Calcium in PDB 7c8h: Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
Enzymatic activity of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
All present enzymatic activity of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate:
4.1.2.22;
Protein crystallography data
The structure of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate, PDB code: 7c8h
was solved by
K.Nakata,
T.Kashiwagi,
E.Nango,
H.Miyano,
T.Mizukoshi,
S.Iwata,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
46.80 /
2.50
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
144.62,
185.8,
162.89,
90,
99.61,
90
|
|
R / Rfree (%)
|
16.1 /
21.8
|
Calcium Binding Sites:
The binding sites of Calcium atom in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
(pdb code 7c8h). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate, PDB code: 7c8h:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 7c8h
Go back to
Calcium Binding Sites List in 7c8h
Calcium binding site 1 out
of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca901
b:60.6
occ:1.00
|
O2B
|
A:TPP900
|
2.1
|
47.0
|
1.0
|
|
O1A
|
A:TPP900
|
2.2
|
47.5
|
1.0
|
|
OD1
|
A:ASP182
|
2.2
|
36.2
|
1.0
|
|
OD1
|
A:ASN215
|
2.3
|
40.5
|
1.0
|
|
O
|
A:TYR217
|
2.3
|
45.0
|
1.0
|
|
O
|
A:HOH1028
|
2.3
|
34.3
|
1.0
|
|
PB
|
A:TPP900
|
3.0
|
40.4
|
1.0
|
|
CG
|
A:ASN215
|
3.1
|
37.4
|
1.0
|
|
PA
|
A:TPP900
|
3.2
|
44.9
|
1.0
|
|
ND2
|
A:ASN215
|
3.3
|
35.8
|
1.0
|
|
O3A
|
A:TPP900
|
3.3
|
46.6
|
1.0
|
|
CG
|
A:ASP182
|
3.4
|
37.9
|
1.0
|
|
O1B
|
A:TPP900
|
3.4
|
48.6
|
1.0
|
|
C
|
A:TYR217
|
3.6
|
40.8
|
1.0
|
|
OD2
|
A:ASP182
|
4.0
|
40.6
|
1.0
|
|
N
|
A:ASP182
|
4.0
|
38.6
|
1.0
|
|
O
|
A:HIS213
|
4.0
|
34.7
|
1.0
|
|
O7
|
A:TPP900
|
4.1
|
43.9
|
1.0
|
|
NZ
|
A:LYS300
|
4.2
|
40.7
|
1.0
|
|
N
|
A:GLY183
|
4.3
|
38.5
|
1.0
|
|
N
|
A:TYR217
|
4.3
|
42.5
|
1.0
|
|
O2A
|
A:TPP900
|
4.3
|
37.7
|
1.0
|
|
O3B
|
A:TPP900
|
4.3
|
42.7
|
1.0
|
|
N
|
A:LYS218
|
4.4
|
37.9
|
1.0
|
|
CD
|
A:LYS300
|
4.4
|
41.1
|
1.0
|
|
CB
|
A:ASN215
|
4.5
|
39.0
|
1.0
|
|
CB
|
A:ASP182
|
4.5
|
39.5
|
1.0
|
|
CA
|
A:LYS218
|
4.5
|
38.9
|
1.0
|
|
CA
|
A:TYR217
|
4.6
|
41.0
|
1.0
|
|
N
|
A:ASN215
|
4.6
|
32.5
|
1.0
|
|
CA
|
A:ASP182
|
4.6
|
39.1
|
1.0
|
|
CG2
|
A:THR223
|
4.7
|
35.3
|
1.0
|
|
CE
|
A:LYS300
|
4.7
|
42.4
|
1.0
|
|
C
|
A:ASN215
|
4.8
|
37.9
|
1.0
|
|
CA
|
A:ASN215
|
4.8
|
35.4
|
1.0
|
|
N
|
A:GLY216
|
4.9
|
37.8
|
1.0
|
|
C
|
A:ASP182
|
4.9
|
37.5
|
1.0
|
|
C
|
A:GLY181
|
4.9
|
38.2
|
1.0
|
|
CA
|
A:GLY181
|
4.9
|
42.3
|
1.0
|
|
Calcium binding site 2 out
of 8 in 7c8h
Go back to
Calcium Binding Sites List in 7c8h
Calcium binding site 2 out
of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca904
b:55.7
occ:1.00
|
O1A
|
B:TPP903
|
2.1
|
43.6
|
1.0
|
|
OD1
|
B:ASP182
|
2.2
|
31.4
|
1.0
|
|
OD1
|
B:ASN215
|
2.2
|
31.4
|
1.0
|
|
O1B
|
B:TPP903
|
2.2
|
39.3
|
1.0
|
|
O
|
B:TYR217
|
2.3
|
37.7
|
1.0
|
|
O
|
B:HOH1010
|
2.5
|
35.4
|
1.0
|
|
PB
|
B:TPP903
|
3.1
|
46.5
|
1.0
|
|
CG
|
B:ASN215
|
3.1
|
38.3
|
1.0
|
|
PA
|
B:TPP903
|
3.3
|
44.9
|
1.0
|
|
CG
|
B:ASP182
|
3.3
|
32.8
|
1.0
|
|
O3A
|
B:TPP903
|
3.4
|
45.3
|
1.0
|
|
ND2
|
B:ASN215
|
3.5
|
36.9
|
1.0
|
|
C
|
B:TYR217
|
3.5
|
33.3
|
1.0
|
|
O2B
|
B:TPP903
|
3.5
|
43.3
|
1.0
|
|
OD2
|
B:ASP182
|
3.9
|
35.5
|
1.0
|
|
N
|
B:ASP182
|
4.0
|
36.5
|
1.0
|
|
O
|
B:HIS213
|
4.1
|
41.6
|
1.0
|
|
N
|
B:TYR217
|
4.1
|
39.4
|
1.0
|
|
O7
|
B:TPP903
|
4.1
|
41.2
|
1.0
|
|
N
|
B:GLY183
|
4.2
|
37.0
|
1.0
|
|
NZ
|
B:LYS300
|
4.2
|
40.0
|
1.0
|
|
N
|
B:LYS218
|
4.4
|
36.9
|
1.0
|
|
O2A
|
B:TPP903
|
4.4
|
37.5
|
1.0
|
|
O3B
|
B:TPP903
|
4.4
|
52.6
|
1.0
|
|
CA
|
B:TYR217
|
4.4
|
35.2
|
1.0
|
|
CB
|
B:ASN215
|
4.5
|
40.0
|
1.0
|
|
CB
|
B:ASP182
|
4.5
|
34.3
|
1.0
|
|
CG2
|
B:THR223
|
4.5
|
39.2
|
1.0
|
|
N
|
B:ASN215
|
4.5
|
35.0
|
1.0
|
|
CA
|
B:LYS218
|
4.6
|
36.7
|
1.0
|
|
CA
|
B:ASP182
|
4.6
|
36.0
|
1.0
|
|
CD
|
B:LYS300
|
4.7
|
36.5
|
1.0
|
|
N
|
B:GLY216
|
4.7
|
41.9
|
1.0
|
|
CA
|
B:ASN215
|
4.8
|
37.5
|
1.0
|
|
C
|
B:ASN215
|
4.8
|
39.0
|
1.0
|
|
C
|
B:ASP182
|
4.8
|
35.5
|
1.0
|
|
CE
|
B:LYS300
|
4.8
|
38.7
|
1.0
|
|
C
|
B:GLY181
|
4.9
|
36.8
|
1.0
|
|
Calcium binding site 3 out
of 8 in 7c8h
Go back to
Calcium Binding Sites List in 7c8h
Calcium binding site 3 out
of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca901
b:70.1
occ:1.00
|
OD1
|
C:ASP182
|
2.1
|
73.6
|
1.0
|
|
O
|
C:TYR217
|
2.2
|
47.2
|
1.0
|
|
O3B
|
C:TPP900
|
2.3
|
57.3
|
1.0
|
|
O2A
|
C:TPP900
|
2.3
|
66.3
|
1.0
|
|
O
|
C:HOH1058
|
2.3
|
42.1
|
1.0
|
|
OD1
|
C:ASN215
|
2.4
|
58.7
|
1.0
|
|
CG
|
C:ASN215
|
3.0
|
57.9
|
1.0
|
|
ND2
|
C:ASN215
|
3.2
|
50.1
|
1.0
|
|
CG
|
C:ASP182
|
3.3
|
60.4
|
1.0
|
|
PB
|
C:TPP900
|
3.4
|
63.3
|
1.0
|
|
C
|
C:TYR217
|
3.4
|
52.1
|
1.0
|
|
PA
|
C:TPP900
|
3.5
|
60.3
|
1.0
|
|
O3A
|
C:TPP900
|
3.7
|
63.7
|
1.0
|
|
O2B
|
C:TPP900
|
3.9
|
53.2
|
1.0
|
|
OD2
|
C:ASP182
|
3.9
|
53.0
|
1.0
|
|
N
|
C:TYR217
|
4.0
|
53.6
|
1.0
|
|
N
|
C:ASP182
|
4.0
|
47.7
|
1.0
|
|
O
|
C:HIS213
|
4.0
|
45.2
|
1.0
|
|
N
|
C:GLY183
|
4.3
|
54.3
|
1.0
|
|
CG2
|
C:THR223
|
4.3
|
57.1
|
1.0
|
|
CB
|
C:ASN215
|
4.3
|
59.6
|
1.0
|
|
N
|
C:LYS218
|
4.3
|
54.1
|
1.0
|
|
O7
|
C:TPP900
|
4.3
|
60.3
|
1.0
|
|
CA
|
C:TYR217
|
4.4
|
53.9
|
1.0
|
|
N
|
C:ASN215
|
4.4
|
59.4
|
1.0
|
|
NZ
|
C:LYS300
|
4.4
|
47.6
|
1.0
|
|
CB
|
C:ASP182
|
4.4
|
56.9
|
1.0
|
|
N
|
C:GLY216
|
4.5
|
45.9
|
1.0
|
|
CA
|
C:LYS218
|
4.5
|
60.2
|
1.0
|
|
C
|
C:ASN215
|
4.6
|
52.2
|
1.0
|
|
O1A
|
C:TPP900
|
4.6
|
65.5
|
1.0
|
|
CA
|
C:ASP182
|
4.6
|
54.4
|
1.0
|
|
CA
|
C:ASN215
|
4.6
|
56.7
|
1.0
|
|
CE
|
C:LYS300
|
4.7
|
46.7
|
1.0
|
|
O1B
|
C:TPP900
|
4.7
|
90.6
|
1.0
|
|
CD
|
C:LYS300
|
4.8
|
51.9
|
1.0
|
|
C
|
C:ASP182
|
4.9
|
52.2
|
1.0
|
|
Calcium binding site 4 out
of 8 in 7c8h
Go back to
Calcium Binding Sites List in 7c8h
Calcium binding site 4 out
of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca904
b:71.6
occ:1.00
|
OD1
|
D:ASP182
|
1.9
|
61.5
|
1.0
|
|
O2A
|
D:TPP903
|
2.1
|
64.1
|
1.0
|
|
O1B
|
D:TPP903
|
2.2
|
58.9
|
1.0
|
|
O
|
D:HOH1049
|
2.2
|
39.3
|
1.0
|
|
O
|
D:TYR217
|
2.4
|
42.6
|
1.0
|
|
OD1
|
D:ASN215
|
2.5
|
48.5
|
1.0
|
|
CG
|
D:ASP182
|
3.0
|
52.2
|
1.0
|
|
CG
|
D:ASN215
|
3.1
|
45.8
|
1.0
|
|
ND2
|
D:ASN215
|
3.2
|
44.6
|
1.0
|
|
PA
|
D:TPP903
|
3.2
|
54.1
|
1.0
|
|
PB
|
D:TPP903
|
3.3
|
55.1
|
1.0
|
|
O3A
|
D:TPP903
|
3.5
|
60.5
|
1.0
|
|
C
|
D:TYR217
|
3.6
|
50.7
|
1.0
|
|
OD2
|
D:ASP182
|
3.6
|
49.5
|
1.0
|
|
N
|
D:ASP182
|
3.7
|
53.5
|
1.0
|
|
O2B
|
D:TPP903
|
3.8
|
50.9
|
1.0
|
|
N
|
D:GLY183
|
3.9
|
47.9
|
1.0
|
|
O
|
D:HIS213
|
4.0
|
44.9
|
1.0
|
|
N
|
D:TYR217
|
4.1
|
48.5
|
1.0
|
|
O1A
|
D:TPP903
|
4.1
|
56.9
|
1.0
|
|
CB
|
D:ASP182
|
4.2
|
57.3
|
1.0
|
|
O7
|
D:TPP903
|
4.3
|
60.0
|
1.0
|
|
CG2
|
D:THR223
|
4.3
|
52.4
|
1.0
|
|
CA
|
D:ASP182
|
4.3
|
56.5
|
1.0
|
|
N
|
D:ASN215
|
4.3
|
54.6
|
1.0
|
|
CB
|
D:ASN215
|
4.4
|
49.1
|
1.0
|
|
CA
|
D:TYR217
|
4.5
|
50.5
|
1.0
|
|
N
|
D:LYS218
|
4.5
|
54.4
|
1.0
|
|
C
|
D:GLY181
|
4.5
|
49.3
|
1.0
|
|
O3B
|
D:TPP903
|
4.6
|
83.1
|
1.0
|
|
C
|
D:ASP182
|
4.6
|
49.5
|
1.0
|
|
N
|
D:GLY216
|
4.6
|
43.5
|
1.0
|
|
CA
|
D:GLY181
|
4.7
|
53.2
|
1.0
|
|
CA
|
D:ASN215
|
4.7
|
53.1
|
1.0
|
|
CA
|
D:LYS218
|
4.7
|
56.0
|
1.0
|
|
NZ
|
D:LYS300
|
4.7
|
53.8
|
1.0
|
|
C
|
D:ASN215
|
4.7
|
48.2
|
1.0
|
|
CE
|
D:LYS300
|
4.8
|
52.5
|
1.0
|
|
CA
|
D:GLY183
|
4.9
|
50.1
|
1.0
|
|
Calcium binding site 5 out
of 8 in 7c8h
Go back to
Calcium Binding Sites List in 7c8h
Calcium binding site 5 out
of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca903
b:62.8
occ:1.00
|
OD1
|
E:ASN215
|
2.1
|
44.7
|
1.0
|
|
O2A
|
E:TPP902
|
2.1
|
49.3
|
1.0
|
|
OD1
|
E:ASP182
|
2.2
|
45.2
|
1.0
|
|
O2B
|
E:TPP902
|
2.2
|
40.5
|
1.0
|
|
O
|
E:TYR217
|
2.2
|
41.7
|
1.0
|
|
O
|
E:HOH1017
|
2.4
|
40.0
|
1.0
|
|
CG
|
E:ASN215
|
2.9
|
40.2
|
1.0
|
|
ND2
|
E:ASN215
|
3.2
|
39.0
|
1.0
|
|
PB
|
E:TPP902
|
3.2
|
43.3
|
1.0
|
|
CG
|
E:ASP182
|
3.3
|
44.4
|
1.0
|
|
PA
|
E:TPP902
|
3.3
|
45.6
|
1.0
|
|
C
|
E:TYR217
|
3.4
|
38.5
|
1.0
|
|
O3A
|
E:TPP902
|
3.5
|
46.0
|
1.0
|
|
O1B
|
E:TPP902
|
3.7
|
45.9
|
1.0
|
|
OD2
|
E:ASP182
|
3.8
|
41.6
|
1.0
|
|
N
|
E:ASP182
|
3.9
|
47.8
|
1.0
|
|
N
|
E:TYR217
|
4.0
|
39.9
|
1.0
|
|
O
|
E:HIS213
|
4.0
|
36.0
|
1.0
|
|
N
|
E:GLY183
|
4.1
|
42.4
|
1.0
|
|
NZ
|
E:LYS300
|
4.2
|
47.4
|
1.0
|
|
O7
|
E:TPP902
|
4.3
|
45.9
|
1.0
|
|
N
|
E:LYS218
|
4.3
|
40.3
|
1.0
|
|
CA
|
E:TYR217
|
4.3
|
37.8
|
1.0
|
|
CB
|
E:ASN215
|
4.3
|
41.4
|
1.0
|
|
O1A
|
E:TPP902
|
4.3
|
46.5
|
1.0
|
|
N
|
E:ASN215
|
4.3
|
41.5
|
1.0
|
|
CG2
|
E:THR223
|
4.4
|
50.7
|
1.0
|
|
CB
|
E:ASP182
|
4.5
|
46.8
|
1.0
|
|
O3B
|
E:TPP902
|
4.5
|
50.4
|
1.0
|
|
N
|
E:GLY216
|
4.5
|
39.9
|
1.0
|
|
CA
|
E:ASP182
|
4.6
|
44.1
|
1.0
|
|
CA
|
E:LYS218
|
4.6
|
39.8
|
1.0
|
|
CD
|
E:LYS300
|
4.6
|
45.4
|
1.0
|
|
CA
|
E:ASN215
|
4.7
|
42.3
|
1.0
|
|
CE
|
E:LYS300
|
4.7
|
43.4
|
1.0
|
|
C
|
E:ASN215
|
4.7
|
38.9
|
1.0
|
|
C
|
E:ASP182
|
4.8
|
42.5
|
1.0
|
|
C
|
E:GLY181
|
4.9
|
49.7
|
1.0
|
|
CA
|
E:GLY181
|
5.0
|
50.0
|
1.0
|
|
CA
|
E:GLY183
|
5.0
|
42.7
|
1.0
|
|
Calcium binding site 6 out
of 8 in 7c8h
Go back to
Calcium Binding Sites List in 7c8h
Calcium binding site 6 out
of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca901
b:79.6
occ:1.00
|
O3B
|
F:TPP900
|
2.0
|
54.1
|
1.0
|
|
OD1
|
F:ASP182
|
2.1
|
45.4
|
1.0
|
|
O1A
|
F:TPP900
|
2.1
|
48.5
|
1.0
|
|
O
|
F:TYR217
|
2.2
|
51.8
|
1.0
|
|
OD1
|
F:ASN215
|
2.3
|
51.5
|
1.0
|
|
O
|
F:HOH1031
|
2.5
|
43.9
|
1.0
|
|
PA
|
F:TPP900
|
3.2
|
52.3
|
1.0
|
|
PB
|
F:TPP900
|
3.2
|
58.6
|
1.0
|
|
CG
|
F:ASN215
|
3.2
|
49.9
|
1.0
|
|
CG
|
F:ASP182
|
3.2
|
47.7
|
1.0
|
|
O3A
|
F:TPP900
|
3.4
|
60.8
|
1.0
|
|
C
|
F:TYR217
|
3.5
|
52.2
|
1.0
|
|
ND2
|
F:ASN215
|
3.5
|
48.5
|
1.0
|
|
O2B
|
F:TPP900
|
3.8
|
63.4
|
1.0
|
|
OD2
|
F:ASP182
|
3.9
|
45.6
|
1.0
|
|
NZ
|
F:LYS300
|
3.9
|
57.0
|
1.0
|
|
N
|
F:ASP182
|
4.0
|
40.8
|
1.0
|
|
O7
|
F:TPP900
|
4.0
|
58.7
|
1.0
|
|
N
|
F:GLY183
|
4.1
|
54.8
|
1.0
|
|
O
|
F:HIS213
|
4.2
|
45.9
|
1.0
|
|
CG2
|
F:THR223
|
4.2
|
45.8
|
1.0
|
|
N
|
F:TYR217
|
4.3
|
45.6
|
1.0
|
|
N
|
F:LYS218
|
4.3
|
56.0
|
1.0
|
|
O2A
|
F:TPP900
|
4.4
|
54.8
|
1.0
|
|
CB
|
F:ASP182
|
4.4
|
47.7
|
1.0
|
|
CA
|
F:LYS218
|
4.4
|
59.9
|
1.0
|
|
O1B
|
F:TPP900
|
4.4
|
69.2
|
1.0
|
|
CA
|
F:TYR217
|
4.5
|
46.6
|
1.0
|
|
CA
|
F:ASP182
|
4.5
|
45.6
|
1.0
|
|
CB
|
F:ASN215
|
4.6
|
51.2
|
1.0
|
|
N
|
F:ASN215
|
4.6
|
46.1
|
1.0
|
|
CD
|
F:LYS300
|
4.7
|
56.7
|
1.0
|
|
C
|
F:ASP182
|
4.7
|
49.0
|
1.0
|
|
C
|
F:GLY181
|
4.8
|
41.2
|
1.0
|
|
CE
|
F:LYS300
|
4.8
|
54.8
|
1.0
|
|
N
|
F:GLY216
|
4.8
|
49.5
|
1.0
|
|
CA
|
F:GLY181
|
4.8
|
41.2
|
1.0
|
|
CA
|
F:ASN215
|
4.9
|
50.9
|
1.0
|
|
CA
|
F:GLY183
|
5.0
|
52.1
|
1.0
|
|
C
|
F:ASN215
|
5.0
|
49.2
|
1.0
|
|
Calcium binding site 7 out
of 8 in 7c8h
Go back to
Calcium Binding Sites List in 7c8h
Calcium binding site 7 out
of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca902
b:70.2
occ:1.00
|
O2A
|
G:TPP901
|
2.1
|
39.8
|
1.0
|
|
OD1
|
G:ASP182
|
2.4
|
42.7
|
1.0
|
|
OD1
|
G:ASN215
|
2.4
|
46.9
|
1.0
|
|
O2B
|
G:TPP901
|
2.4
|
44.5
|
1.0
|
|
O
|
G:TYR217
|
2.5
|
41.2
|
1.0
|
|
CG
|
G:ASN215
|
3.1
|
45.9
|
1.0
|
|
PB
|
G:TPP901
|
3.2
|
39.3
|
1.0
|
|
O1B
|
G:TPP901
|
3.2
|
38.1
|
1.0
|
|
PA
|
G:TPP901
|
3.3
|
41.0
|
1.0
|
|
ND2
|
G:ASN215
|
3.3
|
50.9
|
1.0
|
|
CG
|
G:ASP182
|
3.4
|
42.4
|
1.0
|
|
O3A
|
G:TPP901
|
3.4
|
41.1
|
1.0
|
|
O
|
G:HIS213
|
3.7
|
38.3
|
1.0
|
|
C
|
G:TYR217
|
3.7
|
38.0
|
1.0
|
|
N
|
G:ASP182
|
3.8
|
40.1
|
1.0
|
|
OD2
|
G:ASP182
|
4.0
|
39.5
|
1.0
|
|
N
|
G:GLY183
|
4.2
|
43.1
|
1.0
|
|
O1A
|
G:TPP901
|
4.2
|
39.2
|
1.0
|
|
O7
|
G:TPP901
|
4.3
|
42.6
|
1.0
|
|
CB
|
G:ASP182
|
4.3
|
43.7
|
1.0
|
|
N
|
G:TYR217
|
4.4
|
39.8
|
1.0
|
|
N
|
G:ASN215
|
4.4
|
41.2
|
1.0
|
|
NZ
|
G:LYS300
|
4.4
|
45.3
|
1.0
|
|
CB
|
G:ASN215
|
4.5
|
43.8
|
1.0
|
|
CA
|
G:ASP182
|
4.5
|
40.4
|
1.0
|
|
N
|
G:LYS218
|
4.6
|
37.8
|
1.0
|
|
O3B
|
G:TPP901
|
4.6
|
42.8
|
1.0
|
|
CA
|
G:GLY181
|
4.7
|
39.7
|
1.0
|
|
CA
|
G:TYR217
|
4.7
|
37.2
|
1.0
|
|
CG2
|
G:THR223
|
4.7
|
37.0
|
1.0
|
|
C
|
G:GLY181
|
4.7
|
40.8
|
1.0
|
|
C
|
G:ASP182
|
4.8
|
44.6
|
1.0
|
|
N
|
G:GLY216
|
4.8
|
42.2
|
1.0
|
|
CA
|
G:LYS218
|
4.8
|
38.0
|
1.0
|
|
CA
|
G:ASN215
|
4.8
|
45.2
|
1.0
|
|
CD
|
G:LYS300
|
4.9
|
35.8
|
1.0
|
|
C
|
G:HIS213
|
4.9
|
37.5
|
1.0
|
|
CE
|
G:LYS300
|
4.9
|
38.0
|
1.0
|
|
C
|
G:ASN215
|
5.0
|
44.4
|
1.0
|
|
Calcium binding site 8 out
of 8 in 7c8h
Go back to
Calcium Binding Sites List in 7c8h
Calcium binding site 8 out
of 8 in the Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca903
b:69.9
occ:1.00
|
O1A
|
H:TPP902
|
2.0
|
49.0
|
1.0
|
|
O1B
|
H:TPP902
|
2.1
|
47.3
|
1.0
|
|
OD1
|
H:ASN215
|
2.2
|
48.6
|
1.0
|
|
O
|
H:TYR217
|
2.2
|
40.4
|
1.0
|
|
OD1
|
H:ASP182
|
2.3
|
41.9
|
1.0
|
|
O
|
H:HOH1019
|
2.4
|
44.9
|
1.0
|
|
PB
|
H:TPP902
|
3.0
|
48.0
|
1.0
|
|
PA
|
H:TPP902
|
3.0
|
43.0
|
1.0
|
|
CG
|
H:ASN215
|
3.1
|
46.2
|
1.0
|
|
O3A
|
H:TPP902
|
3.1
|
47.3
|
1.0
|
|
ND2
|
H:ASN215
|
3.3
|
45.5
|
1.0
|
|
CG
|
H:ASP182
|
3.4
|
40.4
|
1.0
|
|
C
|
H:TYR217
|
3.5
|
39.6
|
1.0
|
|
O2B
|
H:TPP902
|
3.5
|
47.0
|
1.0
|
|
N
|
H:ASP182
|
3.9
|
34.9
|
1.0
|
|
O7
|
H:TPP902
|
4.0
|
47.4
|
1.0
|
|
OD2
|
H:ASP182
|
4.1
|
36.9
|
1.0
|
|
N
|
H:GLY183
|
4.1
|
43.5
|
1.0
|
|
O2A
|
H:TPP902
|
4.2
|
48.0
|
1.0
|
|
NZ
|
H:LYS300
|
4.2
|
47.0
|
1.0
|
|
O
|
H:HIS213
|
4.2
|
40.8
|
1.0
|
|
N
|
H:TYR217
|
4.2
|
37.0
|
1.0
|
|
N
|
H:LYS218
|
4.3
|
43.7
|
1.0
|
|
O3B
|
H:TPP902
|
4.4
|
47.6
|
1.0
|
|
CG2
|
H:THR223
|
4.4
|
43.2
|
1.0
|
|
CB
|
H:ASN215
|
4.5
|
47.2
|
1.0
|
|
CA
|
H:TYR217
|
4.5
|
41.1
|
1.0
|
|
CA
|
H:LYS218
|
4.5
|
48.8
|
1.0
|
|
CB
|
H:ASP182
|
4.6
|
41.6
|
1.0
|
|
CA
|
H:ASP182
|
4.6
|
38.1
|
1.0
|
|
N
|
H:ASN215
|
4.7
|
44.2
|
1.0
|
|
CD
|
H:LYS300
|
4.7
|
43.5
|
1.0
|
|
CE
|
H:LYS300
|
4.7
|
44.7
|
1.0
|
|
CA
|
H:GLY181
|
4.8
|
40.3
|
1.0
|
|
C
|
H:GLY181
|
4.8
|
37.4
|
1.0
|
|
C
|
H:ASP182
|
4.8
|
43.0
|
1.0
|
|
CA
|
H:ASN215
|
4.9
|
45.3
|
1.0
|
|
N
|
H:GLY216
|
5.0
|
44.6
|
1.0
|
|
C
|
H:ASN215
|
5.0
|
43.8
|
1.0
|
|
Reference:
K.Nakata,
T.Kashiwagi,
E.Nango,
H.Miyano,
T.Mizukoshi,
S.Iwata.
Ambient Temperature Structure of Bifidobacterium Longum Phosphoketolase with Thiamine Diphosphate To Be Published.
Page generated: Thu Jul 18 23:29:53 2024
|
