Calcium in PDB 6tj9: Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate
Enzymatic activity of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate
All present enzymatic activity of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate:
2.2.1.1;
Protein crystallography data
The structure of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate, PDB code: 6tj9
was solved by
F.Rabe Von Pappenheim,
K.Tittmann,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
47.66 /
0.95
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.760,
102.080,
133.130,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
9.9 /
11
|
Other elements in 6tj9:
The structure of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate
(pdb code 6tj9). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the
Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate, PDB code: 6tj9:
Jump to Calcium binding site number:
1;
2;
Calcium binding site 1 out
of 2 in 6tj9
Go back to
Calcium Binding Sites List in 6tj9
Calcium binding site 1 out
of 2 in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca703
b:5.1
occ:1.00
|
O13
|
A:NDQ702
|
2.1
|
7.1
|
0.3
|
O22
|
A:NDQ702
|
2.2
|
6.2
|
0.7
|
O
|
A:ILE187
|
2.3
|
6.3
|
1.0
|
OD2
|
A:ASP155
|
2.3
|
6.5
|
1.0
|
O13
|
A:NDQ702
|
2.4
|
6.1
|
0.7
|
OD1
|
A:ASN185
|
2.4
|
5.5
|
1.0
|
O
|
A:HOH924
|
2.4
|
6.1
|
1.0
|
O22
|
A:NDQ702
|
2.4
|
6.0
|
0.3
|
HD21
|
A:ASN185
|
3.0
|
7.3
|
1.0
|
HB2
|
A:ASP155
|
3.2
|
6.8
|
1.0
|
CG
|
A:ASN185
|
3.3
|
5.5
|
1.0
|
H
|
A:ASP155
|
3.3
|
6.0
|
1.0
|
H
|
A:ILE187
|
3.3
|
6.9
|
1.0
|
P1
|
A:NDQ702
|
3.4
|
6.6
|
0.3
|
CG
|
A:ASP155
|
3.4
|
5.4
|
1.0
|
P2
|
A:NDQ702
|
3.4
|
6.4
|
0.7
|
C
|
A:ILE187
|
3.5
|
5.6
|
1.0
|
ND2
|
A:ASN185
|
3.5
|
6.0
|
1.0
|
P1
|
A:NDQ702
|
3.5
|
6.1
|
0.7
|
P2
|
A:NDQ702
|
3.6
|
6.8
|
0.3
|
O11
|
A:NDQ702
|
3.7
|
7.5
|
0.3
|
O11
|
A:NDQ702
|
3.7
|
8.5
|
0.7
|
CB
|
A:ASP155
|
3.8
|
5.7
|
1.0
|
O5G
|
A:NDQ702
|
4.0
|
10.7
|
0.3
|
O23
|
A:NDQ702
|
4.0
|
8.4
|
0.7
|
N
|
A:ILE187
|
4.0
|
5.7
|
1.0
|
HA
|
A:SER188
|
4.1
|
7.1
|
1.0
|
N
|
A:ASP155
|
4.1
|
5.0
|
1.0
|
HB
|
A:ILE187
|
4.1
|
8.1
|
1.0
|
H
|
A:ASN185
|
4.1
|
6.9
|
1.0
|
CA
|
A:ILE187
|
4.3
|
5.8
|
1.0
|
HD22
|
A:ASN185
|
4.3
|
7.3
|
1.0
|
O
|
A:HOH808
|
4.4
|
9.8
|
1.0
|
O12
|
A:NDQ702
|
4.4
|
11.0
|
0.7
|
HB3
|
A:SER188
|
4.4
|
7.4
|
1.0
|
O
|
A:ASP183
|
4.4
|
6.5
|
1.0
|
OD1
|
A:ASP155
|
4.5
|
6.9
|
1.0
|
O21
|
A:NDQ702
|
4.5
|
8.4
|
0.3
|
N
|
A:SER188
|
4.5
|
5.6
|
1.0
|
HD12
|
A:ILE247
|
4.5
|
9.0
|
1.0
|
O12
|
A:NDQ702
|
4.5
|
6.8
|
0.3
|
HB3
|
A:ASP155
|
4.6
|
6.8
|
1.0
|
CA
|
A:ASP155
|
4.6
|
4.9
|
1.0
|
HG22
|
A:ILE187
|
4.6
|
9.6
|
1.0
|
H
|
A:GLY186
|
4.6
|
6.8
|
1.0
|
CB
|
A:ASN185
|
4.7
|
5.8
|
1.0
|
CA
|
A:SER188
|
4.7
|
5.9
|
1.0
|
HG11
|
A:VAL193
|
4.7
|
10.5
|
1.0
|
O21
|
A:NDQ702
|
4.7
|
8.1
|
0.7
|
CB
|
A:ILE187
|
4.7
|
6.7
|
1.0
|
HA3
|
A:GLY154
|
4.7
|
6.5
|
1.0
|
O5G
|
A:NDQ702
|
4.7
|
10.0
|
0.7
|
O23
|
A:NDQ702
|
4.8
|
7.4
|
0.3
|
C5B
|
A:NDQ702
|
4.8
|
12.4
|
0.7
|
N
|
A:GLY186
|
4.8
|
5.7
|
1.0
|
N
|
A:ASN185
|
4.9
|
5.7
|
1.0
|
H
|
A:GLY156
|
4.9
|
6.0
|
1.0
|
|
Calcium binding site 2 out
of 2 in 6tj9
Go back to
Calcium Binding Sites List in 6tj9
Calcium binding site 2 out
of 2 in the Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca702
b:5.5
occ:1.00
|
O12
|
B:NDQ701
|
2.1
|
8.6
|
0.3
|
O22
|
B:NDQ701
|
2.3
|
7.0
|
0.7
|
O
|
B:ILE187
|
2.3
|
6.5
|
1.0
|
OD2
|
B:ASP155
|
2.3
|
6.8
|
1.0
|
O22
|
B:NDQ701
|
2.3
|
5.6
|
0.3
|
O13
|
B:NDQ701
|
2.4
|
6.9
|
0.7
|
OD1
|
B:ASN185
|
2.4
|
5.9
|
1.0
|
O
|
B:HOH933
|
2.4
|
6.7
|
1.0
|
HD21
|
B:ASN185
|
3.0
|
7.3
|
1.0
|
HB2
|
B:ASP155
|
3.2
|
6.8
|
1.0
|
CG
|
B:ASN185
|
3.3
|
5.7
|
1.0
|
H
|
B:ASP155
|
3.3
|
6.5
|
1.0
|
H
|
B:ILE187
|
3.3
|
7.0
|
1.0
|
CG
|
B:ASP155
|
3.4
|
6.0
|
1.0
|
P1
|
B:NDQ701
|
3.4
|
7.8
|
0.3
|
P2
|
B:NDQ701
|
3.5
|
6.9
|
0.7
|
C
|
B:ILE187
|
3.5
|
5.8
|
1.0
|
ND2
|
B:ASN185
|
3.5
|
6.1
|
1.0
|
P1
|
B:NDQ701
|
3.5
|
6.4
|
0.7
|
P2
|
B:NDQ701
|
3.6
|
6.8
|
0.3
|
O11
|
B:NDQ701
|
3.7
|
7.5
|
0.3
|
O11
|
B:NDQ701
|
3.7
|
8.9
|
0.7
|
CB
|
B:ASP155
|
3.8
|
5.7
|
1.0
|
O5G
|
B:NDQ701
|
3.9
|
11.7
|
0.3
|
N
|
B:ILE187
|
4.0
|
5.8
|
1.0
|
HA
|
B:SER188
|
4.1
|
7.3
|
1.0
|
O23
|
B:NDQ701
|
4.1
|
8.5
|
0.7
|
HB
|
B:ILE187
|
4.1
|
8.5
|
1.0
|
H
|
B:ASN185
|
4.1
|
7.2
|
1.0
|
N
|
B:ASP155
|
4.1
|
5.4
|
1.0
|
CA
|
B:ILE187
|
4.3
|
6.1
|
1.0
|
HD22
|
B:ASN185
|
4.3
|
7.3
|
1.0
|
O12
|
B:NDQ701
|
4.4
|
11.5
|
0.7
|
O
|
B:HOH801
|
4.4
|
10.6
|
1.0
|
O
|
B:ASP183
|
4.4
|
6.7
|
0.7
|
HB3
|
B:SER188
|
4.4
|
7.6
|
1.0
|
OD1
|
B:ASP155
|
4.5
|
7.2
|
1.0
|
O21
|
B:NDQ701
|
4.5
|
8.7
|
0.3
|
N
|
B:SER188
|
4.5
|
5.8
|
1.0
|
HD12
|
B:ILE247
|
4.5
|
9.5
|
1.0
|
O
|
B:ASP183
|
4.5
|
7.3
|
0.3
|
HB3
|
B:ASP155
|
4.5
|
6.8
|
1.0
|
O13
|
B:NDQ701
|
4.6
|
6.8
|
0.3
|
CA
|
B:ASP155
|
4.6
|
5.3
|
1.0
|
HG22
|
B:ILE187
|
4.6
|
10.2
|
1.0
|
H
|
B:GLY186
|
4.6
|
7.0
|
1.0
|
CB
|
B:ASN185
|
4.7
|
6.3
|
1.0
|
CB
|
B:ILE187
|
4.7
|
7.1
|
1.0
|
HG11
|
B:VAL193
|
4.7
|
10.7
|
1.0
|
CA
|
B:SER188
|
4.7
|
6.0
|
1.0
|
O21
|
B:NDQ701
|
4.7
|
8.7
|
0.7
|
O5G
|
B:NDQ701
|
4.7
|
10.8
|
0.7
|
O23
|
B:NDQ701
|
4.7
|
7.6
|
0.3
|
HA3
|
B:GLY154
|
4.7
|
7.0
|
1.0
|
C5B
|
B:NDQ701
|
4.8
|
13.3
|
0.7
|
N
|
B:GLY186
|
4.9
|
5.8
|
1.0
|
N
|
B:ASN185
|
4.9
|
6.0
|
1.0
|
H
|
B:GLY156
|
4.9
|
6.5
|
1.0
|
C
|
B:ASN185
|
5.0
|
6.2
|
1.0
|
|
Reference:
F.Rabe Von Pappenheim,
M.Aldeghi,
B.Shome,
T.Begley,
B.L.De Groot,
K.Tittmann.
Structural Basis For Antibiotic Action of the B 1 Antivitamin 2'-Methoxy-Thiamine. Nat.Chem.Biol. V. 16 1237 2020.
ISSN: ESSN 1552-4469
PubMed: 32839604
DOI: 10.1038/S41589-020-0628-4
Page generated: Tue Jul 16 15:19:46 2024
|