Sodium in PDB 6rjc: E.Coli Transketolase Apoenzyme
Enzymatic activity of E.Coli Transketolase Apoenzyme
All present enzymatic activity of E.Coli Transketolase Apoenzyme:
2.2.1.1;
Protein crystallography data
The structure of E.Coli Transketolase Apoenzyme, PDB code: 6rjc
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)
|
80.95 /
1.05
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
89.905,
102.048,
132.933,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
10.4 /
12.3
|
Other elements in 6rjc:
The structure of E.Coli Transketolase Apoenzyme also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the E.Coli Transketolase Apoenzyme
(pdb code 6rjc). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
E.Coli Transketolase Apoenzyme, PDB code: 6rjc:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 6rjc
Go back to
Sodium Binding Sites List in 6rjc
Sodium binding site 1 out
of 2 in the E.Coli Transketolase Apoenzyme
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of E.Coli Transketolase Apoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na725
b:10.3
occ:0.64
|
O
|
A:HOH1217
|
2.3
|
6.1
|
0.3
|
O
|
A:VAL234
|
2.3
|
17.2
|
1.0
|
O
|
A:GLY176
|
2.3
|
10.8
|
1.0
|
O
|
A:HOH1217
|
2.4
|
11.0
|
0.7
|
O
|
A:HOH1013
|
2.4
|
15.4
|
1.0
|
O
|
A:ALA231
|
2.4
|
11.6
|
1.0
|
HA
|
A:ARG232
|
3.3
|
13.9
|
1.0
|
C
|
A:VAL234
|
3.4
|
12.7
|
1.0
|
C
|
A:GLY176
|
3.4
|
8.9
|
1.0
|
HA
|
A:THR235
|
3.5
|
16.3
|
1.0
|
C
|
A:ALA231
|
3.5
|
10.2
|
1.0
|
HE2
|
A:TYR148
|
3.5
|
16.8
|
1.0
|
HD11
|
A:ILE179
|
3.6
|
12.5
|
1.0
|
HA2
|
A:GLY176
|
3.8
|
11.5
|
1.0
|
H
|
A:VAL234
|
3.8
|
13.8
|
1.0
|
HB
|
A:VAL234
|
3.8
|
16.5
|
1.0
|
CA
|
A:ARG232
|
4.0
|
11.6
|
1.0
|
HA
|
A:LYS177
|
4.0
|
10.4
|
1.0
|
O
|
A:ARG232
|
4.0
|
15.6
|
1.0
|
O
|
A:LYS237
|
4.0
|
9.1
|
1.0
|
CA
|
A:GLY176
|
4.1
|
9.6
|
1.0
|
HG12
|
A:ILE179
|
4.1
|
10.7
|
1.0
|
C
|
A:ARG232
|
4.1
|
12.0
|
1.0
|
HA3
|
A:GLY176
|
4.2
|
11.5
|
1.0
|
N
|
A:VAL234
|
4.2
|
11.5
|
1.0
|
N
|
A:ARG232
|
4.2
|
10.4
|
1.0
|
CA
|
A:VAL234
|
4.2
|
11.7
|
1.0
|
HG13
|
A:ILE179
|
4.3
|
10.7
|
1.0
|
OG
|
A:SER239
|
4.3
|
9.5
|
1.0
|
N
|
A:THR235
|
4.3
|
12.3
|
1.0
|
CA
|
A:THR235
|
4.3
|
13.6
|
1.0
|
HG12
|
A:VAL234
|
4.4
|
19.0
|
1.0
|
CD1
|
A:ILE179
|
4.5
|
10.4
|
1.0
|
CE2
|
A:TYR148
|
4.5
|
14.0
|
1.0
|
CB
|
A:VAL234
|
4.5
|
13.7
|
1.0
|
HB1
|
A:ALA231
|
4.5
|
12.3
|
1.0
|
CG1
|
A:ILE179
|
4.5
|
8.9
|
1.0
|
N
|
A:LYS177
|
4.5
|
8.1
|
1.0
|
O
|
A:HOH1428
|
4.5
|
22.6
|
0.9
|
HA
|
A:ALA231
|
4.6
|
12.4
|
1.0
|
CA
|
A:ALA231
|
4.6
|
10.4
|
1.0
|
HG22
|
A:THR235
|
4.7
|
23.9
|
1.0
|
CA
|
A:LYS177
|
4.7
|
8.6
|
1.0
|
HG
|
A:SER239
|
4.7
|
11.4
|
1.0
|
OH
|
A:TYR148
|
4.8
|
22.1
|
1.0
|
HB2
|
A:SER239
|
4.9
|
10.1
|
1.0
|
N
|
A:ALA233
|
4.9
|
11.3
|
1.0
|
H
|
A:LYS237
|
4.9
|
11.8
|
0.7
|
H
|
A:LYS237
|
4.9
|
11.8
|
0.3
|
HD13
|
A:ILE179
|
5.0
|
12.5
|
1.0
|
CG1
|
A:VAL234
|
5.0
|
15.8
|
1.0
|
|
Sodium binding site 2 out
of 2 in 6rjc
Go back to
Sodium Binding Sites List in 6rjc
Sodium binding site 2 out
of 2 in the E.Coli Transketolase Apoenzyme
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of E.Coli Transketolase Apoenzyme within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na723
b:8.7
occ:0.80
|
O
|
B:VAL234
|
2.2
|
12.2
|
1.0
|
O
|
B:GLY176
|
2.3
|
10.1
|
1.0
|
O
|
B:ALA231
|
2.3
|
10.3
|
1.0
|
O
|
B:HOH1033
|
2.4
|
10.5
|
1.0
|
O
|
B:HOH998
|
2.4
|
12.5
|
1.0
|
HA
|
B:ARG232
|
3.4
|
12.8
|
1.0
|
C
|
B:VAL234
|
3.4
|
10.3
|
1.0
|
C
|
B:GLY176
|
3.4
|
8.4
|
1.0
|
C
|
B:ALA231
|
3.5
|
10.3
|
1.0
|
HA
|
B:THR235
|
3.6
|
12.6
|
1.0
|
HD11
|
B:ILE179
|
3.6
|
11.9
|
1.0
|
HE2
|
B:TYR148
|
3.7
|
16.2
|
1.0
|
HB
|
B:VAL234
|
3.7
|
13.5
|
1.0
|
HA2
|
B:GLY176
|
3.8
|
10.2
|
1.0
|
H
|
B:VAL234
|
3.8
|
12.9
|
1.0
|
O
|
B:LYS237
|
4.0
|
8.0
|
1.0
|
CA
|
B:ARG232
|
4.0
|
10.7
|
1.0
|
CA
|
B:GLY176
|
4.1
|
8.5
|
1.0
|
HA
|
B:LYS177
|
4.1
|
9.8
|
1.0
|
HG12
|
B:ILE179
|
4.1
|
10.7
|
1.0
|
HA3
|
B:GLY176
|
4.2
|
10.2
|
1.0
|
N
|
B:VAL234
|
4.2
|
10.8
|
1.0
|
CA
|
B:VAL234
|
4.2
|
10.7
|
1.0
|
O
|
B:ARG232
|
4.2
|
13.1
|
1.0
|
N
|
B:ARG232
|
4.2
|
10.2
|
1.0
|
C
|
B:ARG232
|
4.2
|
11.2
|
1.0
|
OG
|
B:SER239
|
4.2
|
9.5
|
1.0
|
HG13
|
B:ILE179
|
4.3
|
10.7
|
1.0
|
N
|
B:THR235
|
4.3
|
9.8
|
1.0
|
CA
|
B:THR235
|
4.4
|
10.5
|
1.0
|
HG12
|
B:VAL234
|
4.4
|
15.4
|
1.0
|
CB
|
B:VAL234
|
4.4
|
11.2
|
1.0
|
O
|
B:HOH1437
|
4.4
|
16.4
|
0.9
|
HB1
|
B:ALA231
|
4.4
|
11.5
|
1.0
|
HA
|
B:ALA231
|
4.4
|
11.3
|
1.0
|
CD1
|
B:ILE179
|
4.5
|
9.9
|
1.0
|
CG1
|
B:ILE179
|
4.5
|
8.9
|
1.0
|
N
|
B:LYS177
|
4.5
|
8.1
|
1.0
|
CA
|
B:ALA231
|
4.6
|
9.4
|
1.0
|
CE2
|
B:TYR148
|
4.6
|
13.5
|
1.0
|
HG
|
B:SER239
|
4.7
|
11.4
|
1.0
|
CA
|
B:LYS177
|
4.8
|
8.2
|
1.0
|
H
|
B:LYS237
|
4.8
|
10.3
|
1.0
|
HD13
|
B:ILE179
|
4.9
|
11.9
|
1.0
|
HB2
|
B:SER239
|
4.9
|
10.6
|
1.0
|
N
|
B:ALA233
|
4.9
|
11.6
|
1.0
|
CG1
|
B:VAL234
|
5.0
|
12.8
|
1.0
|
OH
|
B:TYR148
|
5.0
|
18.7
|
1.0
|
|
Reference:
S.Dai,
L.M.Funk,
F.R.Von Pappenheim,
V.Sautner,
M.Paulikat,
B.Schroder,
J.Uranga,
R.A.Mata,
K.Tittmann.
Low-Barrier Hydrogen Bonds in Enzyme Cooperativity. Nature V. 573 609 2019.
ISSN: ESSN 1476-4687
PubMed: 31534226
DOI: 10.1038/S41586-019-1581-9
Page generated: Tue Oct 8 13:14:25 2024
|