C
|
A:GLY164
|
3.6
|
38.9
|
1.0
|
CG
|
A:ASN143
|
3.8
|
63.5
|
1.0
|
CB
|
A:ASP166
|
3.8
|
43.2
|
1.0
|
N
|
A:ASP144
|
4.0
|
44.6
|
1.0
|
CA
|
A:PRO141
|
4.0
|
71.0
|
1.0
|
N
|
A:PRO141
|
4.1
|
68.0
|
1.0
|
CA
|
A:GLY164
|
4.2
|
33.4
|
1.0
|
N
|
A:ASN140
|
4.2
|
53.8
|
1.0
|
OD2
|
A:ASP144
|
4.3
|
50.9
|
1.0
|
CB
|
A:ASN138
|
4.3
|
47.5
|
1.0
|
CA
|
A:ASP144
|
4.3
|
43.5
|
1.0
|
CA
|
A:ASN140
|
4.3
|
58.9
|
1.0
|
ND2
|
A:ASN143
|
4.4
|
64.4
|
1.0
|
O
|
A:ARG214
|
4.4
|
41.6
|
1.0
|
O
|
A:GLY165
|
4.4
|
44.4
|
1.0
|
C
|
A:GLY165
|
4.4
|
33.8
|
1.0
|
OD1
|
A:ASP166
|
4.4
|
45.8
|
1.0
|
CA
|
A:ASN138
|
4.5
|
46.9
|
1.0
|
CB
|
A:ASP144
|
4.5
|
36.1
|
1.0
|
C
|
A:ASN143
|
4.5
|
52.5
|
1.0
|
C
|
A:PRO141
|
4.6
|
60.4
|
1.0
|
N
|
A:GLY165
|
4.7
|
41.1
|
1.0
|
N
|
A:ASP166
|
4.7
|
36.1
|
1.0
|
N
|
A:ASN143
|
4.8
|
64.8
|
1.0
|
O
|
A:PRO141
|
4.8
|
69.7
|
1.0
|
N
|
A:GLY139
|
4.8
|
41.1
|
1.0
|
CB
|
A:ASN140
|
4.8
|
62.0
|
1.0
|
CA
|
A:GLY165
|
4.9
|
35.8
|
1.0
|
CA
|
A:ASP166
|
4.9
|
35.3
|
1.0
|
C
|
A:ASN138
|
4.9
|
46.0
|
1.0
|
CA
|
A:ASN143
|
5.0
|
56.4
|
1.0
|
CB
|
A:ASN143
|
5.0
|
59.4
|
1.0
|
|
Calcium binding site 2 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 2 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca707
b:43.2
occ:1.00
|
OD2
|
A:ASP300
|
2.3
|
39.7
|
1.0
|
O
|
A:HOH934
|
2.3
|
39.6
|
1.0
|
O
|
A:ILE290
|
2.4
|
49.6
|
1.0
|
OD1
|
A:ASN242
|
2.4
|
39.8
|
1.0
|
O
|
A:TYR335
|
2.4
|
42.2
|
1.0
|
O
|
A:HOH848
|
2.6
|
39.4
|
1.0
|
O
|
A:HOH821
|
2.6
|
36.2
|
1.0
|
OD1
|
A:ASP300
|
2.7
|
39.0
|
1.0
|
CG
|
A:ASP300
|
2.8
|
42.3
|
1.0
|
CG
|
A:ASN242
|
3.4
|
41.0
|
1.0
|
C
|
A:TYR335
|
3.5
|
34.1
|
1.0
|
C
|
A:ILE290
|
3.5
|
50.3
|
1.0
|
ND2
|
A:ASN242
|
3.9
|
47.5
|
1.0
|
CB
|
A:ASP300
|
4.3
|
46.0
|
1.0
|
CB
|
A:TYR335
|
4.3
|
35.1
|
1.0
|
CA
|
A:ALA336
|
4.3
|
44.4
|
1.0
|
N
|
A:ALA336
|
4.4
|
39.2
|
1.0
|
CA
|
A:ILE290
|
4.4
|
50.3
|
1.0
|
ND2
|
A:ASN261
|
4.4
|
33.0
|
1.0
|
O
|
A:GLY292
|
4.4
|
49.6
|
1.0
|
O
|
A:ASN242
|
4.4
|
35.0
|
1.0
|
N
|
A:ASP291
|
4.5
|
46.4
|
1.0
|
CA
|
A:TYR335
|
4.5
|
43.1
|
1.0
|
O
|
A:PHE301
|
4.5
|
45.1
|
1.0
|
CA
|
A:ASP291
|
4.5
|
47.7
|
1.0
|
CB
|
A:ASN242
|
4.7
|
38.5
|
1.0
|
CG2
|
A:ILE290
|
4.7
|
36.0
|
1.0
|
OE1
|
A:GLN303
|
4.7
|
48.5
|
1.0
|
NE2
|
A:GLN303
|
4.8
|
50.2
|
1.0
|
C
|
A:ASP291
|
4.8
|
54.5
|
1.0
|
CA
|
A:ASN242
|
4.9
|
36.5
|
1.0
|
|
Calcium binding site 3 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 3 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca704
b:73.3
occ:1.00
|
O
|
B:HOH844
|
2.3
|
56.6
|
1.0
|
OD1
|
B:ASP144
|
2.3
|
71.3
|
1.0
|
OD2
|
B:ASP166
|
2.4
|
72.6
|
1.0
|
O
|
B:GLY164
|
2.4
|
47.2
|
1.0
|
OD1
|
B:ASN138
|
2.4
|
58.8
|
1.0
|
OD1
|
B:ASN143
|
2.7
|
79.1
|
1.0
|
O
|
B:ASN140
|
2.7
|
77.0
|
1.0
|
CG
|
B:ASN138
|
3.1
|
62.5
|
1.0
|
CG
|
B:ASP166
|
3.4
|
65.2
|
1.0
|
C
|
B:GLY164
|
3.5
|
56.3
|
1.0
|
ND2
|
B:ASN138
|
3.5
|
46.0
|
1.0
|
CG
|
B:ASP144
|
3.5
|
57.5
|
1.0
|
C
|
B:ASN140
|
3.6
|
74.1
|
1.0
|
CB
|
B:ASP166
|
3.8
|
53.9
|
1.0
|
CG
|
B:ASN143
|
3.9
|
74.4
|
1.0
|
N
|
B:ASP144
|
4.0
|
53.5
|
1.0
|
CA
|
B:GLY164
|
4.1
|
55.5
|
1.0
|
CA
|
B:PRO141
|
4.1
|
71.7
|
1.0
|
N
|
B:PRO141
|
4.2
|
81.9
|
1.0
|
OD2
|
B:ASP144
|
4.3
|
60.8
|
1.0
|
CA
|
B:ASP144
|
4.3
|
57.0
|
1.0
|
CB
|
B:ASN138
|
4.3
|
58.7
|
1.0
|
N
|
B:ASN140
|
4.3
|
69.8
|
1.0
|
O
|
B:GLY165
|
4.3
|
55.9
|
1.0
|
C
|
B:GLY165
|
4.4
|
50.1
|
1.0
|
O
|
B:ARG214
|
4.4
|
68.4
|
1.0
|
CA
|
B:ASN138
|
4.5
|
59.3
|
1.0
|
CB
|
B:ASP144
|
4.5
|
60.0
|
1.0
|
OD1
|
B:ASP166
|
4.5
|
78.0
|
1.0
|
CA
|
B:ASN140
|
4.5
|
70.5
|
1.0
|
ND2
|
B:ASN143
|
4.5
|
64.6
|
1.0
|
C
|
B:ASN143
|
4.5
|
54.9
|
1.0
|
N
|
B:GLY165
|
4.5
|
55.7
|
1.0
|
N
|
B:ASP166
|
4.6
|
46.5
|
1.0
|
C
|
B:PRO141
|
4.6
|
66.4
|
1.0
|
CA
|
B:GLY165
|
4.8
|
50.8
|
1.0
|
CA
|
B:ASP166
|
4.8
|
50.4
|
1.0
|
N
|
B:ASN143
|
4.9
|
67.6
|
1.0
|
O
|
B:PRO141
|
4.9
|
65.8
|
1.0
|
N
|
B:GLY139
|
4.9
|
54.1
|
1.0
|
C
|
B:ASN138
|
4.9
|
56.9
|
1.0
|
CB
|
B:ASN140
|
5.0
|
65.3
|
1.0
|
|
Calcium binding site 4 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 4 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca705
b:93.9
occ:1.00
|
O
|
B:HOH821
|
2.7
|
52.3
|
1.0
|
O
|
B:TYR335
|
3.0
|
68.2
|
1.0
|
O
|
B:HOH874
|
3.4
|
75.8
|
1.0
|
OD2
|
B:ASP300
|
3.7
|
83.1
|
1.0
|
CD2
|
B:TYR335
|
3.7
|
93.6
|
1.0
|
C
|
B:TYR335
|
4.0
|
71.2
|
1.0
|
CB
|
B:ASN242
|
4.1
|
51.1
|
1.0
|
CG
|
B:ASP300
|
4.2
|
67.6
|
1.0
|
O
|
B:ILE290
|
4.2
|
86.1
|
1.0
|
OE1
|
B:GLN303
|
4.3
|
82.8
|
1.0
|
CB
|
B:TYR335
|
4.4
|
85.4
|
1.0
|
CG
|
B:TYR335
|
4.5
|
94.9
|
1.0
|
CE2
|
B:TYR335
|
4.5
|
75.3
|
1.0
|
OD1
|
B:ASP300
|
4.5
|
80.6
|
1.0
|
NE2
|
B:GLN303
|
4.6
|
97.6
|
1.0
|
O
|
B:ASN242
|
4.7
|
47.0
|
1.0
|
CA
|
B:ASN242
|
4.7
|
46.8
|
1.0
|
CA
|
B:ALA336
|
4.8
|
79.5
|
1.0
|
N
|
B:ALA336
|
4.8
|
72.6
|
1.0
|
CA
|
B:TYR335
|
4.8
|
82.9
|
1.0
|
CB
|
B:ASP300
|
4.9
|
60.2
|
1.0
|
O
|
B:PHE301
|
4.9
|
49.3
|
1.0
|
CD
|
B:GLN303
|
4.9
|
75.4
|
1.0
|
|
Calcium binding site 5 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 5 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca706
b:102.7
occ:1.00
|
OD2
|
C:ASP166
|
2.3
|
103.4
|
1.0
|
O
|
C:GLY164
|
2.3
|
83.1
|
1.0
|
OD1
|
C:ASP144
|
2.4
|
100.4
|
1.0
|
OD1
|
C:ASN138
|
2.5
|
75.8
|
1.0
|
OD1
|
C:ASN143
|
2.6
|
107.0
|
1.0
|
O
|
C:ASN140
|
2.7
|
65.0
|
1.0
|
CG
|
C:ASN138
|
3.2
|
79.5
|
1.0
|
CG
|
C:ASP166
|
3.3
|
84.3
|
1.0
|
C
|
C:GLY164
|
3.4
|
87.0
|
1.0
|
ND2
|
C:ASN138
|
3.5
|
78.5
|
1.0
|
CG
|
C:ASP144
|
3.6
|
86.8
|
1.0
|
C
|
C:ASN140
|
3.6
|
89.5
|
1.0
|
CB
|
C:ASP166
|
3.7
|
82.3
|
1.0
|
CG
|
C:ASN143
|
3.8
|
117.7
|
1.0
|
CA
|
C:GLY164
|
4.1
|
78.5
|
1.0
|
N
|
C:ASP144
|
4.1
|
85.4
|
1.0
|
CA
|
C:PRO141
|
4.2
|
84.4
|
1.0
|
N
|
C:PRO141
|
4.2
|
93.7
|
1.0
|
O
|
C:GLY165
|
4.3
|
83.2
|
1.0
|
C
|
C:GLY165
|
4.3
|
73.7
|
1.0
|
CB
|
C:ASN138
|
4.3
|
72.3
|
1.0
|
OD2
|
C:ASP144
|
4.3
|
100.3
|
1.0
|
CA
|
C:ASP144
|
4.3
|
88.0
|
1.0
|
N
|
C:ASN140
|
4.3
|
77.1
|
1.0
|
O
|
C:ARG214
|
4.4
|
112.5
|
1.0
|
ND2
|
C:ASN143
|
4.4
|
123.5
|
1.0
|
OD1
|
C:ASP166
|
4.4
|
88.1
|
1.0
|
CA
|
C:ASN138
|
4.5
|
78.8
|
1.0
|
CA
|
C:ASN140
|
4.5
|
88.2
|
1.0
|
N
|
C:GLY165
|
4.5
|
77.9
|
1.0
|
CB
|
C:ASP144
|
4.5
|
86.2
|
1.0
|
N
|
C:ASP166
|
4.5
|
68.4
|
1.0
|
C
|
C:ASN143
|
4.5
|
89.2
|
1.0
|
C
|
C:PRO141
|
4.7
|
72.6
|
1.0
|
CA
|
C:GLY165
|
4.7
|
80.5
|
1.0
|
CA
|
C:ASP166
|
4.8
|
84.5
|
1.0
|
N
|
C:ASN143
|
4.9
|
97.0
|
1.0
|
N
|
C:GLY139
|
4.9
|
68.2
|
1.0
|
O
|
C:PRO141
|
4.9
|
87.2
|
1.0
|
CB
|
C:ASN140
|
5.0
|
98.4
|
1.0
|
C
|
C:ASN138
|
5.0
|
63.6
|
1.0
|
|
Calcium binding site 6 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 6 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca707
b:135.1
occ:1.00
|
O
|
C:ILE290
|
2.5
|
149.8
|
1.0
|
OD1
|
C:ASN242
|
2.6
|
108.1
|
1.0
|
O
|
C:TYR335
|
2.9
|
116.9
|
1.0
|
CG
|
C:ASN242
|
3.6
|
88.5
|
1.0
|
C
|
C:ILE290
|
3.7
|
136.8
|
1.0
|
O
|
C:PHE301
|
3.8
|
97.8
|
1.0
|
ND2
|
C:ASN261
|
4.0
|
111.3
|
1.0
|
C
|
C:TYR335
|
4.0
|
106.8
|
1.0
|
O
|
C:ASN242
|
4.0
|
81.1
|
1.0
|
CB
|
C:ASP300
|
4.0
|
78.2
|
1.0
|
OE1
|
C:GLN303
|
4.0
|
81.8
|
1.0
|
NE2
|
C:GLN303
|
4.1
|
86.9
|
1.0
|
ND2
|
C:ASN242
|
4.1
|
105.6
|
1.0
|
CA
|
C:ALA336
|
4.4
|
92.0
|
1.0
|
CD
|
C:GLN303
|
4.5
|
83.9
|
1.0
|
CA
|
C:ASP291
|
4.6
|
111.9
|
1.0
|
N
|
C:ASP291
|
4.6
|
112.9
|
1.0
|
CA
|
C:ILE290
|
4.6
|
126.7
|
1.0
|
N
|
C:ALA336
|
4.6
|
95.0
|
1.0
|
CA
|
C:ASN242
|
4.6
|
70.2
|
1.0
|
CB
|
C:ASN242
|
4.6
|
75.1
|
1.0
|
C
|
C:ASN242
|
4.7
|
76.3
|
1.0
|
CA
|
C:ASP300
|
4.7
|
87.7
|
1.0
|
O
|
C:GLY292
|
4.8
|
112.6
|
1.0
|
CB
|
C:TYR335
|
4.9
|
92.4
|
1.0
|
N
|
C:PHE301
|
4.9
|
100.0
|
1.0
|
C
|
C:PHE301
|
4.9
|
93.5
|
1.0
|
C
|
C:ASP300
|
4.9
|
97.5
|
1.0
|
CG2
|
C:ILE290
|
5.0
|
90.9
|
1.0
|
C
|
C:ASP291
|
5.0
|
110.0
|
1.0
|
|
Calcium binding site 7 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 7 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca706
b:106.0
occ:1.00
|
OD1
|
D:ASP144
|
2.3
|
97.2
|
1.0
|
OD1
|
D:ASN143
|
2.4
|
124.2
|
1.0
|
OD2
|
D:ASP166
|
2.5
|
108.3
|
1.0
|
O
|
D:GLY164
|
2.5
|
104.4
|
1.0
|
OD1
|
D:ASN138
|
2.6
|
78.1
|
1.0
|
O
|
D:ASN140
|
2.7
|
97.7
|
1.0
|
CG
|
D:ASN138
|
3.3
|
86.0
|
1.0
|
CG
|
D:ASP166
|
3.5
|
107.1
|
1.0
|
CG
|
D:ASP144
|
3.5
|
85.0
|
1.0
|
C
|
D:ASN140
|
3.6
|
101.5
|
1.0
|
C
|
D:GLY164
|
3.6
|
100.7
|
1.0
|
CG
|
D:ASN143
|
3.6
|
124.2
|
1.0
|
ND2
|
D:ASN138
|
3.7
|
68.7
|
1.0
|
CB
|
D:ASP166
|
3.8
|
100.6
|
1.0
|
N
|
D:ASP144
|
3.9
|
97.3
|
1.0
|
CA
|
D:GLY164
|
4.1
|
92.3
|
1.0
|
CA
|
D:PRO141
|
4.1
|
76.5
|
1.0
|
CA
|
D:ASP144
|
4.2
|
76.6
|
1.0
|
O
|
D:ARG214
|
4.2
|
93.9
|
1.0
|
N
|
D:PRO141
|
4.2
|
88.1
|
1.0
|
ND2
|
D:ASN143
|
4.3
|
113.2
|
1.0
|
C
|
D:ASN143
|
4.3
|
121.1
|
1.0
|
OD2
|
D:ASP144
|
4.3
|
95.2
|
1.0
|
O
|
D:GLY165
|
4.4
|
69.9
|
1.0
|
CB
|
D:ASP144
|
4.4
|
80.2
|
1.0
|
N
|
D:ASN140
|
4.4
|
78.1
|
1.0
|
C
|
D:GLY165
|
4.4
|
81.8
|
1.0
|
CA
|
D:ASN140
|
4.5
|
84.2
|
1.0
|
CB
|
D:ASN138
|
4.5
|
83.7
|
1.0
|
C
|
D:PRO141
|
4.6
|
81.3
|
1.0
|
OD1
|
D:ASP166
|
4.6
|
80.0
|
1.0
|
N
|
D:GLY165
|
4.7
|
98.7
|
1.0
|
N
|
D:ASN143
|
4.7
|
118.0
|
1.0
|
CA
|
D:ASN138
|
4.7
|
91.1
|
1.0
|
N
|
D:ASP166
|
4.7
|
87.2
|
1.0
|
CA
|
D:ASN143
|
4.8
|
128.0
|
1.0
|
O
|
D:PRO141
|
4.8
|
72.7
|
1.0
|
CB
|
D:ASN143
|
4.8
|
128.1
|
1.0
|
O
|
D:ASN143
|
4.8
|
121.1
|
1.0
|
CA
|
D:ASP166
|
4.9
|
93.3
|
1.0
|
CA
|
D:GLY165
|
4.9
|
92.5
|
1.0
|
CB
|
D:ASN140
|
5.0
|
95.7
|
1.0
|
|
Calcium binding site 8 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 8 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca707
b:75.6
occ:1.00
|
OD1
|
D:ASN242
|
2.3
|
76.4
|
1.0
|
OD2
|
D:ASP300
|
2.3
|
56.5
|
1.0
|
O
|
D:ILE290
|
2.4
|
83.5
|
1.0
|
O
|
D:TYR335
|
2.4
|
66.5
|
1.0
|
O
|
D:HOH811
|
2.5
|
63.6
|
1.0
|
O
|
D:HOH817
|
2.6
|
70.7
|
1.0
|
OD1
|
D:ASP300
|
2.7
|
64.3
|
1.0
|
CG
|
D:ASP300
|
2.8
|
74.7
|
1.0
|
CG
|
D:ASN242
|
3.4
|
82.2
|
1.0
|
C
|
D:TYR335
|
3.5
|
62.9
|
1.0
|
C
|
D:ILE290
|
3.6
|
74.5
|
1.0
|
ND2
|
D:ASN242
|
3.9
|
80.0
|
1.0
|
CB
|
D:TYR335
|
4.2
|
59.7
|
1.0
|
CB
|
D:ASP300
|
4.3
|
64.7
|
1.0
|
CA
|
D:ALA336
|
4.3
|
69.9
|
1.0
|
N
|
D:ALA336
|
4.3
|
70.3
|
1.0
|
CA
|
D:ILE290
|
4.4
|
81.7
|
1.0
|
O
|
D:ASN242
|
4.4
|
66.7
|
1.0
|
ND2
|
D:ASN261
|
4.4
|
48.2
|
1.0
|
O
|
D:GLY292
|
4.4
|
69.8
|
1.0
|
CA
|
D:TYR335
|
4.5
|
60.3
|
1.0
|
O
|
D:PHE301
|
4.5
|
48.0
|
1.0
|
N
|
D:ASP291
|
4.5
|
59.2
|
1.0
|
CB
|
D:ASN242
|
4.6
|
81.3
|
1.0
|
CA
|
D:ASP291
|
4.6
|
55.4
|
1.0
|
OE1
|
D:GLN303
|
4.6
|
77.1
|
1.0
|
CG2
|
D:ILE290
|
4.6
|
82.7
|
1.0
|
NE2
|
D:GLN303
|
4.7
|
89.6
|
1.0
|
CA
|
D:ASN242
|
4.8
|
75.9
|
1.0
|
C
|
D:ASP291
|
4.9
|
62.8
|
1.0
|
|
Calcium binding site 9 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 9 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 9 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca704
b:77.2
occ:1.00
|
OD2
|
E:ASP300
|
2.4
|
69.8
|
1.0
|
OD1
|
E:ASN242
|
2.5
|
84.2
|
1.0
|
O
|
E:TYR335
|
2.5
|
64.3
|
1.0
|
O
|
E:ILE290
|
2.5
|
77.5
|
1.0
|
O
|
E:HOH811
|
2.7
|
66.4
|
1.0
|
OD1
|
E:ASP300
|
2.8
|
70.4
|
1.0
|
CG
|
E:ASP300
|
2.9
|
63.9
|
1.0
|
CG
|
E:ASN242
|
3.5
|
88.2
|
1.0
|
C
|
E:TYR335
|
3.6
|
69.4
|
1.0
|
C
|
E:ILE290
|
3.7
|
67.6
|
1.0
|
CA
|
E:ALA336
|
4.1
|
79.9
|
1.0
|
ND2
|
E:ASN242
|
4.1
|
84.2
|
1.0
|
O
|
E:PHE301
|
4.1
|
67.2
|
1.0
|
OE1
|
E:GLN303
|
4.2
|
66.0
|
1.0
|
ND2
|
E:ASN261
|
4.2
|
74.2
|
1.0
|
N
|
E:ALA336
|
4.3
|
78.6
|
1.0
|
O
|
E:ASN242
|
4.3
|
57.7
|
1.0
|
NE2
|
E:GLN303
|
4.3
|
76.2
|
1.0
|
CB
|
E:ASP300
|
4.3
|
66.8
|
1.0
|
CB
|
E:TYR335
|
4.6
|
66.7
|
1.0
|
CA
|
E:ILE290
|
4.6
|
76.2
|
1.0
|
CG2
|
E:ILE290
|
4.6
|
77.2
|
1.0
|
CB
|
E:ASN242
|
4.6
|
90.2
|
1.0
|
N
|
E:ASP291
|
4.6
|
69.5
|
1.0
|
CD
|
E:GLN303
|
4.7
|
66.6
|
1.0
|
CA
|
E:TYR335
|
4.7
|
66.7
|
1.0
|
CA
|
E:ASP291
|
4.7
|
61.5
|
1.0
|
CA
|
E:ASN242
|
4.7
|
75.1
|
1.0
|
O
|
E:GLY292
|
4.8
|
75.3
|
1.0
|
CB
|
E:ALA336
|
4.9
|
86.2
|
1.0
|
C
|
E:ASN242
|
4.9
|
67.7
|
1.0
|
|
Calcium binding site 10 out
of 12 in 9fyz
Go back to
Calcium Binding Sites List in 9fyz
Calcium binding site 10 out
of 12 in the Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 10 of Crystal Structure of Susa Amylase From Bacteroides Thetaiotaomicron Covalently Bound to Alpha-1,6 Branched Pseudo-Trisaccharide Activity- Based Probe within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca705
b:131.6
occ:1.00
|
OD1
|
E:ASP144
|
2.3
|
97.9
|
1.0
|
OD2
|
E:ASP166
|
2.3
|
142.8
|
1.0
|
O
|
E:ASN140
|
2.4
|
137.0
|
1.0
|
OD1
|
E:ASN138
|
2.4
|
119.7
|
1.0
|
OD1
|
E:ASN143
|
2.5
|
107.9
|
1.0
|
O
|
E:GLY164
|
2.7
|
100.2
|
1.0
|
CG
|
E:ASN138
|
3.2
|
102.5
|
1.0
|
C
|
E:ASN140
|
3.2
|
118.0
|
1.0
|
CG
|
E:ASP166
|
3.4
|
121.0
|
1.0
|
CG
|
E:ASP144
|
3.5
|
101.0
|
1.0
|
ND2
|
E:ASN138
|
3.6
|
93.7
|
1.0
|
CG
|
E:ASN143
|
3.7
|
105.7
|
1.0
|
C
|
E:GLY164
|
3.8
|
113.4
|
1.0
|
CA
|
E:PRO141
|
3.9
|
113.8
|
1.0
|
CB
|
E:ASP166
|
3.9
|
100.2
|
1.0
|
N
|
E:PRO141
|
3.9
|
124.0
|
1.0
|
N
|
E:ASP144
|
4.0
|
98.3
|
1.0
|
N
|
E:ASN140
|
4.1
|
108.7
|
1.0
|
CA
|
E:ASN140
|
4.2
|
111.9
|
1.0
|
ND2
|
E:ASN143
|
4.3
|
108.5
|
1.0
|
CA
|
E:ASP144
|
4.3
|
92.3
|
1.0
|
OD2
|
E:ASP144
|
4.3
|
95.7
|
1.0
|
CA
|
E:GLY164
|
4.4
|
127.8
|
1.0
|
C
|
E:PRO141
|
4.4
|
109.5
|
1.0
|
C
|
E:ASN143
|
4.4
|
108.7
|
1.0
|
CB
|
E:ASN138
|
4.4
|
90.6
|
1.0
|
O
|
E:ARG214
|
4.5
|
112.0
|
1.0
|
OD1
|
E:ASP166
|
4.5
|
128.5
|
1.0
|
CB
|
E:ASP144
|
4.5
|
92.1
|
1.0
|
N
|
E:ASN143
|
4.6
|
137.6
|
1.0
|
CA
|
E:ASN138
|
4.6
|
106.9
|
1.0
|
O
|
E:GLY165
|
4.6
|
121.4
|
1.0
|
C
|
E:GLY165
|
4.6
|
98.8
|
1.0
|
O
|
E:PRO141
|
4.7
|
115.8
|
1.0
|
CB
|
E:ASN140
|
4.7
|
107.7
|
1.0
|
CA
|
E:ASN143
|
4.8
|
122.8
|
1.0
|
CB
|
E:ASN143
|
4.8
|
107.8
|
1.0
|
N
|
E:ASP166
|
4.8
|
87.4
|
1.0
|
N
|
E:GLY165
|
4.9
|
101.0
|
1.0
|
N
|
E:GLY139
|
4.9
|
138.6
|
1.0
|
C
|
E:ASN138
|
5.0
|
133.1
|
1.0
|
N
|
E:SER142
|
5.0
|
115.2
|
1.0
|
|
Reference:
I.B.Pickles,
Y.Chen,
O.Moroz,
H.A.Brown,
C.De Boer,
Z.Armstrong,
N.G.S.Mcgregor,
M.Artola,
J.D.C.Codee,
N.M.Koropatkin,
H.S.Overkleeft,
G.J.Davies.
Precision Activity-Based Alpha-Amylase Probes For Dissection and Annotation of Linear and Branched-Chain Starch-Degrading Enzymes. Angew.Chem.Int.Ed.Engl. 15219 2024.
ISSN: ESSN 1521-3773
PubMed: 39601378
DOI: 10.1002/ANIE.202415219
Page generated: Sun Dec 15 09:47:24 2024
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