Calcium in PDB 6lxv: Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
Enzymatic activity of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
All present enzymatic activity of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum:
4.1.2.22;
Calcium Binding Sites:
The binding sites of Calcium atom in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
(pdb code 6lxv). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 8 binding sites of Calcium where determined in the
Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum, PDB code: 6lxv:
Jump to Calcium binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Calcium binding site 1 out
of 8 in 6lxv
Go back to
Calcium Binding Sites List in 6lxv
Calcium binding site 1 out
of 8 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca901
b:18.9
occ:1.00
|
O
|
A:TYR217
|
2.3
|
14.2
|
1.0
|
|
OD1
|
A:ASP182
|
2.3
|
13.5
|
1.0
|
|
OD1
|
A:ASN215
|
2.3
|
15.7
|
1.0
|
|
O1B
|
A:TPP900
|
2.3
|
20.4
|
1.0
|
|
O2A
|
A:TPP900
|
2.3
|
20.4
|
1.0
|
|
O
|
A:HOH1059
|
2.4
|
12.7
|
1.0
|
|
CG
|
A:ASN215
|
3.1
|
15.7
|
1.0
|
|
PA
|
A:TPP900
|
3.2
|
20.4
|
1.0
|
|
PB
|
A:TPP900
|
3.3
|
20.4
|
1.0
|
|
ND2
|
A:ASN215
|
3.4
|
15.7
|
1.0
|
|
CG
|
A:ASP182
|
3.4
|
13.5
|
1.0
|
|
C
|
A:TYR217
|
3.4
|
14.2
|
1.0
|
|
O2B
|
A:TPP900
|
3.5
|
20.4
|
1.0
|
|
O3A
|
A:TPP900
|
3.5
|
20.4
|
1.0
|
|
N
|
A:ASP182
|
3.9
|
13.5
|
1.0
|
|
OD2
|
A:ASP182
|
4.0
|
13.5
|
1.0
|
|
O
|
A:HIS213
|
4.0
|
15.7
|
1.0
|
|
O7
|
A:TPP900
|
4.1
|
20.4
|
1.0
|
|
N
|
A:GLY183
|
4.1
|
14.7
|
1.0
|
|
N
|
A:TYR217
|
4.2
|
14.2
|
1.0
|
|
NZ
|
A:LYS300
|
4.2
|
15.3
|
1.0
|
|
N
|
A:LYS218
|
4.3
|
16.1
|
1.0
|
|
O1A
|
A:TPP900
|
4.3
|
20.4
|
1.0
|
|
O3B
|
A:TPP900
|
4.4
|
20.4
|
1.0
|
|
CA
|
A:TYR217
|
4.4
|
14.2
|
1.0
|
|
CB
|
A:ASN215
|
4.5
|
15.7
|
1.0
|
|
CB
|
A:ASP182
|
4.5
|
13.5
|
1.0
|
|
CG2
|
A:THR223
|
4.5
|
15.0
|
1.0
|
|
CA
|
A:LYS218
|
4.5
|
16.1
|
1.0
|
|
N
|
A:ASN215
|
4.5
|
15.7
|
1.0
|
|
CA
|
A:ASP182
|
4.5
|
13.5
|
1.0
|
|
C
|
A:ASP182
|
4.7
|
13.5
|
1.0
|
|
N
|
A:GLY216
|
4.8
|
20.4
|
1.0
|
|
C
|
A:GLY181
|
4.8
|
14.1
|
1.0
|
|
CA
|
A:ASN215
|
4.8
|
15.7
|
1.0
|
|
CE
|
A:LYS300
|
4.8
|
15.3
|
1.0
|
|
C
|
A:ASN215
|
4.9
|
15.7
|
1.0
|
|
CA
|
A:GLY181
|
5.0
|
14.1
|
1.0
|
|
CD
|
A:LYS300
|
5.0
|
15.3
|
1.0
|
|
Calcium binding site 2 out
of 8 in 6lxv
Go back to
Calcium Binding Sites List in 6lxv
Calcium binding site 2 out
of 8 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca901
b:18.8
occ:1.00
|
O
|
B:TYR217
|
2.3
|
14.4
|
1.0
|
|
OD1
|
B:ASP182
|
2.3
|
13.4
|
1.0
|
|
OD1
|
B:ASN215
|
2.3
|
16.0
|
1.0
|
|
O3B
|
B:TPP900
|
2.3
|
20.4
|
1.0
|
|
O1A
|
B:TPP900
|
2.3
|
20.4
|
1.0
|
|
O
|
B:HOH1062
|
2.4
|
12.8
|
1.0
|
|
CG
|
B:ASN215
|
3.1
|
16.0
|
1.0
|
|
PA
|
B:TPP900
|
3.2
|
20.4
|
1.0
|
|
PB
|
B:TPP900
|
3.3
|
20.4
|
1.0
|
|
ND2
|
B:ASN215
|
3.4
|
16.0
|
1.0
|
|
CG
|
B:ASP182
|
3.4
|
13.4
|
1.0
|
|
C
|
B:TYR217
|
3.4
|
14.4
|
1.0
|
|
O2B
|
B:TPP900
|
3.5
|
20.4
|
1.0
|
|
O3A
|
B:TPP900
|
3.5
|
20.4
|
1.0
|
|
N
|
B:ASP182
|
3.9
|
13.4
|
1.0
|
|
OD2
|
B:ASP182
|
4.0
|
13.4
|
1.0
|
|
O
|
B:HIS213
|
4.0
|
15.0
|
1.0
|
|
O7
|
B:TPP900
|
4.1
|
20.4
|
1.0
|
|
N
|
B:GLY183
|
4.1
|
14.7
|
1.0
|
|
N
|
B:TYR217
|
4.2
|
14.4
|
1.0
|
|
NZ
|
B:LYS300
|
4.2
|
15.3
|
1.0
|
|
N
|
B:LYS218
|
4.3
|
15.8
|
1.0
|
|
O2A
|
B:TPP900
|
4.3
|
20.4
|
1.0
|
|
O1B
|
B:TPP900
|
4.4
|
20.4
|
1.0
|
|
CA
|
B:TYR217
|
4.4
|
14.4
|
1.0
|
|
CB
|
B:ASN215
|
4.5
|
16.0
|
1.0
|
|
CB
|
B:ASP182
|
4.5
|
13.4
|
1.0
|
|
CG2
|
B:THR223
|
4.5
|
15.2
|
1.0
|
|
CA
|
B:LYS218
|
4.5
|
15.8
|
1.0
|
|
N
|
B:ASN215
|
4.5
|
16.0
|
1.0
|
|
CA
|
B:ASP182
|
4.5
|
13.4
|
1.0
|
|
C
|
B:ASP182
|
4.7
|
13.4
|
1.0
|
|
N
|
B:GLY216
|
4.8
|
20.4
|
1.0
|
|
C
|
B:GLY181
|
4.8
|
14.3
|
1.0
|
|
CA
|
B:ASN215
|
4.8
|
16.0
|
1.0
|
|
CE
|
B:LYS300
|
4.8
|
15.3
|
1.0
|
|
C
|
B:ASN215
|
4.9
|
16.0
|
1.0
|
|
CA
|
B:GLY181
|
5.0
|
14.3
|
1.0
|
|
CD
|
B:LYS300
|
5.0
|
15.3
|
1.0
|
|
Calcium binding site 3 out
of 8 in 6lxv
Go back to
Calcium Binding Sites List in 6lxv
Calcium binding site 3 out
of 8 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Ca901
b:18.9
occ:1.00
|
O
|
C:TYR217
|
2.3
|
14.7
|
1.0
|
|
OD1
|
C:ASP182
|
2.3
|
13.2
|
1.0
|
|
OD1
|
C:ASN215
|
2.3
|
15.8
|
1.0
|
|
O1B
|
C:TPP900
|
2.3
|
20.4
|
1.0
|
|
O2A
|
C:TPP900
|
2.4
|
20.4
|
1.0
|
|
O
|
C:HOH1062
|
2.4
|
12.7
|
1.0
|
|
CG
|
C:ASN215
|
3.1
|
15.8
|
1.0
|
|
PA
|
C:TPP900
|
3.2
|
20.4
|
1.0
|
|
PB
|
C:TPP900
|
3.3
|
20.4
|
1.0
|
|
ND2
|
C:ASN215
|
3.4
|
15.8
|
1.0
|
|
CG
|
C:ASP182
|
3.4
|
13.2
|
1.0
|
|
C
|
C:TYR217
|
3.4
|
14.7
|
1.0
|
|
O2B
|
C:TPP900
|
3.5
|
20.4
|
1.0
|
|
O3A
|
C:TPP900
|
3.5
|
20.4
|
1.0
|
|
N
|
C:ASP182
|
3.9
|
13.2
|
1.0
|
|
OD2
|
C:ASP182
|
4.0
|
13.2
|
1.0
|
|
O
|
C:HIS213
|
4.0
|
15.6
|
1.0
|
|
O7
|
C:TPP900
|
4.1
|
20.4
|
1.0
|
|
N
|
C:GLY183
|
4.1
|
14.8
|
1.0
|
|
N
|
C:TYR217
|
4.2
|
14.7
|
1.0
|
|
NZ
|
C:LYS300
|
4.2
|
15.5
|
1.0
|
|
N
|
C:LYS218
|
4.3
|
15.9
|
1.0
|
|
O1A
|
C:TPP900
|
4.3
|
20.4
|
1.0
|
|
O3B
|
C:TPP900
|
4.4
|
20.4
|
1.0
|
|
CA
|
C:TYR217
|
4.4
|
14.7
|
1.0
|
|
CB
|
C:ASN215
|
4.5
|
15.8
|
1.0
|
|
CB
|
C:ASP182
|
4.5
|
13.2
|
1.0
|
|
CG2
|
C:THR223
|
4.5
|
15.3
|
1.0
|
|
CA
|
C:LYS218
|
4.5
|
15.9
|
1.0
|
|
N
|
C:ASN215
|
4.5
|
15.8
|
1.0
|
|
CA
|
C:ASP182
|
4.5
|
13.2
|
1.0
|
|
C
|
C:ASP182
|
4.7
|
13.2
|
1.0
|
|
N
|
C:GLY216
|
4.8
|
20.4
|
1.0
|
|
C
|
C:GLY181
|
4.8
|
14.1
|
1.0
|
|
CA
|
C:ASN215
|
4.8
|
15.8
|
1.0
|
|
CE
|
C:LYS300
|
4.8
|
15.5
|
1.0
|
|
C
|
C:ASN215
|
4.9
|
15.8
|
1.0
|
|
CA
|
C:GLY181
|
5.0
|
14.1
|
1.0
|
|
CD
|
C:LYS300
|
5.0
|
15.5
|
1.0
|
|
Calcium binding site 4 out
of 8 in 6lxv
Go back to
Calcium Binding Sites List in 6lxv
Calcium binding site 4 out
of 8 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Ca901
b:18.8
occ:1.00
|
O
|
D:TYR217
|
2.3
|
14.7
|
1.0
|
|
OD1
|
D:ASP182
|
2.3
|
13.3
|
1.0
|
|
OD1
|
D:ASN215
|
2.3
|
15.5
|
1.0
|
|
O3B
|
D:TPP900
|
2.3
|
20.4
|
1.0
|
|
O1A
|
D:TPP900
|
2.3
|
20.4
|
1.0
|
|
O
|
D:HOH1062
|
2.4
|
12.8
|
1.0
|
|
CG
|
D:ASN215
|
3.1
|
15.5
|
1.0
|
|
PA
|
D:TPP900
|
3.2
|
20.4
|
1.0
|
|
PB
|
D:TPP900
|
3.3
|
20.4
|
1.0
|
|
ND2
|
D:ASN215
|
3.4
|
15.5
|
1.0
|
|
CG
|
D:ASP182
|
3.4
|
13.3
|
1.0
|
|
C
|
D:TYR217
|
3.4
|
14.7
|
1.0
|
|
O2B
|
D:TPP900
|
3.5
|
20.4
|
1.0
|
|
O3A
|
D:TPP900
|
3.5
|
20.4
|
1.0
|
|
N
|
D:ASP182
|
3.9
|
13.3
|
1.0
|
|
OD2
|
D:ASP182
|
4.0
|
13.3
|
1.0
|
|
O
|
D:HIS213
|
4.0
|
15.5
|
1.0
|
|
O7
|
D:TPP900
|
4.1
|
20.4
|
1.0
|
|
N
|
D:GLY183
|
4.1
|
14.6
|
1.0
|
|
N
|
D:TYR217
|
4.2
|
14.7
|
1.0
|
|
NZ
|
D:LYS300
|
4.2
|
15.2
|
1.0
|
|
N
|
D:LYS218
|
4.3
|
15.9
|
1.0
|
|
O2A
|
D:TPP900
|
4.3
|
20.4
|
1.0
|
|
O1B
|
D:TPP900
|
4.4
|
20.4
|
1.0
|
|
CA
|
D:TYR217
|
4.4
|
14.7
|
1.0
|
|
CB
|
D:ASN215
|
4.5
|
15.5
|
1.0
|
|
CB
|
D:ASP182
|
4.5
|
13.3
|
1.0
|
|
CG2
|
D:THR223
|
4.5
|
15.2
|
1.0
|
|
CA
|
D:LYS218
|
4.5
|
15.9
|
1.0
|
|
N
|
D:ASN215
|
4.5
|
15.5
|
1.0
|
|
CA
|
D:ASP182
|
4.5
|
13.3
|
1.0
|
|
C
|
D:ASP182
|
4.7
|
13.3
|
1.0
|
|
N
|
D:GLY216
|
4.8
|
20.4
|
1.0
|
|
C
|
D:GLY181
|
4.8
|
14.2
|
1.0
|
|
CA
|
D:ASN215
|
4.8
|
15.5
|
1.0
|
|
CE
|
D:LYS300
|
4.8
|
15.2
|
1.0
|
|
C
|
D:ASN215
|
4.9
|
15.5
|
1.0
|
|
CA
|
D:GLY181
|
5.0
|
14.2
|
1.0
|
|
CD
|
D:LYS300
|
5.0
|
15.2
|
1.0
|
|
Calcium binding site 5 out
of 8 in 6lxv
Go back to
Calcium Binding Sites List in 6lxv
Calcium binding site 5 out
of 8 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 5 of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:Ca901
b:18.7
occ:1.00
|
O
|
E:TYR217
|
2.3
|
14.5
|
1.0
|
|
OD1
|
E:ASP182
|
2.3
|
13.3
|
1.0
|
|
OD1
|
E:ASN215
|
2.3
|
15.7
|
1.0
|
|
O1B
|
E:TPP900
|
2.3
|
20.4
|
1.0
|
|
O2A
|
E:TPP900
|
2.3
|
20.4
|
1.0
|
|
O
|
E:HOH1061
|
2.4
|
12.8
|
1.0
|
|
CG
|
E:ASN215
|
3.1
|
15.7
|
1.0
|
|
PA
|
E:TPP900
|
3.2
|
20.4
|
1.0
|
|
PB
|
E:TPP900
|
3.3
|
20.4
|
1.0
|
|
ND2
|
E:ASN215
|
3.4
|
15.7
|
1.0
|
|
CG
|
E:ASP182
|
3.4
|
13.3
|
1.0
|
|
C
|
E:TYR217
|
3.4
|
14.5
|
1.0
|
|
O2B
|
E:TPP900
|
3.5
|
20.4
|
1.0
|
|
O3A
|
E:TPP900
|
3.5
|
20.4
|
1.0
|
|
N
|
E:ASP182
|
3.9
|
13.3
|
1.0
|
|
OD2
|
E:ASP182
|
4.0
|
13.3
|
1.0
|
|
O
|
E:HIS213
|
4.0
|
15.5
|
1.0
|
|
O7
|
E:TPP900
|
4.1
|
20.4
|
1.0
|
|
N
|
E:GLY183
|
4.1
|
14.7
|
1.0
|
|
N
|
E:TYR217
|
4.2
|
14.5
|
1.0
|
|
NZ
|
E:LYS300
|
4.2
|
15.4
|
1.0
|
|
N
|
E:LYS218
|
4.3
|
16.0
|
1.0
|
|
O1A
|
E:TPP900
|
4.3
|
20.4
|
1.0
|
|
O3B
|
E:TPP900
|
4.4
|
20.4
|
1.0
|
|
CA
|
E:TYR217
|
4.4
|
14.5
|
1.0
|
|
CB
|
E:ASN215
|
4.5
|
15.7
|
1.0
|
|
CB
|
E:ASP182
|
4.5
|
13.3
|
1.0
|
|
CG2
|
E:THR223
|
4.5
|
15.2
|
1.0
|
|
CA
|
E:LYS218
|
4.5
|
16.0
|
1.0
|
|
N
|
E:ASN215
|
4.5
|
15.7
|
1.0
|
|
CA
|
E:ASP182
|
4.5
|
13.3
|
1.0
|
|
C
|
E:ASP182
|
4.7
|
13.3
|
1.0
|
|
N
|
E:GLY216
|
4.8
|
20.4
|
1.0
|
|
C
|
E:GLY181
|
4.8
|
14.1
|
1.0
|
|
CA
|
E:ASN215
|
4.8
|
15.7
|
1.0
|
|
CE
|
E:LYS300
|
4.8
|
15.4
|
1.0
|
|
C
|
E:ASN215
|
4.9
|
15.7
|
1.0
|
|
CA
|
E:GLY181
|
5.0
|
14.1
|
1.0
|
|
CD
|
E:LYS300
|
5.0
|
15.4
|
1.0
|
|
Calcium binding site 6 out
of 8 in 6lxv
Go back to
Calcium Binding Sites List in 6lxv
Calcium binding site 6 out
of 8 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 6 of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:Ca901
b:18.9
occ:1.00
|
O
|
F:TYR217
|
2.3
|
14.6
|
1.0
|
|
OD1
|
F:ASP182
|
2.3
|
13.4
|
1.0
|
|
OD1
|
F:ASN215
|
2.3
|
16.1
|
1.0
|
|
O3B
|
F:TPP900
|
2.3
|
20.4
|
1.0
|
|
O1A
|
F:TPP900
|
2.3
|
20.4
|
1.0
|
|
O
|
F:HOH1062
|
2.4
|
12.6
|
1.0
|
|
CG
|
F:ASN215
|
3.1
|
16.1
|
1.0
|
|
PA
|
F:TPP900
|
3.2
|
20.4
|
1.0
|
|
PB
|
F:TPP900
|
3.3
|
20.4
|
1.0
|
|
ND2
|
F:ASN215
|
3.4
|
16.1
|
1.0
|
|
CG
|
F:ASP182
|
3.4
|
13.4
|
1.0
|
|
C
|
F:TYR217
|
3.4
|
14.6
|
1.0
|
|
O2B
|
F:TPP900
|
3.5
|
20.4
|
1.0
|
|
O3A
|
F:TPP900
|
3.5
|
20.4
|
1.0
|
|
N
|
F:ASP182
|
3.9
|
13.4
|
1.0
|
|
OD2
|
F:ASP182
|
4.0
|
13.4
|
1.0
|
|
O
|
F:HIS213
|
4.0
|
15.2
|
1.0
|
|
O7
|
F:TPP900
|
4.1
|
20.4
|
1.0
|
|
N
|
F:GLY183
|
4.1
|
14.7
|
1.0
|
|
N
|
F:TYR217
|
4.2
|
14.6
|
1.0
|
|
NZ
|
F:LYS300
|
4.2
|
15.2
|
1.0
|
|
N
|
F:LYS218
|
4.3
|
15.8
|
1.0
|
|
O2A
|
F:TPP900
|
4.3
|
20.4
|
1.0
|
|
O1B
|
F:TPP900
|
4.4
|
20.4
|
1.0
|
|
CA
|
F:TYR217
|
4.4
|
14.6
|
1.0
|
|
CB
|
F:ASP182
|
4.5
|
13.4
|
1.0
|
|
CB
|
F:ASN215
|
4.5
|
16.1
|
1.0
|
|
CG2
|
F:THR223
|
4.5
|
15.4
|
1.0
|
|
CA
|
F:LYS218
|
4.5
|
15.8
|
1.0
|
|
N
|
F:ASN215
|
4.5
|
16.1
|
1.0
|
|
CA
|
F:ASP182
|
4.5
|
13.4
|
1.0
|
|
C
|
F:ASP182
|
4.7
|
13.4
|
1.0
|
|
N
|
F:GLY216
|
4.8
|
20.4
|
1.0
|
|
C
|
F:GLY181
|
4.8
|
14.2
|
1.0
|
|
CA
|
F:ASN215
|
4.8
|
16.1
|
1.0
|
|
CE
|
F:LYS300
|
4.8
|
15.2
|
1.0
|
|
C
|
F:ASN215
|
4.9
|
16.1
|
1.0
|
|
CA
|
F:GLY181
|
5.0
|
14.2
|
1.0
|
|
CD
|
F:LYS300
|
5.0
|
15.2
|
1.0
|
|
Calcium binding site 7 out
of 8 in 6lxv
Go back to
Calcium Binding Sites List in 6lxv
Calcium binding site 7 out
of 8 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 7 of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
G:Ca901
b:19.0
occ:1.00
|
O
|
G:TYR217
|
2.3
|
14.6
|
1.0
|
|
OD1
|
G:ASP182
|
2.3
|
13.0
|
1.0
|
|
OD1
|
G:ASN215
|
2.3
|
16.0
|
1.0
|
|
O3B
|
G:TPP900
|
2.3
|
20.4
|
1.0
|
|
O1A
|
G:TPP900
|
2.3
|
20.4
|
1.0
|
|
O
|
G:HOH1059
|
2.4
|
12.8
|
1.0
|
|
CG
|
G:ASN215
|
3.1
|
16.0
|
1.0
|
|
PA
|
G:TPP900
|
3.2
|
20.4
|
1.0
|
|
PB
|
G:TPP900
|
3.3
|
20.4
|
1.0
|
|
ND2
|
G:ASN215
|
3.3
|
16.0
|
1.0
|
|
CG
|
G:ASP182
|
3.4
|
13.0
|
1.0
|
|
C
|
G:TYR217
|
3.4
|
14.6
|
1.0
|
|
O2B
|
G:TPP900
|
3.5
|
20.4
|
1.0
|
|
O3A
|
G:TPP900
|
3.5
|
20.4
|
1.0
|
|
N
|
G:ASP182
|
3.9
|
13.0
|
1.0
|
|
OD2
|
G:ASP182
|
4.0
|
13.0
|
1.0
|
|
O
|
G:HIS213
|
4.0
|
15.5
|
1.0
|
|
O7
|
G:TPP900
|
4.1
|
20.4
|
1.0
|
|
N
|
G:GLY183
|
4.1
|
14.7
|
1.0
|
|
N
|
G:TYR217
|
4.2
|
14.6
|
1.0
|
|
NZ
|
G:LYS300
|
4.2
|
15.3
|
1.0
|
|
N
|
G:LYS218
|
4.3
|
15.9
|
1.0
|
|
O2A
|
G:TPP900
|
4.3
|
20.4
|
1.0
|
|
O1B
|
G:TPP900
|
4.4
|
20.4
|
1.0
|
|
CA
|
G:TYR217
|
4.4
|
14.6
|
1.0
|
|
CB
|
G:ASN215
|
4.5
|
16.0
|
1.0
|
|
CB
|
G:ASP182
|
4.5
|
13.0
|
1.0
|
|
CG2
|
G:THR223
|
4.5
|
15.3
|
1.0
|
|
CA
|
G:LYS218
|
4.5
|
15.9
|
1.0
|
|
N
|
G:ASN215
|
4.5
|
16.0
|
1.0
|
|
CA
|
G:ASP182
|
4.5
|
13.0
|
1.0
|
|
C
|
G:ASP182
|
4.7
|
13.0
|
1.0
|
|
N
|
G:GLY216
|
4.8
|
20.4
|
1.0
|
|
C
|
G:GLY181
|
4.8
|
14.3
|
1.0
|
|
CA
|
G:ASN215
|
4.8
|
16.0
|
1.0
|
|
CE
|
G:LYS300
|
4.8
|
15.3
|
1.0
|
|
C
|
G:ASN215
|
4.9
|
16.0
|
1.0
|
|
CA
|
G:GLY181
|
5.0
|
14.3
|
1.0
|
|
CD
|
G:LYS300
|
5.0
|
15.3
|
1.0
|
|
Calcium binding site 8 out
of 8 in 6lxv
Go back to
Calcium Binding Sites List in 6lxv
Calcium binding site 8 out
of 8 in the Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum
 Mono view
 Stereo pair view
|
|
A full contact list of Calcium with other atoms in the Ca binding
site number 8 of Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
H:Ca901
b:18.9
occ:1.00
|
O
|
H:TYR217
|
2.3
|
14.1
|
1.0
|
|
OD1
|
H:ASP182
|
2.3
|
13.3
|
1.0
|
|
OD1
|
H:ASN215
|
2.3
|
15.9
|
1.0
|
|
O1B
|
H:TPP900
|
2.3
|
20.4
|
1.0
|
|
O2A
|
H:TPP900
|
2.3
|
20.4
|
1.0
|
|
O
|
H:HOH1062
|
2.4
|
12.7
|
1.0
|
|
CG
|
H:ASN215
|
3.1
|
15.9
|
1.0
|
|
PA
|
H:TPP900
|
3.2
|
20.4
|
1.0
|
|
PB
|
H:TPP900
|
3.3
|
20.4
|
1.0
|
|
ND2
|
H:ASN215
|
3.4
|
15.9
|
1.0
|
|
CG
|
H:ASP182
|
3.4
|
13.3
|
1.0
|
|
C
|
H:TYR217
|
3.4
|
14.1
|
1.0
|
|
O2B
|
H:TPP900
|
3.5
|
20.4
|
1.0
|
|
O3A
|
H:TPP900
|
3.5
|
20.4
|
1.0
|
|
N
|
H:ASP182
|
3.9
|
13.3
|
1.0
|
|
OD2
|
H:ASP182
|
4.0
|
13.3
|
1.0
|
|
O
|
H:HIS213
|
4.0
|
15.9
|
1.0
|
|
O7
|
H:TPP900
|
4.1
|
20.4
|
1.0
|
|
N
|
H:GLY183
|
4.1
|
14.7
|
1.0
|
|
N
|
H:TYR217
|
4.2
|
14.1
|
1.0
|
|
NZ
|
H:LYS300
|
4.2
|
15.5
|
1.0
|
|
N
|
H:LYS218
|
4.3
|
16.0
|
1.0
|
|
O1A
|
H:TPP900
|
4.3
|
20.4
|
1.0
|
|
O3B
|
H:TPP900
|
4.4
|
20.4
|
1.0
|
|
CA
|
H:TYR217
|
4.4
|
14.1
|
1.0
|
|
CB
|
H:ASN215
|
4.5
|
15.9
|
1.0
|
|
CB
|
H:ASP182
|
4.5
|
13.3
|
1.0
|
|
CG2
|
H:THR223
|
4.5
|
15.0
|
1.0
|
|
CA
|
H:LYS218
|
4.5
|
16.0
|
1.0
|
|
N
|
H:ASN215
|
4.5
|
15.9
|
1.0
|
|
CA
|
H:ASP182
|
4.5
|
13.3
|
1.0
|
|
C
|
H:ASP182
|
4.7
|
13.3
|
1.0
|
|
N
|
H:GLY216
|
4.8
|
20.4
|
1.0
|
|
C
|
H:GLY181
|
4.8
|
14.0
|
1.0
|
|
CA
|
H:ASN215
|
4.8
|
15.9
|
1.0
|
|
CE
|
H:LYS300
|
4.8
|
15.5
|
1.0
|
|
C
|
H:ASN215
|
4.9
|
15.9
|
1.0
|
|
CA
|
H:GLY181
|
5.0
|
14.0
|
1.0
|
|
CD
|
H:LYS300
|
5.0
|
15.5
|
1.0
|
|
Reference:
K.Nakata,
N.Miyazaki,
H.Yamaguchi,
M.Hirose,
H.Miyano,
T.Mizukoshi,
T.Kashiwagi,
K.Iwasaki.
Cryo-Em Structure of Phosphoketolase From Bifidobacterium Longum To Be Published.
Page generated: Wed Jul 9 15:58:25 2025
|
