Potassium in PDB 8fsi: The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
Enzymatic activity of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
All present enzymatic activity of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam:
1.97.1.4;
Protein crystallography data
The structure of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam, PDB code: 8fsi
was solved by
J.D.Moody,
A.Galambas,
C.M.Lawrence,
J.B.Broderick,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
41.77 /
1.46
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
46.405,
59.094,
83.545,
90,
90,
90
|
R / Rfree (%)
|
15.1 /
17.3
|
Other elements in 8fsi:
The structure of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam also contains other interesting chemical elements:
Potassium Binding Sites:
The binding sites of Potassium atom in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
(pdb code 8fsi). This binding sites where shown within
5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the
The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam, PDB code: 8fsi:
Jump to Potassium binding site number:
1;
2;
Potassium binding site 1 out
of 2 in 8fsi
Go back to
Potassium Binding Sites List in 8fsi
Potassium binding site 1 out
of 2 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 1 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K303
b:13.8
occ:1.00
|
OXT
|
A:SAM302
|
2.6
|
14.7
|
1.0
|
OD1
|
A:ASP104
|
2.7
|
14.9
|
1.0
|
OD1
|
A:ASP129
|
2.7
|
13.5
|
1.0
|
O
|
A:MET127
|
2.8
|
13.4
|
1.0
|
H
|
A:ASP129
|
2.9
|
14.4
|
1.0
|
O
|
A:THR105
|
3.0
|
13.4
|
1.0
|
H
|
A:THR105
|
3.0
|
13.9
|
1.0
|
O
|
A:HOH490
|
3.0
|
17.0
|
1.0
|
N
|
A:ASP129
|
3.3
|
12.0
|
1.0
|
N
|
A:THR105
|
3.4
|
11.6
|
1.0
|
HB2
|
A:ASP129
|
3.4
|
15.5
|
1.0
|
CG
|
A:ASP129
|
3.5
|
13.9
|
1.0
|
H3'
|
A:SAM302
|
3.6
|
15.3
|
1.0
|
C
|
A:THR105
|
3.6
|
12.0
|
1.0
|
HB2
|
A:SAM302
|
3.7
|
17.0
|
1.0
|
C
|
A:MET127
|
3.7
|
12.8
|
1.0
|
HA
|
A:LEU128
|
3.8
|
15.4
|
1.0
|
C
|
A:SAM302
|
3.8
|
13.8
|
1.0
|
HA
|
A:ASP104
|
3.8
|
14.1
|
1.0
|
CB
|
A:ASP129
|
3.8
|
12.9
|
1.0
|
CG
|
A:ASP104
|
3.8
|
13.2
|
1.0
|
C
|
A:ASP104
|
3.9
|
12.2
|
1.0
|
C
|
A:LEU128
|
3.9
|
12.6
|
1.0
|
HB2
|
A:ARG166
|
4.0
|
19.3
|
1.0
|
CA
|
A:ASP129
|
4.0
|
11.5
|
1.0
|
O3'
|
A:SAM302
|
4.0
|
14.9
|
1.0
|
CA
|
A:THR105
|
4.0
|
11.9
|
1.0
|
HG3
|
A:ARG166
|
4.1
|
22.5
|
1.0
|
HB2
|
A:MET127
|
4.1
|
15.2
|
1.0
|
HA
|
A:SAM302
|
4.1
|
17.6
|
1.0
|
HA
|
A:ASP129
|
4.2
|
13.8
|
1.0
|
CA
|
A:LEU128
|
4.2
|
12.9
|
1.0
|
HB3
|
A:MET127
|
4.2
|
15.2
|
1.0
|
N
|
A:LEU128
|
4.3
|
13.0
|
1.0
|
CA
|
A:ASP104
|
4.3
|
11.8
|
1.0
|
C3'
|
A:SAM302
|
4.3
|
12.8
|
1.0
|
CA
|
A:SAM302
|
4.4
|
14.7
|
1.0
|
HA
|
A:THR105
|
4.4
|
14.2
|
1.0
|
CB
|
A:SAM302
|
4.5
|
14.2
|
1.0
|
H5'2
|
A:SAM302
|
4.5
|
19.2
|
1.0
|
CB
|
A:MET127
|
4.5
|
12.6
|
1.0
|
N
|
A:ASN106
|
4.6
|
12.2
|
1.0
|
OD2
|
A:ASP129
|
4.6
|
15.8
|
1.0
|
HA
|
A:ASN106
|
4.6
|
16.7
|
1.0
|
O
|
A:ASP104
|
4.6
|
14.4
|
1.0
|
CB
|
A:ASP104
|
4.7
|
12.0
|
1.0
|
OD2
|
A:ASP104
|
4.7
|
16.1
|
1.0
|
O
|
A:SAM302
|
4.7
|
14.3
|
1.0
|
CA
|
A:MET127
|
4.8
|
11.7
|
1.0
|
HB3
|
A:ASP129
|
4.8
|
15.5
|
1.0
|
O
|
A:LEU128
|
4.8
|
12.4
|
1.0
|
CB
|
A:ARG166
|
4.8
|
16.1
|
1.0
|
CG
|
A:ARG166
|
4.9
|
18.8
|
1.0
|
HE3
|
A:MET127
|
4.9
|
19.4
|
1.0
|
H4'
|
A:SAM302
|
5.0
|
17.6
|
1.0
|
HB1
|
A:SAM302
|
5.0
|
17.0
|
1.0
|
|
Potassium binding site 2 out
of 2 in 8fsi
Go back to
Potassium Binding Sites List in 8fsi
Potassium binding site 2 out
of 2 in the The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam
 Mono view
 Stereo pair view
|
A full contact list of Potassium with other atoms in the K binding
site number 2 of The Structure of A Crystallizable Variant of E. Coli Pyruvate Formate- Lyase Activating Enzyme Bound to Sam within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:K305
b:34.5
occ:0.52
|
HH
|
A:TYR216
|
2.5
|
25.3
|
1.0
|
O
|
A:LEU204
|
2.8
|
34.3
|
1.0
|
O
|
A:TYR35
|
2.9
|
17.5
|
1.0
|
OH
|
A:TYR216
|
3.0
|
21.1
|
1.0
|
HA
|
A:HIS37
|
3.1
|
20.6
|
1.0
|
HN61
|
A:SAM302
|
3.1
|
17.5
|
1.0
|
HE1
|
A:TYR216
|
3.2
|
28.1
|
1.0
|
CZ
|
A:TYR216
|
3.5
|
21.5
|
1.0
|
O
|
A:CYS36
|
3.5
|
17.3
|
1.0
|
CE1
|
A:TYR216
|
3.6
|
23.4
|
1.0
|
HB3
|
A:HIS37
|
3.6
|
22.9
|
1.0
|
HN62
|
A:SAM302
|
3.6
|
17.5
|
1.0
|
O
|
A:GLU203
|
3.7
|
41.6
|
1.0
|
N6
|
A:SAM302
|
3.7
|
14.6
|
1.0
|
C
|
A:TYR35
|
3.8
|
14.1
|
1.0
|
HE1
|
A:TRP209
|
3.8
|
26.4
|
1.0
|
C
|
A:LEU204
|
3.8
|
26.1
|
1.0
|
CA
|
A:HIS37
|
3.9
|
17.1
|
1.0
|
C
|
A:CYS36
|
3.9
|
16.7
|
1.0
|
HA
|
A:GLU203
|
3.9
|
28.5
|
1.0
|
HA
|
A:TYR35
|
4.0
|
19.4
|
1.0
|
HA3
|
A:GLY205
|
4.0
|
40.2
|
1.0
|
C
|
A:GLU203
|
4.0
|
33.8
|
1.0
|
N
|
A:HIS37
|
4.0
|
15.9
|
1.0
|
O
|
A:HIS202
|
4.1
|
20.1
|
1.0
|
H
|
A:LYS206
|
4.1
|
44.5
|
1.0
|
N
|
A:LYS206
|
4.1
|
37.1
|
1.0
|
CB
|
A:HIS37
|
4.2
|
19.1
|
1.0
|
C
|
A:GLY205
|
4.2
|
34.4
|
1.0
|
HH
|
A:TYR201
|
4.2
|
28.4
|
1.0
|
HA
|
A:LYS206
|
4.2
|
43.9
|
1.0
|
HE1
|
A:TYR201
|
4.2
|
20.9
|
1.0
|
HB2
|
A:HIS37
|
4.4
|
22.9
|
1.0
|
CA
|
A:GLY205
|
4.4
|
33.5
|
1.0
|
CA
|
A:TYR35
|
4.5
|
16.2
|
1.0
|
NE1
|
A:TRP209
|
4.5
|
22.0
|
1.0
|
CA
|
A:GLU203
|
4.5
|
23.7
|
1.0
|
N
|
A:GLY205
|
4.5
|
30.0
|
1.0
|
HB2
|
A:TYR35
|
4.6
|
18.6
|
1.0
|
N
|
A:LEU204
|
4.6
|
31.9
|
1.0
|
N
|
A:CYS36
|
4.6
|
15.1
|
1.0
|
H
|
A:HIS37
|
4.6
|
19.0
|
1.0
|
CE2
|
A:TYR216
|
4.6
|
25.1
|
1.0
|
HB2
|
A:LYS206
|
4.6
|
41.2
|
1.0
|
O
|
A:GLY205
|
4.6
|
30.0
|
1.0
|
O
|
A:HOH431
|
4.7
|
17.7
|
1.0
|
CA
|
A:LYS206
|
4.7
|
36.6
|
1.0
|
CD1
|
A:TYR216
|
4.7
|
23.7
|
1.0
|
HD2
|
A:HIS202
|
4.7
|
27.4
|
1.0
|
HD1
|
A:TRP209
|
4.7
|
28.6
|
1.0
|
CA
|
A:LEU204
|
4.9
|
36.8
|
1.0
|
CA
|
A:CYS36
|
4.9
|
15.7
|
1.0
|
OH
|
A:TYR201
|
4.9
|
23.7
|
1.0
|
CE1
|
A:TYR201
|
4.9
|
17.5
|
1.0
|
HG3
|
A:GLU203
|
4.9
|
44.7
|
1.0
|
C6
|
A:SAM302
|
4.9
|
14.0
|
1.0
|
CD1
|
A:TRP209
|
5.0
|
23.8
|
1.0
|
HE2
|
A:TYR216
|
5.0
|
30.1
|
1.0
|
|
Reference:
J.D.Moody,
S.Hill,
M.N.Lundahl,
A.J.Saxton,
A.Galambas,
W.E.Broderick,
C.M.Lawrence,
J.B.Broderick.
Computational Engineering of Previously Crystallized Pyruvate Formate-Lyase Activating Enzyme Reveals Insights Into Sam Binding and Reductive Cleavage. J.Biol.Chem. 04791 2023.
ISSN: ESSN 1083-351X
PubMed: 37156396
DOI: 10.1016/J.JBC.2023.104791
Page generated: Mon Aug 12 23:43:53 2024
|