Sodium 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:
Sodium Binding Sites:
The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where determined in the
Escherichia Coli Transketolase in Complex with Cofactor Analog 2'- Methoxythiamine and Substrate Xylulose 5-Phosphate, PDB code: 6tj9:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 6tj9
Go back to
Sodium Binding Sites List in 6tj9
Sodium 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 Sodium with other atoms in the Na 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:Na717
b:7.4
occ:0.29
|
O
|
A:HOH820
|
1.8
|
9.7
|
0.7
|
O
|
A:VAL234
|
2.1
|
12.1
|
1.0
|
O
|
A:HOH820
|
2.1
|
6.5
|
0.3
|
O
|
A:GLY176
|
2.2
|
9.0
|
1.0
|
O
|
A:HOH1104
|
2.3
|
16.8
|
1.0
|
O
|
A:ALA231
|
2.4
|
8.8
|
1.0
|
HA
|
A:ARG232
|
3.3
|
11.2
|
0.4
|
HA
|
A:ARG232
|
3.3
|
10.5
|
0.6
|
C
|
A:VAL234
|
3.3
|
9.2
|
1.0
|
C
|
A:GLY176
|
3.4
|
6.7
|
1.0
|
HE2
|
A:TYR148
|
3.5
|
13.1
|
1.0
|
HA
|
A:THR235
|
3.5
|
12.3
|
1.0
|
HD11
|
A:ILE179
|
3.5
|
10.4
|
1.0
|
C
|
A:ALA231
|
3.6
|
7.6
|
1.0
|
HB
|
A:VAL234
|
3.7
|
11.3
|
1.0
|
H
|
A:VAL234
|
3.8
|
11.3
|
1.0
|
HA2
|
A:GLY176
|
3.8
|
8.3
|
1.0
|
O
|
A:ARG232
|
3.8
|
11.1
|
0.6
|
CA
|
A:ARG232
|
4.0
|
8.8
|
0.6
|
CA
|
A:ARG232
|
4.0
|
9.3
|
0.4
|
HA
|
A:LYS177
|
4.0
|
7.7
|
1.0
|
C
|
A:ARG232
|
4.0
|
9.4
|
0.6
|
CA
|
A:GLY176
|
4.1
|
6.9
|
1.0
|
O
|
A:LYS237
|
4.1
|
7.0
|
0.5
|
HG12
|
A:ILE179
|
4.1
|
8.7
|
1.0
|
HA3
|
A:GLY176
|
4.1
|
8.3
|
1.0
|
O
|
A:LYS237
|
4.1
|
6.4
|
0.5
|
HG
|
A:SER239
|
4.1
|
8.7
|
1.0
|
N
|
A:VAL234
|
4.1
|
9.4
|
1.0
|
CA
|
A:VAL234
|
4.2
|
8.9
|
1.0
|
C
|
A:ARG232
|
4.2
|
9.8
|
0.4
|
HG13
|
A:ILE179
|
4.2
|
8.7
|
1.0
|
N
|
A:ARG232
|
4.2
|
7.4
|
0.6
|
N
|
A:ARG232
|
4.2
|
8.1
|
0.4
|
OG
|
A:SER239
|
4.2
|
7.3
|
1.0
|
HG12
|
A:VAL234
|
4.3
|
12.9
|
1.0
|
O
|
A:ARG232
|
4.3
|
11.1
|
0.4
|
N
|
A:THR235
|
4.3
|
9.1
|
1.0
|
CA
|
A:THR235
|
4.3
|
10.3
|
1.0
|
CB
|
A:VAL234
|
4.4
|
9.4
|
1.0
|
CD1
|
A:ILE179
|
4.4
|
8.7
|
1.0
|
CE2
|
A:TYR148
|
4.4
|
10.9
|
1.0
|
CG1
|
A:ILE179
|
4.4
|
7.3
|
1.0
|
N
|
A:LYS177
|
4.5
|
6.1
|
1.0
|
HB1
|
A:ALA231
|
4.6
|
9.3
|
1.0
|
HA
|
A:ALA231
|
4.6
|
9.0
|
1.0
|
CA
|
A:ALA231
|
4.7
|
7.5
|
1.0
|
CA
|
A:LYS177
|
4.7
|
6.4
|
1.0
|
OH
|
A:TYR148
|
4.7
|
17.7
|
1.0
|
HG22
|
A:THR235
|
4.8
|
21.2
|
1.0
|
O
|
A:HOH1418
|
4.8
|
29.6
|
1.0
|
HD13
|
A:ILE179
|
4.9
|
10.4
|
1.0
|
CG1
|
A:VAL234
|
4.9
|
10.7
|
1.0
|
N
|
A:ALA233
|
4.9
|
9.9
|
1.0
|
H
|
A:LYS237
|
5.0
|
9.1
|
0.5
|
HB2
|
A:SER239
|
5.0
|
7.4
|
1.0
|
H
|
A:LYS237
|
5.0
|
9.3
|
0.5
|
|
Sodium binding site 2 out
of 2 in 6tj9
Go back to
Sodium Binding Sites List in 6tj9
Sodium 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 Sodium with other atoms in the Na 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:Na717
b:7.3
occ:0.52
|
O
|
B:HOH1084
|
1.8
|
6.0
|
0.5
|
O
|
B:VAL234
|
2.2
|
10.9
|
1.0
|
O
|
B:GLY176
|
2.3
|
9.0
|
1.0
|
O
|
B:ALA231
|
2.3
|
9.2
|
1.0
|
O
|
B:HOH820
|
2.4
|
15.2
|
1.0
|
O
|
B:HOH1084
|
2.4
|
7.3
|
0.5
|
HA
|
B:ARG232
|
3.3
|
12.2
|
0.5
|
C
|
B:VAL234
|
3.3
|
8.8
|
1.0
|
HA
|
B:ARG232
|
3.4
|
12.1
|
0.6
|
C
|
B:GLY176
|
3.4
|
7.0
|
1.0
|
C
|
B:ALA231
|
3.5
|
8.3
|
1.0
|
HE2
|
B:TYR148
|
3.6
|
14.1
|
1.0
|
HD11
|
B:ILE179
|
3.6
|
11.1
|
1.0
|
HB
|
B:VAL234
|
3.6
|
11.4
|
1.0
|
HA
|
B:THR235
|
3.7
|
10.8
|
1.0
|
H
|
B:VAL234
|
3.7
|
11.6
|
1.0
|
HA2
|
B:GLY176
|
3.8
|
8.3
|
1.0
|
O
|
B:ARG232
|
3.9
|
12.7
|
0.6
|
CA
|
B:ARG232
|
4.0
|
10.1
|
0.6
|
CA
|
B:ARG232
|
4.0
|
10.2
|
0.5
|
HA
|
B:LYS177
|
4.0
|
7.6
|
1.0
|
HG
|
B:SER239
|
4.0
|
9.9
|
1.0
|
O
|
B:LYS237
|
4.1
|
6.7
|
1.0
|
C
|
B:ARG232
|
4.1
|
10.8
|
0.6
|
CA
|
B:GLY176
|
4.1
|
6.9
|
1.0
|
N
|
B:VAL234
|
4.1
|
9.6
|
1.0
|
HG12
|
B:ILE179
|
4.1
|
9.5
|
1.0
|
HA3
|
B:GLY176
|
4.1
|
8.3
|
1.0
|
CA
|
B:VAL234
|
4.1
|
9.0
|
1.0
|
N
|
B:ARG232
|
4.2
|
9.0
|
0.6
|
N
|
B:ARG232
|
4.2
|
9.0
|
0.5
|
C
|
B:ARG232
|
4.2
|
11.0
|
0.5
|
OG
|
B:SER239
|
4.2
|
8.3
|
1.0
|
HG13
|
B:ILE179
|
4.3
|
9.5
|
1.0
|
CB
|
B:VAL234
|
4.3
|
9.5
|
1.0
|
N
|
B:THR235
|
4.3
|
8.7
|
1.0
|
HG12
|
B:VAL234
|
4.3
|
13.3
|
1.0
|
O
|
B:ARG232
|
4.4
|
11.7
|
0.5
|
CA
|
B:THR235
|
4.4
|
9.0
|
1.0
|
CD1
|
B:ILE179
|
4.4
|
9.2
|
1.0
|
HA
|
B:ALA231
|
4.5
|
10.1
|
1.0
|
HB1
|
B:ALA231
|
4.5
|
10.2
|
1.0
|
O
|
B:HOH1449
|
4.5
|
19.5
|
1.0
|
CE2
|
B:TYR148
|
4.5
|
11.8
|
1.0
|
CG1
|
B:ILE179
|
4.5
|
7.9
|
1.0
|
N
|
B:LYS177
|
4.5
|
6.3
|
1.0
|
CA
|
B:ALA231
|
4.6
|
8.4
|
1.0
|
CA
|
B:LYS177
|
4.7
|
6.3
|
1.0
|
N
|
B:ALA233
|
4.8
|
11.5
|
1.0
|
CG1
|
B:VAL234
|
4.9
|
11.1
|
1.0
|
OH
|
B:TYR148
|
4.9
|
17.4
|
1.0
|
H
|
B:LYS237
|
4.9
|
8.3
|
1.0
|
HD13
|
B:ILE179
|
4.9
|
11.1
|
1.0
|
HB2
|
B:SER239
|
5.0
|
9.0
|
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 Oct 8 13:58:20 2024
|