Sodium in PDB 7p1s: Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.
Protein crystallography data
The structure of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid., PDB code: 7p1s
was solved by
T.M.Gloster,
S.A.Mcmahon,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
179.01 /
1.92
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.646,
179.008,
97.292,
90,
104.04,
90
|
R / Rfree (%)
|
26 /
28.9
|
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.
(pdb code 7p1s). This binding sites where shown within
5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the
Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid., PDB code: 7p1s:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7p1s
Go back to
Sodium Binding Sites List in 7p1s
Sodium binding site 1 out
of 4 in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na502
b:37.5
occ:1.00
|
OD1
|
A:ASP90
|
1.9
|
35.4
|
1.0
|
O
|
A:HOH625
|
2.2
|
37.1
|
1.0
|
O
|
A:HOH698
|
2.5
|
37.6
|
1.0
|
O
|
A:GLY121
|
2.5
|
37.9
|
1.0
|
OD1
|
A:ASN92
|
2.6
|
32.6
|
1.0
|
O
|
A:HOH702
|
2.8
|
30.4
|
1.0
|
O
|
A:GLY119
|
2.9
|
35.4
|
1.0
|
CG
|
A:ASP90
|
2.9
|
30.9
|
1.0
|
OD2
|
A:ASP90
|
3.3
|
37.5
|
1.0
|
CG
|
A:ASN92
|
3.6
|
31.4
|
1.0
|
C
|
A:GLY121
|
3.7
|
34.5
|
1.0
|
C
|
A:GLY119
|
3.8
|
33.2
|
1.0
|
ND2
|
A:ASN92
|
4.0
|
32.5
|
1.0
|
O
|
D:HOH678
|
4.0
|
32.7
|
1.0
|
CB
|
A:ASP90
|
4.3
|
30.9
|
1.0
|
O
|
A:HIS123
|
4.3
|
24.1
|
1.0
|
CA
|
A:GLY119
|
4.3
|
31.1
|
1.0
|
CA
|
A:PRO122
|
4.3
|
30.2
|
1.0
|
N
|
A:PRO122
|
4.4
|
31.0
|
1.0
|
N
|
A:HIS123
|
4.5
|
25.6
|
1.0
|
N
|
A:ILE91
|
4.5
|
28.7
|
1.0
|
CA
|
A:ASP90
|
4.5
|
29.5
|
1.0
|
O
|
A:THR120
|
4.6
|
34.1
|
1.0
|
C
|
A:PRO122
|
4.6
|
27.5
|
1.0
|
O
|
A:ILE91
|
4.6
|
23.9
|
1.0
|
C
|
A:ASP90
|
4.6
|
30.3
|
1.0
|
C
|
A:THR120
|
4.7
|
37.8
|
1.0
|
CD
|
A:ARG82
|
4.7
|
39.8
|
1.0
|
N
|
A:GLY121
|
4.8
|
35.6
|
1.0
|
C
|
A:ILE91
|
4.8
|
25.8
|
1.0
|
N
|
A:THR120
|
4.8
|
36.8
|
1.0
|
CA
|
A:GLY121
|
4.9
|
35.6
|
1.0
|
NH1
|
A:ARG82
|
5.0
|
44.4
|
1.0
|
CB
|
A:ASN92
|
5.0
|
30.4
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7p1s
Go back to
Sodium Binding Sites List in 7p1s
Sodium binding site 2 out
of 4 in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na502
b:23.0
occ:1.00
|
O
|
B:HOH672
|
1.9
|
30.1
|
1.0
|
O
|
B:GLY119
|
2.3
|
22.5
|
1.0
|
O
|
B:GLY121
|
2.3
|
20.7
|
1.0
|
OD1
|
B:ASP90
|
2.5
|
15.4
|
1.0
|
O
|
B:HOH759
|
2.5
|
36.2
|
1.0
|
OD1
|
B:ASN92
|
2.7
|
17.9
|
1.0
|
C
|
B:GLY119
|
3.3
|
22.4
|
1.0
|
CG
|
B:ASP90
|
3.5
|
16.0
|
1.0
|
C
|
B:GLY121
|
3.6
|
19.6
|
1.0
|
CG
|
B:ASN92
|
3.7
|
17.4
|
1.0
|
OD2
|
B:ASP90
|
3.9
|
16.8
|
1.0
|
CA
|
B:GLY119
|
3.9
|
22.6
|
1.0
|
ND2
|
B:ASN92
|
4.0
|
18.9
|
1.0
|
O
|
C:HOH602
|
4.0
|
22.6
|
1.0
|
O
|
B:THR120
|
4.1
|
18.7
|
1.0
|
C
|
B:THR120
|
4.1
|
21.5
|
1.0
|
N
|
B:GLY121
|
4.3
|
20.2
|
1.0
|
N
|
B:THR120
|
4.3
|
21.9
|
1.0
|
N
|
B:PRO122
|
4.4
|
18.4
|
1.0
|
CA
|
B:GLY121
|
4.5
|
20.8
|
1.0
|
CA
|
B:PRO122
|
4.5
|
18.4
|
1.0
|
O
|
B:HIS123
|
4.5
|
21.0
|
1.0
|
N
|
B:HIS123
|
4.6
|
18.6
|
1.0
|
CA
|
B:THR120
|
4.6
|
23.0
|
1.0
|
O
|
B:ILE91
|
4.8
|
14.3
|
1.0
|
C
|
B:PRO122
|
4.8
|
19.1
|
1.0
|
O
|
B:HOH752
|
4.9
|
30.4
|
1.0
|
CB
|
B:ASP90
|
4.9
|
14.8
|
1.0
|
N
|
B:ILE91
|
5.0
|
14.0
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7p1s
Go back to
Sodium Binding Sites List in 7p1s
Sodium binding site 3 out
of 4 in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na502
b:22.7
occ:1.00
|
O
|
C:HOH614
|
1.9
|
12.0
|
1.0
|
O
|
C:HOH627
|
2.2
|
34.5
|
1.0
|
OD1
|
C:ASN92
|
2.3
|
18.9
|
1.0
|
OD1
|
C:ASP90
|
2.4
|
13.9
|
1.0
|
O
|
C:GLY119
|
2.4
|
17.9
|
1.0
|
O
|
C:GLY121
|
2.6
|
18.8
|
1.0
|
O
|
C:HOH711
|
2.8
|
27.1
|
1.0
|
C
|
C:GLY119
|
3.3
|
20.1
|
1.0
|
CG
|
C:ASN92
|
3.3
|
19.2
|
1.0
|
CG
|
C:ASP90
|
3.5
|
15.5
|
1.0
|
ND2
|
C:ASN92
|
3.7
|
19.3
|
1.0
|
CA
|
C:GLY119
|
3.8
|
19.2
|
1.0
|
C
|
C:GLY121
|
3.8
|
18.0
|
1.0
|
OD2
|
C:ASP90
|
4.0
|
16.8
|
1.0
|
O
|
C:THR120
|
4.2
|
22.6
|
1.0
|
O
|
B:HOH621
|
4.3
|
20.3
|
1.0
|
C
|
C:THR120
|
4.3
|
21.8
|
1.0
|
O
|
C:HIS123
|
4.3
|
15.7
|
1.0
|
N
|
C:THR120
|
4.4
|
20.5
|
1.0
|
O
|
C:ILE91
|
4.5
|
14.8
|
1.0
|
N
|
C:GLY121
|
4.5
|
20.5
|
1.0
|
N
|
C:HIS123
|
4.6
|
17.1
|
1.0
|
N
|
C:PRO122
|
4.6
|
17.2
|
1.0
|
CA
|
C:PRO122
|
4.7
|
17.0
|
1.0
|
CB
|
C:ASN92
|
4.7
|
17.3
|
1.0
|
N
|
C:ILE91
|
4.7
|
12.5
|
1.0
|
C
|
C:ILE91
|
4.8
|
14.0
|
1.0
|
CA
|
C:GLY121
|
4.8
|
19.8
|
1.0
|
CB
|
C:ASP90
|
4.8
|
14.1
|
1.0
|
CA
|
C:THR120
|
4.8
|
21.8
|
1.0
|
C
|
C:PRO122
|
4.9
|
17.0
|
1.0
|
CD1
|
C:TRP125
|
4.9
|
17.3
|
1.0
|
CA
|
C:ASP90
|
5.0
|
13.9
|
1.0
|
CA
|
C:ASN92
|
5.0
|
17.1
|
1.0
|
C
|
C:ASP90
|
5.0
|
13.7
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7p1s
Go back to
Sodium Binding Sites List in 7p1s
Sodium binding site 4 out
of 4 in the Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid.
Mono view
Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3- Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na502
b:31.0
occ:1.00
|
O
|
D:HOH618
|
2.1
|
18.3
|
1.0
|
OD1
|
D:ASP90
|
2.1
|
28.3
|
1.0
|
OD1
|
D:ASN92
|
2.4
|
40.8
|
1.0
|
O
|
D:GLY121
|
2.6
|
35.5
|
1.0
|
O
|
D:GLY119
|
2.6
|
35.9
|
1.0
|
O
|
D:HOH679
|
2.8
|
44.5
|
1.0
|
CG
|
D:ASP90
|
3.2
|
29.3
|
1.0
|
CG
|
D:ASN92
|
3.4
|
36.4
|
1.0
|
C
|
D:GLY119
|
3.6
|
33.4
|
1.0
|
OD2
|
D:ASP90
|
3.6
|
33.7
|
1.0
|
C
|
D:GLY121
|
3.8
|
31.2
|
1.0
|
ND2
|
D:ASN92
|
3.8
|
39.6
|
1.0
|
CA
|
D:GLY119
|
4.0
|
32.9
|
1.0
|
O
|
D:HIS123
|
4.3
|
25.7
|
1.0
|
O
|
D:THR120
|
4.4
|
31.1
|
1.0
|
C
|
D:THR120
|
4.5
|
36.4
|
1.0
|
CA
|
D:PRO122
|
4.5
|
26.2
|
1.0
|
O
|
D:ILE91
|
4.5
|
25.6
|
1.0
|
CB
|
D:ASP90
|
4.5
|
28.2
|
1.0
|
N
|
D:PRO122
|
4.6
|
27.0
|
1.0
|
N
|
D:HIS123
|
4.6
|
23.9
|
1.0
|
N
|
D:THR120
|
4.6
|
34.6
|
1.0
|
N
|
D:ILE91
|
4.6
|
28.7
|
1.0
|
N
|
D:GLY121
|
4.6
|
34.0
|
1.0
|
O
|
D:HOH696
|
4.7
|
35.4
|
1.0
|
C
|
D:PRO122
|
4.8
|
24.2
|
1.0
|
CA
|
D:ASP90
|
4.8
|
26.9
|
1.0
|
C
|
D:ILE91
|
4.8
|
26.6
|
1.0
|
CB
|
D:ASN92
|
4.8
|
32.5
|
1.0
|
CD
|
D:ARG82
|
4.8
|
44.6
|
1.0
|
CA
|
D:GLY121
|
4.8
|
32.2
|
1.0
|
C
|
D:ASP90
|
4.8
|
29.0
|
1.0
|
|
Reference:
T.M.Gloster,
S.A.Mcmahon.
Structure of Kdnase From Trichophyton Rubrum in Complex with 2,3-Didehydro-2,3-Dideoxy-D-Glycero-D-Galacto-Nonulosonic Acid. To Be Published.
Page generated: Tue Oct 8 18:26:14 2024
|