Sodium in PDB 6ok1: LTP2-CHSH2(DUF35) Aldolase
Protein crystallography data
The structure of LTP2-CHSH2(DUF35) Aldolase, PDB code: 6ok1
was solved by
M.S.Kimber,
E.Mallette,
R.Aggett,
S.Y.K.Seah,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
42.83 /
1.70
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
91.680,
110.560,
120.140,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
14.4 /
16.8
|
Other elements in 6ok1:
The structure of LTP2-CHSH2(DUF35) Aldolase also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the LTP2-CHSH2(DUF35) Aldolase
(pdb code 6ok1). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the
LTP2-CHSH2(DUF35) Aldolase, PDB code: 6ok1:
Jump to Sodium binding site number:
1;
2;
Sodium binding site 1 out
of 2 in 6ok1
Go back to
Sodium Binding Sites List in 6ok1
Sodium binding site 1 out
of 2 in the LTP2-CHSH2(DUF35) Aldolase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of LTP2-CHSH2(DUF35) Aldolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na501
b:27.8
occ:1.00
|
O
|
A:ILE70
|
2.2
|
26.5
|
1.0
|
O
|
A:HOH738
|
2.3
|
44.7
|
1.0
|
O
|
A:VAL48
|
2.4
|
26.2
|
1.0
|
O
|
A:GLU72
|
2.4
|
24.7
|
1.0
|
O
|
A:HOH862
|
2.5
|
36.2
|
1.0
|
HG23
|
A:ILE70
|
3.4
|
29.5
|
1.0
|
HA
|
A:ASP49
|
3.4
|
28.5
|
1.0
|
C
|
A:ILE70
|
3.4
|
27.0
|
1.0
|
H
|
A:GLU72
|
3.4
|
31.1
|
0.4
|
H
|
A:GLU72
|
3.4
|
31.1
|
0.6
|
C
|
A:GLU72
|
3.4
|
24.6
|
1.0
|
N
|
A:GLU72
|
3.5
|
25.9
|
1.0
|
HG2
|
A:GLU72
|
3.5
|
35.5
|
0.4
|
HG22
|
A:ILE70
|
3.5
|
29.5
|
1.0
|
C
|
A:VAL48
|
3.6
|
25.7
|
1.0
|
HG3
|
A:GLU72
|
3.7
|
35.5
|
0.4
|
C
|
A:GLY71
|
3.9
|
28.8
|
1.0
|
HB2
|
A:GLU72
|
3.9
|
22.3
|
0.6
|
CG2
|
A:ILE70
|
3.9
|
24.6
|
1.0
|
O
|
A:SER46
|
4.0
|
34.7
|
1.0
|
CA
|
A:GLU72
|
4.0
|
25.9
|
0.6
|
CA
|
A:GLU72
|
4.0
|
21.8
|
0.4
|
CG
|
A:GLU72
|
4.0
|
29.5
|
0.4
|
HA3
|
A:GLY71
|
4.0
|
40.2
|
1.0
|
HD23
|
A:LEU73
|
4.1
|
28.6
|
1.0
|
HA
|
A:SER46
|
4.1
|
34.2
|
1.0
|
HA
|
A:ILE70
|
4.2
|
39.5
|
1.0
|
CA
|
A:ASP49
|
4.2
|
23.7
|
1.0
|
N
|
A:GLY71
|
4.3
|
28.7
|
1.0
|
CA
|
A:GLY71
|
4.3
|
33.5
|
1.0
|
HB3
|
A:ASP49
|
4.3
|
27.0
|
1.0
|
CA
|
A:ILE70
|
4.3
|
32.9
|
1.0
|
N
|
A:ASP49
|
4.4
|
24.0
|
1.0
|
O
|
A:GLY71
|
4.4
|
25.9
|
1.0
|
HA
|
A:LEU73
|
4.4
|
26.3
|
1.0
|
O
|
A:HOH728
|
4.4
|
38.1
|
1.0
|
CB
|
A:GLU72
|
4.5
|
18.7
|
0.6
|
HB
|
A:VAL48
|
4.5
|
31.2
|
1.0
|
O
|
A:HOH607
|
4.5
|
45.8
|
1.0
|
C
|
A:SER46
|
4.6
|
34.7
|
1.0
|
CB
|
A:GLU72
|
4.6
|
57.9
|
0.4
|
H
|
A:VAL48
|
4.6
|
31.8
|
1.0
|
N
|
A:LEU73
|
4.6
|
24.7
|
1.0
|
CA
|
A:VAL48
|
4.6
|
21.4
|
1.0
|
O
|
A:HOH813
|
4.6
|
53.2
|
1.0
|
N
|
A:VAL48
|
4.6
|
26.5
|
1.0
|
HG21
|
A:ILE70
|
4.6
|
29.5
|
1.0
|
O
|
A:PRO45
|
4.7
|
29.2
|
1.0
|
CB
|
A:ILE70
|
4.8
|
23.7
|
1.0
|
CB
|
A:ASP49
|
4.8
|
22.4
|
1.0
|
CA
|
A:SER46
|
4.9
|
28.5
|
1.0
|
HA
|
A:GLU72
|
4.9
|
26.2
|
0.4
|
HA
|
A:GLU72
|
4.9
|
31.1
|
0.6
|
HB3
|
A:GLU72
|
5.0
|
22.3
|
0.6
|
CD2
|
A:LEU73
|
5.0
|
23.8
|
1.0
|
HG12
|
A:VAL48
|
5.0
|
29.2
|
1.0
|
|
Sodium binding site 2 out
of 2 in 6ok1
Go back to
Sodium Binding Sites List in 6ok1
Sodium binding site 2 out
of 2 in the LTP2-CHSH2(DUF35) Aldolase
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of LTP2-CHSH2(DUF35) Aldolase within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na501
b:24.8
occ:1.00
|
O
|
C:ILE70
|
2.3
|
21.6
|
1.0
|
O
|
C:VAL48
|
2.3
|
22.3
|
1.0
|
O
|
C:GLU72
|
2.3
|
22.1
|
1.0
|
O
|
C:HOH859
|
2.4
|
35.1
|
1.0
|
O
|
C:HOH808
|
2.5
|
47.7
|
1.0
|
HA
|
C:ASP49
|
3.3
|
19.8
|
1.0
|
HG23
|
C:ILE70
|
3.4
|
30.3
|
1.0
|
C
|
C:GLU72
|
3.4
|
22.1
|
1.0
|
C
|
C:ILE70
|
3.4
|
22.6
|
1.0
|
H
|
C:GLU72
|
3.5
|
27.0
|
0.6
|
H
|
C:GLU72
|
3.5
|
27.0
|
0.4
|
C
|
C:VAL48
|
3.5
|
19.9
|
1.0
|
HG22
|
C:ILE70
|
3.5
|
30.3
|
1.0
|
HG2
|
C:GLU72
|
3.5
|
46.1
|
0.6
|
N
|
C:GLU72
|
3.6
|
22.5
|
1.0
|
HG3
|
C:GLU72
|
3.7
|
46.1
|
0.6
|
HB2
|
C:GLU72
|
3.8
|
18.3
|
0.4
|
C
|
C:GLY71
|
3.9
|
24.1
|
1.0
|
CG2
|
C:ILE70
|
3.9
|
25.3
|
1.0
|
O
|
C:SER46
|
3.9
|
29.3
|
1.0
|
CA
|
C:GLU72
|
4.0
|
37.7
|
0.4
|
CA
|
C:GLU72
|
4.0
|
16.1
|
0.6
|
CG
|
C:GLU72
|
4.0
|
38.4
|
0.6
|
HA3
|
C:GLY71
|
4.1
|
29.5
|
1.0
|
HA
|
C:SER46
|
4.1
|
28.8
|
1.0
|
HD23
|
C:LEU73
|
4.1
|
25.7
|
1.0
|
CA
|
C:ASP49
|
4.2
|
16.4
|
1.0
|
HB3
|
C:ASP49
|
4.2
|
24.7
|
1.0
|
HA
|
C:ILE70
|
4.2
|
27.8
|
1.0
|
N
|
C:ASP49
|
4.3
|
20.4
|
1.0
|
CA
|
C:GLY71
|
4.3
|
24.6
|
1.0
|
N
|
C:GLY71
|
4.3
|
23.4
|
1.0
|
HA
|
C:LEU73
|
4.4
|
25.1
|
1.0
|
CA
|
C:ILE70
|
4.4
|
23.1
|
1.0
|
O
|
C:HOH843
|
4.4
|
47.8
|
1.0
|
O
|
C:GLY71
|
4.4
|
24.1
|
1.0
|
CB
|
C:GLU72
|
4.4
|
15.2
|
0.4
|
HB
|
C:VAL48
|
4.5
|
24.5
|
1.0
|
H
|
C:VAL48
|
4.6
|
25.8
|
1.0
|
C
|
C:SER46
|
4.6
|
26.8
|
1.0
|
CA
|
C:VAL48
|
4.6
|
18.5
|
1.0
|
N
|
C:VAL48
|
4.6
|
21.5
|
1.0
|
N
|
C:LEU73
|
4.6
|
19.8
|
1.0
|
O
|
C:HOH780
|
4.6
|
30.5
|
1.0
|
O
|
C:HOH606
|
4.6
|
47.2
|
1.0
|
CB
|
C:GLU72
|
4.6
|
34.8
|
0.6
|
HG21
|
C:ILE70
|
4.6
|
30.3
|
1.0
|
CB
|
C:ASP49
|
4.7
|
20.5
|
1.0
|
O
|
C:PRO45
|
4.7
|
23.7
|
1.0
|
CB
|
C:ILE70
|
4.8
|
21.5
|
1.0
|
CA
|
C:SER46
|
4.8
|
23.9
|
1.0
|
HA
|
C:GLU72
|
4.9
|
45.3
|
0.4
|
HA
|
C:GLU72
|
4.9
|
19.4
|
0.6
|
HB3
|
C:GLU72
|
4.9
|
18.3
|
0.4
|
HG12
|
C:VAL48
|
4.9
|
27.0
|
1.0
|
CA
|
C:LEU73
|
5.0
|
20.9
|
1.0
|
|
Reference:
R.Aggett,
E.Mallette,
S.E.Gilbert,
M.A.Vachon,
K.L.Schroeter,
M.S.Kimber,
S.Y.K.Seah.
The Steroid Side-Chain-Cleaving Aldolase LTP2-CHSH2DUF35IS A Thiolase Superfamily Member with A Radically Repurposed Active Site. J.Biol.Chem. V. 294 11934 2019.
ISSN: ESSN 1083-351X
PubMed: 31209106
DOI: 10.1074/JBC.RA119.008889
Page generated: Tue Oct 8 12:31:03 2024
|