Sodium in PDB 6ef6: Structure of the Microcompartment-Associated Aminopropanol Kinase
Protein crystallography data
The structure of Structure of the Microcompartment-Associated Aminopropanol Kinase, PDB code: 6ef6
was solved by
E.Mallette,
M.S.Kimber,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.83 /
1.35
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
72.010,
70.050,
60.720,
90.00,
95.12,
90.00
|
R / Rfree (%)
|
14.9 /
16.8
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of the Microcompartment-Associated Aminopropanol Kinase
(pdb code 6ef6). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
Structure of the Microcompartment-Associated Aminopropanol Kinase, PDB code: 6ef6:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 6ef6
Go back to
Sodium Binding Sites List in 6ef6
Sodium binding site 1 out
of 2 in the Structure of the Microcompartment-Associated Aminopropanol Kinase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of the Microcompartment-Associated Aminopropanol Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na403
b:44.0
occ:1.00
|
O
|
A:HOH557
|
2.0
|
45.1
|
1.0
|
O
|
A:HOH661
|
2.2
|
24.4
|
1.0
|
OD2
|
A:ASP211
|
2.2
|
19.7
|
1.0
|
O
|
A:HOH658
|
2.5
|
30.4
|
1.0
|
OD2
|
A:ASP232
|
2.6
|
27.0
|
1.0
|
HH21
|
A:ARG213
|
3.0
|
30.6
|
0.5
|
CG
|
A:ASP211
|
3.3
|
17.7
|
1.0
|
CG
|
A:ASP232
|
3.4
|
25.9
|
1.0
|
OD1
|
A:ASP232
|
3.6
|
24.5
|
1.0
|
HD21
|
A:ASN216
|
3.7
|
23.5
|
1.0
|
HB3
|
A:ASP211
|
3.7
|
19.3
|
1.0
|
NH2
|
A:ARG213
|
3.8
|
25.6
|
0.5
|
HB2
|
A:ASP211
|
3.8
|
19.3
|
1.0
|
OD2
|
A:ASP235
|
3.8
|
23.3
|
1.0
|
H
|
A:GLU33
|
3.8
|
44.1
|
1.0
|
CB
|
A:ASP211
|
3.9
|
16.2
|
1.0
|
HH22
|
A:ARG213
|
3.9
|
30.6
|
0.5
|
H151
|
A:JFN402
|
4.0
|
58.6
|
1.0
|
HA
|
A:SER32
|
4.0
|
40.9
|
1.0
|
HH21
|
A:ARG213
|
4.1
|
29.4
|
0.5
|
O
|
A:HOH572
|
4.1
|
31.7
|
1.0
|
OD1
|
A:ASP211
|
4.3
|
19.6
|
1.0
|
O
|
A:HOH522
|
4.3
|
34.3
|
1.0
|
NH2
|
A:ARG213
|
4.4
|
24.6
|
0.5
|
HB2
|
A:GLU33
|
4.4
|
70.9
|
1.0
|
ND2
|
A:ASN216
|
4.5
|
19.6
|
1.0
|
CG
|
A:ASP235
|
4.5
|
25.1
|
1.0
|
HH22
|
A:ARG213
|
4.5
|
29.4
|
0.5
|
HB2
|
A:ASP235
|
4.5
|
25.4
|
1.0
|
HG3
|
A:GLU33
|
4.5
|
85.4
|
1.0
|
H091
|
A:JFN402
|
4.6
|
68.8
|
1.0
|
N
|
A:GLU33
|
4.6
|
36.8
|
1.0
|
HB3
|
A:ASP232
|
4.7
|
25.4
|
1.0
|
HE
|
A:ARG213
|
4.7
|
25.7
|
0.5
|
HD22
|
A:ASN216
|
4.7
|
23.5
|
1.0
|
H153
|
A:JFN402
|
4.7
|
58.6
|
1.0
|
CB
|
A:ASP232
|
4.7
|
21.2
|
1.0
|
HB3
|
A:ASP234
|
4.7
|
26.3
|
1.0
|
N04
|
A:JFN402
|
4.8
|
57.5
|
1.0
|
H1
|
A:JFN402
|
4.8
|
68.9
|
1.0
|
O
|
A:ASP232
|
4.8
|
16.9
|
1.0
|
C15
|
A:JFN402
|
4.8
|
48.9
|
1.0
|
H
|
A:ASP235
|
4.9
|
21.8
|
1.0
|
CZ
|
A:ARG213
|
5.0
|
21.9
|
0.5
|
O
|
A:HOH575
|
5.0
|
17.0
|
1.0
|
CA
|
A:SER32
|
5.0
|
34.2
|
1.0
|
OD1
|
A:ASP235
|
5.0
|
23.8
|
1.0
|
|
Sodium binding site 2 out
of 2 in 6ef6
Go back to
Sodium Binding Sites List in 6ef6
Sodium binding site 2 out
of 2 in the Structure of the Microcompartment-Associated Aminopropanol Kinase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of the Microcompartment-Associated Aminopropanol Kinase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na404
b:23.1
occ:1.00
|
O
|
A:GLN171
|
2.2
|
18.4
|
1.0
|
O
|
A:HOH573
|
2.3
|
21.1
|
1.0
|
O
|
A:VAL176
|
2.3
|
20.3
|
1.0
|
O
|
A:HOH598
|
2.3
|
24.3
|
1.0
|
O
|
A:HOH686
|
2.8
|
45.6
|
1.0
|
HB
|
A:VAL176
|
3.4
|
15.8
|
1.0
|
C
|
A:GLN171
|
3.5
|
15.9
|
1.0
|
C
|
A:VAL176
|
3.5
|
17.0
|
1.0
|
HA
|
A:ASP172
|
3.6
|
23.2
|
1.0
|
HG12
|
A:VAL176
|
3.6
|
20.7
|
1.0
|
O
|
A:HOH710
|
3.9
|
32.9
|
1.0
|
HA2
|
A:GLY177
|
4.0
|
19.3
|
1.0
|
CB
|
A:VAL176
|
4.1
|
13.2
|
1.0
|
O
|
A:HOH719
|
4.2
|
31.4
|
1.0
|
HB3
|
A:GLN171
|
4.2
|
19.8
|
1.0
|
HA
|
A:GLN171
|
4.2
|
19.3
|
1.0
|
OG1
|
A:THR181
|
4.2
|
15.9
|
1.0
|
HG1
|
A:THR181
|
4.3
|
19.0
|
1.0
|
CG1
|
A:VAL176
|
4.3
|
17.3
|
1.0
|
O
|
A:HOH645
|
4.3
|
39.2
|
1.0
|
CA
|
A:ASP172
|
4.3
|
19.4
|
1.0
|
N
|
A:ASP172
|
4.3
|
16.1
|
1.0
|
CA
|
A:VAL176
|
4.3
|
15.2
|
1.0
|
O
|
A:ALA173
|
4.4
|
18.9
|
1.0
|
CA
|
A:GLN171
|
4.4
|
16.1
|
1.0
|
HG11
|
A:VAL176
|
4.5
|
20.7
|
1.0
|
N
|
A:GLY177
|
4.5
|
16.0
|
1.0
|
H
|
A:VAL176
|
4.6
|
18.4
|
1.0
|
CA
|
A:GLY177
|
4.7
|
16.1
|
1.0
|
C
|
A:ASP172
|
4.7
|
20.0
|
1.0
|
CB
|
A:GLN171
|
4.8
|
16.6
|
1.0
|
H
|
A:ALA173
|
4.9
|
21.7
|
1.0
|
N
|
A:VAL176
|
4.9
|
15.4
|
1.0
|
N
|
A:ALA173
|
5.0
|
18.1
|
1.0
|
|
Reference:
E.Mallette,
M.S.Kimber.
Structural and Kinetic Characterization of (S)-1-Amino-2-Propanol Kinase From the Aminoacetone Utilization Microcompartment Ofmycobacterium Smegmatis. J.Biol.Chem. V. 293 19909 2018.
ISSN: ESSN 1083-351X
PubMed: 30361441
DOI: 10.1074/JBC.RA118.005485
Page generated: Tue Oct 8 08:22:49 2024
|