Calcium in PDB 3ai7: Crystal Structure of Bifidobacterium Longum Phosphoketolase
Enzymatic activity of Crystal Structure of Bifidobacterium Longum Phosphoketolase
All present enzymatic activity of Crystal Structure of Bifidobacterium Longum Phosphoketolase:
4.1.2.22;
Protein crystallography data
The structure of Crystal Structure of Bifidobacterium Longum Phosphoketolase, PDB code: 3ai7
was solved by
K.Takahashi,
U.Tagami,
N.Shimba,
T.Kashiwagi,
K.Ishikawa,
E.Suzuki,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
47.87 /
2.20
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
142.260,
184.410,
157.440,
90.00,
97.31,
90.00
|
|
R / Rfree (%)
|
14.7 /
20.6
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
(pdb code 3ai7). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Crystal Structure of Bifidobacterium Longum Phosphoketolase, PDB code: 3ai7:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 3ai7
Go back to
Calcium Binding Sites List in 3ai7
Calcium binding site 1 out
of 8 in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
 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 Bifidobacterium Longum Phosphoketolase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca901
b:11.0
occ:1.00
|
O2A
|
A:TPP900
|
2.0
|
17.0
|
1.0
|
|
OD1
|
A:ASP182
|
2.2
|
11.3
|
1.0
|
|
O
|
A:TYR217
|
2.2
|
16.2
|
1.0
|
|
OD1
|
A:ASN215
|
2.2
|
13.9
|
1.0
|
|
O1B
|
A:TPP900
|
2.2
|
11.9
|
1.0
|
|
O
|
A:HOH5052
|
2.3
|
20.9
|
1.0
|
|
CG
|
A:ASN215
|
3.1
|
13.0
|
1.0
|
|
PB
|
A:TPP900
|
3.3
|
11.6
|
1.0
|
|
PA
|
A:TPP900
|
3.4
|
16.3
|
1.0
|
|
ND2
|
A:ASN215
|
3.4
|
15.8
|
1.0
|
|
CG
|
A:ASP182
|
3.4
|
11.7
|
1.0
|
|
C
|
A:TYR217
|
3.4
|
15.3
|
1.0
|
|
O2B
|
A:TPP900
|
3.7
|
17.9
|
1.0
|
|
O3A
|
A:TPP900
|
3.7
|
15.8
|
1.0
|
|
N
|
A:TYR217
|
4.0
|
11.5
|
1.0
|
|
OD2
|
A:ASP182
|
4.0
|
13.4
|
1.0
|
|
N
|
A:ASP182
|
4.1
|
12.5
|
1.0
|
|
NZ
|
A:LYS300
|
4.2
|
14.6
|
1.0
|
|
O7
|
A:TPP900
|
4.2
|
16.6
|
1.0
|
|
N
|
A:GLY183
|
4.3
|
12.7
|
1.0
|
|
O
|
A:HIS213
|
4.3
|
14.6
|
1.0
|
|
CA
|
A:TYR217
|
4.3
|
13.0
|
1.0
|
|
N
|
A:LYS218
|
4.4
|
15.3
|
1.0
|
|
CG2
|
A:THR223
|
4.4
|
12.7
|
1.0
|
|
CB
|
A:ASN215
|
4.5
|
10.9
|
1.0
|
|
N
|
A:GLY216
|
4.5
|
13.2
|
1.0
|
|
CA
|
A:LYS218
|
4.5
|
15.6
|
1.0
|
|
O1A
|
A:TPP900
|
4.5
|
15.5
|
1.0
|
|
CB
|
A:ASP182
|
4.6
|
11.2
|
1.0
|
|
N
|
A:ASN215
|
4.6
|
12.2
|
1.0
|
|
CA
|
A:ASP182
|
4.7
|
11.9
|
1.0
|
|
C
|
A:ASN215
|
4.7
|
13.2
|
1.0
|
|
CE
|
A:LYS300
|
4.8
|
13.0
|
1.0
|
|
O3B
|
A:TPP900
|
4.8
|
17.5
|
1.0
|
|
CD
|
A:LYS300
|
4.8
|
17.0
|
1.0
|
|
CA
|
A:ASN215
|
4.8
|
13.4
|
1.0
|
|
C
|
A:ASP182
|
4.9
|
12.6
|
1.0
|
|
Calcium binding site 2 out
of 8 in 3ai7
Go back to
Calcium Binding Sites List in 3ai7
Calcium binding site 2 out
of 8 in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
 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 Bifidobacterium Longum Phosphoketolase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca901
b:13.4
occ:1.00
|
O1A
|
B:TPP900
|
2.1
|
17.2
|
1.0
|
|
O3B
|
B:TPP900
|
2.2
|
18.2
|
1.0
|
|
OD2
|
B:ASP182
|
2.2
|
13.8
|
1.0
|
|
OD1
|
B:ASN215
|
2.2
|
16.0
|
1.0
|
|
O
|
B:HOH5051
|
2.3
|
15.9
|
1.0
|
|
O
|
B:TYR217
|
2.3
|
14.3
|
1.0
|
|
CG
|
B:ASN215
|
3.2
|
14.2
|
1.0
|
|
PB
|
B:TPP900
|
3.3
|
11.7
|
1.0
|
|
PA
|
B:TPP900
|
3.4
|
13.9
|
1.0
|
|
CG
|
B:ASP182
|
3.4
|
13.9
|
1.0
|
|
ND2
|
B:ASN215
|
3.5
|
14.7
|
1.0
|
|
C
|
B:TYR217
|
3.5
|
13.1
|
1.0
|
|
O3A
|
B:TPP900
|
3.7
|
16.3
|
1.0
|
|
O2B
|
B:TPP900
|
3.8
|
16.2
|
1.0
|
|
N
|
B:ASP182
|
3.9
|
12.5
|
1.0
|
|
OD1
|
B:ASP182
|
4.0
|
15.5
|
1.0
|
|
N
|
B:TYR217
|
4.1
|
11.6
|
1.0
|
|
N
|
B:GLY183
|
4.1
|
15.4
|
1.0
|
|
O
|
B:HIS213
|
4.1
|
13.9
|
1.0
|
|
O7
|
B:TPP900
|
4.2
|
18.8
|
1.0
|
|
CG2
|
B:THR223
|
4.2
|
15.2
|
1.0
|
|
NZ
|
B:LYS300
|
4.3
|
12.0
|
1.0
|
|
CA
|
B:TYR217
|
4.4
|
12.3
|
1.0
|
|
N
|
B:LYS218
|
4.4
|
14.8
|
1.0
|
|
N
|
B:GLY216
|
4.4
|
12.5
|
1.0
|
|
N
|
B:ASN215
|
4.5
|
12.0
|
1.0
|
|
CB
|
B:ASN215
|
4.5
|
12.2
|
1.0
|
|
CB
|
B:ASP182
|
4.6
|
13.3
|
1.0
|
|
CA
|
B:ASP182
|
4.6
|
13.7
|
1.0
|
|
CD
|
B:LYS300
|
4.6
|
18.8
|
1.0
|
|
CA
|
B:LYS218
|
4.6
|
13.2
|
1.0
|
|
O2A
|
B:TPP900
|
4.7
|
14.0
|
1.0
|
|
O1B
|
B:TPP900
|
4.7
|
19.0
|
1.0
|
|
C
|
B:ASN215
|
4.7
|
13.4
|
1.0
|
|
C
|
B:ASP182
|
4.8
|
14.4
|
1.0
|
|
CA
|
B:ASN215
|
4.8
|
13.1
|
1.0
|
|
CE
|
B:LYS300
|
4.8
|
12.4
|
1.0
|
|
C
|
B:GLY181
|
4.9
|
12.9
|
1.0
|
|
CA
|
B:GLY181
|
5.0
|
13.6
|
1.0
|
|
Calcium binding site 3 out
of 8 in 3ai7
Go back to
Calcium Binding Sites List in 3ai7
Calcium binding site 3 out
of 8 in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
 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 Bifidobacterium Longum Phosphoketolase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca901
b:12.3
occ:1.00
|
O1A
|
C:TPP900
|
2.2
|
19.9
|
1.0
|
|
O
|
C:HOH5053
|
2.2
|
14.0
|
1.0
|
|
O
|
C:TYR217
|
2.2
|
11.1
|
1.0
|
|
O2B
|
C:TPP900
|
2.2
|
14.5
|
1.0
|
|
OD1
|
C:ASP182
|
2.3
|
19.1
|
1.0
|
|
OD1
|
C:ASN215
|
2.4
|
14.2
|
1.0
|
|
PB
|
C:TPP900
|
3.2
|
14.8
|
1.0
|
|
CG
|
C:ASN215
|
3.3
|
16.0
|
1.0
|
|
PA
|
C:TPP900
|
3.4
|
16.8
|
1.0
|
|
C
|
C:TYR217
|
3.4
|
12.6
|
1.0
|
|
CG
|
C:ASP182
|
3.5
|
18.2
|
1.0
|
|
O3A
|
C:TPP900
|
3.6
|
21.4
|
1.0
|
|
ND2
|
C:ASN215
|
3.7
|
20.4
|
1.0
|
|
O1B
|
C:TPP900
|
3.7
|
15.2
|
1.0
|
|
N
|
C:TYR217
|
3.9
|
13.6
|
1.0
|
|
N
|
C:GLY183
|
4.0
|
13.4
|
1.0
|
|
OD2
|
C:ASP182
|
4.1
|
20.7
|
1.0
|
|
N
|
C:ASP182
|
4.1
|
15.5
|
1.0
|
|
O7
|
C:TPP900
|
4.2
|
25.2
|
1.0
|
|
NZ
|
C:LYS300
|
4.2
|
16.9
|
1.0
|
|
CG2
|
C:THR223
|
4.3
|
18.3
|
1.0
|
|
CA
|
C:TYR217
|
4.3
|
13.2
|
1.0
|
|
N
|
C:LYS218
|
4.3
|
12.9
|
1.0
|
|
O
|
C:HIS213
|
4.4
|
14.4
|
1.0
|
|
CA
|
C:LYS218
|
4.5
|
16.1
|
1.0
|
|
CD
|
C:LYS300
|
4.6
|
16.0
|
1.0
|
|
N
|
C:ASN215
|
4.6
|
16.8
|
1.0
|
|
CB
|
C:ASP182
|
4.6
|
16.3
|
1.0
|
|
CA
|
C:ASP182
|
4.6
|
15.6
|
1.0
|
|
N
|
C:GLY216
|
4.6
|
15.9
|
1.0
|
|
CB
|
C:ASN215
|
4.6
|
15.5
|
1.0
|
|
O2A
|
C:TPP900
|
4.7
|
20.1
|
1.0
|
|
C
|
C:ASP182
|
4.8
|
14.0
|
1.0
|
|
O3B
|
C:TPP900
|
4.8
|
19.7
|
1.0
|
|
C
|
C:ASN215
|
4.8
|
16.0
|
1.0
|
|
CE
|
C:LYS300
|
4.9
|
13.3
|
1.0
|
|
CA
|
C:ASN215
|
4.9
|
15.8
|
1.0
|
|
CA
|
C:GLY183
|
4.9
|
13.7
|
1.0
|
|
C
|
C:GLY181
|
5.0
|
16.2
|
1.0
|
|
Calcium binding site 4 out
of 8 in 3ai7
Go back to
Calcium Binding Sites List in 3ai7
Calcium binding site 4 out
of 8 in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
 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 Bifidobacterium Longum Phosphoketolase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca901
b:12.9
occ:1.00
|
O1A
|
D:TPP900
|
2.1
|
20.5
|
1.0
|
|
O3B
|
D:TPP900
|
2.1
|
13.0
|
1.0
|
|
O
|
D:TYR217
|
2.2
|
11.8
|
1.0
|
|
O
|
D:HOH1179
|
2.2
|
10.9
|
1.0
|
|
OD1
|
D:ASN215
|
2.3
|
17.0
|
1.0
|
|
OD1
|
D:ASP182
|
2.3
|
19.1
|
1.0
|
|
PB
|
D:TPP900
|
3.3
|
13.9
|
1.0
|
|
CG
|
D:ASN215
|
3.3
|
16.2
|
1.0
|
|
PA
|
D:TPP900
|
3.4
|
19.2
|
1.0
|
|
C
|
D:TYR217
|
3.4
|
13.5
|
1.0
|
|
CG
|
D:ASP182
|
3.6
|
20.8
|
1.0
|
|
O3A
|
D:TPP900
|
3.7
|
19.6
|
1.0
|
|
ND2
|
D:ASN215
|
3.7
|
15.7
|
1.0
|
|
O2B
|
D:TPP900
|
3.8
|
15.6
|
1.0
|
|
N
|
D:GLY183
|
4.0
|
15.9
|
1.0
|
|
N
|
D:TYR217
|
4.0
|
12.4
|
1.0
|
|
N
|
D:ASP182
|
4.1
|
17.3
|
1.0
|
|
O7
|
D:TPP900
|
4.2
|
24.9
|
1.0
|
|
OD2
|
D:ASP182
|
4.2
|
21.1
|
1.0
|
|
O
|
D:HIS213
|
4.2
|
17.7
|
1.0
|
|
NZ
|
D:LYS300
|
4.3
|
18.7
|
1.0
|
|
CG2
|
D:THR223
|
4.3
|
16.4
|
1.0
|
|
N
|
D:LYS218
|
4.3
|
11.8
|
1.0
|
|
CA
|
D:TYR217
|
4.3
|
14.2
|
1.0
|
|
CA
|
D:LYS218
|
4.4
|
13.8
|
1.0
|
|
N
|
D:ASN215
|
4.6
|
14.1
|
1.0
|
|
CA
|
D:ASP182
|
4.6
|
17.8
|
1.0
|
|
CD
|
D:LYS300
|
4.6
|
17.1
|
1.0
|
|
CB
|
D:ASN215
|
4.6
|
12.9
|
1.0
|
|
O1B
|
D:TPP900
|
4.7
|
17.0
|
1.0
|
|
CB
|
D:ASP182
|
4.7
|
17.4
|
1.0
|
|
O2A
|
D:TPP900
|
4.7
|
26.6
|
1.0
|
|
N
|
D:GLY216
|
4.7
|
13.4
|
1.0
|
|
C
|
D:ASP182
|
4.7
|
16.4
|
1.0
|
|
C
|
D:ASN215
|
4.8
|
13.3
|
1.0
|
|
CE
|
D:LYS300
|
4.9
|
16.2
|
1.0
|
|
C
|
D:GLY181
|
4.9
|
17.5
|
1.0
|
|
CA
|
D:GLY183
|
4.9
|
14.1
|
1.0
|
|
CA
|
D:ASN215
|
4.9
|
13.7
|
1.0
|
|
CA
|
D:GLY181
|
5.0
|
17.8
|
1.0
|
|
Calcium binding site 5 out
of 8 in 3ai7
Go back to
Calcium Binding Sites List in 3ai7
Calcium binding site 5 out
of 8 in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
 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 Bifidobacterium Longum Phosphoketolase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca901
b:12.1
occ:1.00
|
O3B
|
E:TPP900
|
2.1
|
19.5
|
1.0
|
|
O1A
|
E:TPP900
|
2.1
|
18.7
|
1.0
|
|
OD1
|
E:ASP182
|
2.2
|
14.2
|
1.0
|
|
OD1
|
E:ASN215
|
2.3
|
13.2
|
1.0
|
|
O
|
E:TYR217
|
2.3
|
12.9
|
1.0
|
|
O
|
E:HOH1452
|
2.4
|
16.9
|
1.0
|
|
CG
|
E:ASN215
|
3.1
|
10.8
|
1.0
|
|
PB
|
E:TPP900
|
3.2
|
15.6
|
1.0
|
|
PA
|
E:TPP900
|
3.3
|
17.1
|
1.0
|
|
ND2
|
E:ASN215
|
3.4
|
15.7
|
1.0
|
|
CG
|
E:ASP182
|
3.4
|
15.4
|
1.0
|
|
O3A
|
E:TPP900
|
3.5
|
23.9
|
1.0
|
|
C
|
E:TYR217
|
3.5
|
11.8
|
1.0
|
|
O2B
|
E:TPP900
|
3.8
|
19.8
|
1.0
|
|
OD2
|
E:ASP182
|
4.0
|
12.5
|
1.0
|
|
N
|
E:GLY183
|
4.0
|
12.5
|
1.0
|
|
N
|
E:TYR217
|
4.0
|
11.2
|
1.0
|
|
N
|
E:ASP182
|
4.1
|
12.5
|
1.0
|
|
O7
|
E:TPP900
|
4.2
|
21.6
|
1.0
|
|
O
|
E:HIS213
|
4.2
|
13.3
|
1.0
|
|
NZ
|
E:LYS300
|
4.3
|
12.4
|
1.0
|
|
CA
|
E:TYR217
|
4.4
|
11.1
|
1.0
|
|
CG2
|
E:THR223
|
4.4
|
11.1
|
1.0
|
|
N
|
E:LYS218
|
4.4
|
12.0
|
1.0
|
|
CA
|
E:LYS218
|
4.5
|
11.3
|
1.0
|
|
O2A
|
E:TPP900
|
4.5
|
25.0
|
1.0
|
|
CB
|
E:ASP182
|
4.6
|
11.8
|
1.0
|
|
CA
|
E:ASP182
|
4.6
|
12.5
|
1.0
|
|
CB
|
E:ASN215
|
4.6
|
9.0
|
1.0
|
|
N
|
E:GLY216
|
4.6
|
11.6
|
1.0
|
|
O1B
|
E:TPP900
|
4.6
|
21.5
|
1.0
|
|
N
|
E:ASN215
|
4.7
|
12.4
|
1.0
|
|
CD
|
E:LYS300
|
4.7
|
9.7
|
1.0
|
|
C
|
E:ASP182
|
4.7
|
12.7
|
1.0
|
|
CE
|
E:LYS300
|
4.9
|
14.4
|
1.0
|
|
C
|
E:GLY181
|
4.9
|
12.7
|
1.0
|
|
C
|
E:ASN215
|
4.9
|
11.8
|
1.0
|
|
CA
|
E:GLY183
|
4.9
|
12.2
|
1.0
|
|
CA
|
E:ASN215
|
5.0
|
10.3
|
1.0
|
|
Calcium binding site 6 out
of 8 in 3ai7
Go back to
Calcium Binding Sites List in 3ai7
Calcium binding site 6 out
of 8 in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
 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 Bifidobacterium Longum Phosphoketolase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca901
b:13.8
occ:1.00
|
O2A
|
F:TPP900
|
2.0
|
19.8
|
1.0
|
|
O1B
|
F:TPP900
|
2.2
|
19.9
|
1.0
|
|
O
|
F:HOH5054
|
2.2
|
15.7
|
1.0
|
|
OD2
|
F:ASP182
|
2.2
|
15.2
|
1.0
|
|
OD1
|
F:ASN215
|
2.3
|
21.5
|
1.0
|
|
O
|
F:TYR217
|
2.4
|
16.2
|
1.0
|
|
PB
|
F:TPP900
|
3.2
|
16.1
|
1.0
|
|
CG
|
F:ASN215
|
3.2
|
19.0
|
1.0
|
|
PA
|
F:TPP900
|
3.4
|
18.6
|
1.0
|
|
CG
|
F:ASP182
|
3.4
|
19.5
|
1.0
|
|
ND2
|
F:ASN215
|
3.5
|
18.8
|
1.0
|
|
C
|
F:TYR217
|
3.6
|
15.0
|
1.0
|
|
O3A
|
F:TPP900
|
3.6
|
20.5
|
1.0
|
|
O3B
|
F:TPP900
|
3.7
|
18.3
|
1.0
|
|
OD1
|
F:ASP182
|
4.0
|
17.6
|
1.0
|
|
N
|
F:TYR217
|
4.0
|
15.4
|
1.0
|
|
N
|
F:GLY183
|
4.1
|
15.4
|
1.0
|
|
N
|
F:ASP182
|
4.1
|
16.1
|
1.0
|
|
O
|
F:HIS213
|
4.2
|
14.7
|
1.0
|
|
NZ
|
F:LYS300
|
4.2
|
16.7
|
1.0
|
|
O7
|
F:TPP900
|
4.2
|
20.9
|
1.0
|
|
CA
|
F:TYR217
|
4.4
|
14.4
|
1.0
|
|
CG2
|
F:THR223
|
4.5
|
13.2
|
1.0
|
|
N
|
F:LYS218
|
4.5
|
14.8
|
1.0
|
|
CB
|
F:ASN215
|
4.6
|
18.9
|
1.0
|
|
CA
|
F:LYS218
|
4.6
|
17.6
|
1.0
|
|
O1A
|
F:TPP900
|
4.6
|
21.9
|
1.0
|
|
CB
|
F:ASP182
|
4.6
|
14.9
|
1.0
|
|
N
|
F:GLY216
|
4.6
|
18.7
|
1.0
|
|
N
|
F:ASN215
|
4.6
|
18.2
|
1.0
|
|
CD
|
F:LYS300
|
4.7
|
17.4
|
1.0
|
|
CA
|
F:ASP182
|
4.7
|
14.9
|
1.0
|
|
O2B
|
F:TPP900
|
4.7
|
22.6
|
1.0
|
|
CE
|
F:LYS300
|
4.8
|
12.9
|
1.0
|
|
C
|
F:ASP182
|
4.8
|
14.9
|
1.0
|
|
C
|
F:ASN215
|
4.8
|
18.5
|
1.0
|
|
CA
|
F:ASN215
|
4.8
|
20.1
|
1.0
|
|
C
|
F:GLY181
|
4.9
|
16.1
|
1.0
|
|
CA
|
F:GLY181
|
4.9
|
16.7
|
1.0
|
|
CA
|
F:GLY183
|
5.0
|
13.4
|
1.0
|
|
Calcium binding site 7 out
of 8 in 3ai7
Go back to
Calcium Binding Sites List in 3ai7
Calcium binding site 7 out
of 8 in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
 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 Bifidobacterium Longum Phosphoketolase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca901
b:11.5
occ:1.00
|
O3B
|
G:TPP900
|
2.0
|
14.2
|
1.0
|
|
O2A
|
G:TPP900
|
2.1
|
14.5
|
1.0
|
|
O
|
G:HOH5056
|
2.2
|
16.8
|
1.0
|
|
OD1
|
G:ASP182
|
2.2
|
12.1
|
1.0
|
|
OD1
|
G:ASN215
|
2.3
|
13.3
|
1.0
|
|
O
|
G:TYR217
|
2.3
|
11.0
|
1.0
|
|
CG
|
G:ASN215
|
3.1
|
10.6
|
1.0
|
|
PB
|
G:TPP900
|
3.2
|
12.7
|
1.0
|
|
PA
|
G:TPP900
|
3.3
|
15.3
|
1.0
|
|
ND2
|
G:ASN215
|
3.4
|
11.5
|
1.0
|
|
CG
|
G:ASP182
|
3.4
|
16.6
|
1.0
|
|
C
|
G:TYR217
|
3.5
|
12.4
|
1.0
|
|
O3A
|
G:TPP900
|
3.6
|
18.8
|
1.0
|
|
O2B
|
G:TPP900
|
3.9
|
16.8
|
1.0
|
|
N
|
G:TYR217
|
4.0
|
11.8
|
1.0
|
|
OD2
|
G:ASP182
|
4.0
|
16.1
|
1.0
|
|
N
|
G:ASP182
|
4.1
|
15.0
|
1.0
|
|
N
|
G:GLY183
|
4.1
|
12.9
|
1.0
|
|
O
|
G:HIS213
|
4.2
|
13.3
|
1.0
|
|
O7
|
G:TPP900
|
4.2
|
17.3
|
1.0
|
|
CA
|
G:TYR217
|
4.3
|
12.2
|
1.0
|
|
NZ
|
G:LYS300
|
4.4
|
10.3
|
1.0
|
|
CG2
|
G:THR223
|
4.4
|
13.0
|
1.0
|
|
N
|
G:LYS218
|
4.4
|
12.7
|
1.0
|
|
O1A
|
G:TPP900
|
4.5
|
22.8
|
1.0
|
|
N
|
G:ASN215
|
4.5
|
15.0
|
1.0
|
|
CB
|
G:ASN215
|
4.5
|
12.2
|
1.0
|
|
CA
|
G:LYS218
|
4.5
|
14.2
|
1.0
|
|
N
|
G:GLY216
|
4.5
|
12.3
|
1.0
|
|
CB
|
G:ASP182
|
4.6
|
13.5
|
1.0
|
|
CA
|
G:ASP182
|
4.6
|
14.5
|
1.0
|
|
O1B
|
G:TPP900
|
4.6
|
18.6
|
1.0
|
|
CE
|
G:LYS300
|
4.8
|
8.3
|
1.0
|
|
C
|
G:ASP182
|
4.8
|
13.6
|
1.0
|
|
C
|
G:ASN215
|
4.8
|
14.7
|
1.0
|
|
CD
|
G:LYS300
|
4.8
|
7.7
|
1.0
|
|
CA
|
G:ASN215
|
4.8
|
13.5
|
1.0
|
|
C
|
G:GLY181
|
4.9
|
15.6
|
1.0
|
|
Calcium binding site 8 out
of 8 in 3ai7
Go back to
Calcium Binding Sites List in 3ai7
Calcium binding site 8 out
of 8 in the Crystal Structure of Bifidobacterium Longum Phosphoketolase
 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 Bifidobacterium Longum Phosphoketolase within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca901
b:14.8
occ:1.00
|
O1A
|
H:TPP900
|
2.0
|
16.0
|
1.0
|
|
O1B
|
H:TPP900
|
2.1
|
12.9
|
1.0
|
|
OD2
|
H:ASP182
|
2.2
|
14.4
|
1.0
|
|
O
|
H:TYR217
|
2.3
|
16.0
|
1.0
|
|
O
|
H:HOH5055
|
2.3
|
16.0
|
1.0
|
|
OD1
|
H:ASN215
|
2.3
|
24.6
|
1.0
|
|
PB
|
H:TPP900
|
3.2
|
14.5
|
1.0
|
|
CG
|
H:ASN215
|
3.3
|
19.1
|
1.0
|
|
PA
|
H:TPP900
|
3.3
|
16.4
|
1.0
|
|
CG
|
H:ASP182
|
3.4
|
18.8
|
1.0
|
|
C
|
H:TYR217
|
3.5
|
15.4
|
1.0
|
|
ND2
|
H:ASN215
|
3.6
|
21.1
|
1.0
|
|
O3A
|
H:TPP900
|
3.6
|
17.8
|
1.0
|
|
O3B
|
H:TPP900
|
3.7
|
18.2
|
1.0
|
|
OD1
|
H:ASP182
|
4.1
|
13.7
|
1.0
|
|
N
|
H:TYR217
|
4.1
|
13.2
|
1.0
|
|
N
|
H:ASP182
|
4.1
|
14.3
|
1.0
|
|
N
|
H:GLY183
|
4.1
|
15.5
|
1.0
|
|
O7
|
H:TPP900
|
4.2
|
21.3
|
1.0
|
|
O
|
H:HIS213
|
4.3
|
15.8
|
1.0
|
|
CG2
|
H:THR223
|
4.4
|
13.0
|
1.0
|
|
NZ
|
H:LYS300
|
4.4
|
16.0
|
1.0
|
|
N
|
H:LYS218
|
4.4
|
16.4
|
1.0
|
|
CA
|
H:TYR217
|
4.4
|
14.0
|
1.0
|
|
CA
|
H:LYS218
|
4.5
|
15.9
|
1.0
|
|
CD
|
H:LYS300
|
4.6
|
12.2
|
1.0
|
|
N
|
H:ASN215
|
4.6
|
17.3
|
1.0
|
|
CB
|
H:ASP182
|
4.6
|
14.1
|
1.0
|
|
CB
|
H:ASN215
|
4.6
|
18.2
|
1.0
|
|
CA
|
H:ASP182
|
4.6
|
15.4
|
1.0
|
|
O2A
|
H:TPP900
|
4.7
|
21.2
|
1.0
|
|
N
|
H:GLY216
|
4.7
|
15.4
|
1.0
|
|
C
|
H:ASP182
|
4.8
|
15.7
|
1.0
|
|
CE
|
H:LYS300
|
4.8
|
17.4
|
1.0
|
|
O2B
|
H:TPP900
|
4.8
|
17.9
|
1.0
|
|
C
|
H:ASN215
|
4.9
|
17.6
|
1.0
|
|
CA
|
H:ASN215
|
4.9
|
18.5
|
1.0
|
|
C
|
H:GLY181
|
5.0
|
15.0
|
1.0
|
|
Reference:
K.Takahashi,
U.Tagami,
N.Shimba,
T.Kashiwagi,
K.Ishikawa,
E.Suzuki.
Crystal Structure of Bifidobacterium Longum Phosphoketolase; Key Enzyme For Glucose Metabolism in Bifidobacterium Febs Lett. V. 584 3855 2010.
ISSN: ISSN 0014-5793
PubMed: 20674574
DOI: 10.1016/J.FEBSLET.2010.07.043
Page generated: Sat Dec 12 04:04:10 2020
|
