Sodium in PDB 7p1r: Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn
Protein crystallography data
The structure of Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn, PDB code: 7p1r
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)
|
95.20 /
1.75
|
Space group
|
P 1 21 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.91,
179.49,
98.07,
90,
103.89,
90
|
R / Rfree (%)
|
18.4 /
21.3
|
Other elements in 7p1r:
The structure of Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn also contains other interesting chemical elements:
Sodium Binding Sites:
The binding sites of Sodium atom in the Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn
(pdb code 7p1r). 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 Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn, PDB code: 7p1r:
Jump to Sodium binding site number:
1;
2;
3;
4;
Sodium binding site 1 out
of 4 in 7p1r
Go back to
Sodium Binding Sites List in 7p1r
Sodium binding site 1 out
of 4 in the Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn
![](/pictures/NA/pdb/p1/7p1r-NA-sphere_01.jpg) Mono view
![](/pictures/NA/pdb/p1/7p1r-NA-sphere_01_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 1 of Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Na503
b:14.2
occ:1.00
|
O
|
A:HOH695
|
2.2
|
21.5
|
1.0
|
O1
|
A:PO4501
|
2.3
|
44.9
|
1.0
|
O
|
A:GLY119
|
2.3
|
20.5
|
1.0
|
OD1
|
A:ASP90
|
2.3
|
20.5
|
1.0
|
O
|
A:GLY121
|
2.4
|
22.8
|
1.0
|
ND2
|
A:ASN92
|
2.4
|
13.7
|
1.0
|
O3
|
A:PO4501
|
2.6
|
45.4
|
1.0
|
P
|
A:PO4501
|
2.9
|
53.3
|
1.0
|
C
|
A:GLY119
|
3.3
|
20.0
|
1.0
|
CG
|
A:ASP90
|
3.4
|
21.6
|
1.0
|
CG
|
A:ASN92
|
3.6
|
16.0
|
1.0
|
O4
|
A:PO4501
|
3.6
|
61.5
|
1.0
|
C
|
A:GLY121
|
3.6
|
20.6
|
1.0
|
OD2
|
A:ASP90
|
3.7
|
25.7
|
1.0
|
OD1
|
A:ASN92
|
3.9
|
22.1
|
1.0
|
CA
|
A:GLY119
|
3.9
|
18.5
|
1.0
|
O
|
A:HOH621
|
4.0
|
35.4
|
1.0
|
C
|
A:THR120
|
4.2
|
21.2
|
1.0
|
N
|
A:GLY121
|
4.2
|
22.9
|
1.0
|
O
|
A:THR120
|
4.3
|
19.7
|
1.0
|
O2
|
A:PO4501
|
4.3
|
51.7
|
1.0
|
N
|
A:THR120
|
4.4
|
21.3
|
1.0
|
CA
|
A:GLY121
|
4.5
|
22.8
|
1.0
|
O
|
A:HIS123
|
4.5
|
16.8
|
1.0
|
N
|
A:PRO122
|
4.6
|
20.8
|
1.0
|
CA
|
A:PRO122
|
4.6
|
20.3
|
1.0
|
CB
|
A:ASP90
|
4.7
|
19.8
|
1.0
|
CA
|
A:THR120
|
4.7
|
22.2
|
1.0
|
N
|
A:HIS123
|
4.7
|
17.7
|
1.0
|
O
|
A:ILE91
|
4.7
|
15.5
|
1.0
|
N
|
A:ILE91
|
4.9
|
13.5
|
1.0
|
CB
|
A:ASN92
|
4.9
|
15.0
|
1.0
|
C
|
A:PRO122
|
4.9
|
18.4
|
1.0
|
CD
|
A:ARG82
|
4.9
|
26.5
|
1.0
|
CA
|
A:ASP90
|
4.9
|
17.9
|
1.0
|
C
|
A:ILE91
|
4.9
|
14.6
|
1.0
|
|
Sodium binding site 2 out
of 4 in 7p1r
Go back to
Sodium Binding Sites List in 7p1r
Sodium binding site 2 out
of 4 in the Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn
![](/pictures/NA/pdb/p1/7p1r-NA-sphere_02.jpg) Mono view
![](/pictures/NA/pdb/p1/7p1r-NA-sphere_02_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 2 of Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Na503
b:10.7
occ:1.00
|
OD1
|
B:ASP90
|
2.3
|
21.1
|
1.0
|
O
|
B:HOH657
|
2.3
|
19.4
|
1.0
|
O
|
B:GLY119
|
2.4
|
19.2
|
1.0
|
OD1
|
B:ASN92
|
2.4
|
18.1
|
1.0
|
O
|
B:GLY121
|
2.4
|
19.9
|
1.0
|
O1
|
B:PO4501
|
2.5
|
36.2
|
1.0
|
O3
|
B:PO4501
|
2.6
|
38.5
|
1.0
|
P
|
B:PO4501
|
3.2
|
37.9
|
1.0
|
CG
|
B:ASP90
|
3.3
|
20.2
|
1.0
|
C
|
B:GLY119
|
3.4
|
18.5
|
1.0
|
CG
|
B:ASN92
|
3.4
|
16.9
|
1.0
|
OD2
|
B:ASP90
|
3.6
|
28.9
|
1.0
|
C
|
B:GLY121
|
3.7
|
19.0
|
1.0
|
ND2
|
B:ASN92
|
3.8
|
18.4
|
1.0
|
CA
|
B:GLY119
|
4.0
|
17.6
|
1.0
|
O
|
B:HOH899
|
4.2
|
31.9
|
1.0
|
C
|
B:THR120
|
4.2
|
20.2
|
0.5
|
C
|
B:THR120
|
4.2
|
21.6
|
0.5
|
N
|
B:GLY121
|
4.2
|
20.5
|
1.0
|
O4
|
B:PO4501
|
4.3
|
36.9
|
1.0
|
O2
|
B:PO4501
|
4.3
|
39.5
|
1.0
|
O
|
B:THR120
|
4.3
|
17.9
|
0.5
|
O
|
B:THR120
|
4.3
|
19.2
|
0.5
|
N
|
B:THR120
|
4.4
|
19.5
|
0.5
|
N
|
B:THR120
|
4.4
|
20.8
|
0.5
|
CA
|
B:GLY121
|
4.5
|
20.4
|
1.0
|
O
|
B:HIS123
|
4.6
|
13.8
|
1.0
|
N
|
B:PRO122
|
4.6
|
18.7
|
1.0
|
CB
|
B:ASP90
|
4.7
|
19.1
|
1.0
|
CA
|
B:PRO122
|
4.7
|
18.2
|
1.0
|
O
|
B:ILE91
|
4.7
|
14.9
|
1.0
|
CA
|
B:THR120
|
4.7
|
21.6
|
0.5
|
CA
|
B:THR120
|
4.8
|
19.5
|
0.5
|
CB
|
B:ASN92
|
4.8
|
15.8
|
1.0
|
N
|
B:ILE91
|
4.8
|
15.2
|
1.0
|
N
|
B:HIS123
|
4.8
|
17.0
|
1.0
|
C
|
B:ILE91
|
4.9
|
14.7
|
1.0
|
CA
|
B:ASP90
|
4.9
|
16.8
|
1.0
|
C
|
B:ASP90
|
4.9
|
16.3
|
1.0
|
C
|
B:PRO122
|
5.0
|
17.6
|
1.0
|
|
Sodium binding site 3 out
of 4 in 7p1r
Go back to
Sodium Binding Sites List in 7p1r
Sodium binding site 3 out
of 4 in the Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn
![](/pictures/NA/pdb/p1/7p1r-NA-sphere_03.jpg) Mono view
![](/pictures/NA/pdb/p1/7p1r-NA-sphere_03_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 3 of Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:Na503
b:15.8
occ:1.00
|
O4
|
C:PO4501
|
2.2
|
45.8
|
1.0
|
OD1
|
C:ASP90
|
2.3
|
20.3
|
1.0
|
O
|
C:HOH743
|
2.3
|
19.0
|
1.0
|
O
|
C:GLY119
|
2.4
|
21.0
|
1.0
|
O
|
C:GLY121
|
2.4
|
19.9
|
1.0
|
ND2
|
C:ASN92
|
2.4
|
16.3
|
1.0
|
O1
|
C:PO4501
|
2.7
|
55.2
|
1.0
|
P
|
C:PO4501
|
2.9
|
67.8
|
1.0
|
CG
|
C:ASP90
|
3.3
|
20.8
|
1.0
|
C
|
C:GLY119
|
3.4
|
20.6
|
1.0
|
CG
|
C:ASN92
|
3.5
|
19.1
|
1.0
|
OD2
|
C:ASP90
|
3.6
|
26.5
|
1.0
|
C
|
C:GLY121
|
3.6
|
19.4
|
1.0
|
O2
|
C:PO4501
|
3.8
|
61.9
|
1.0
|
O
|
C:HOH611
|
3.8
|
34.2
|
1.0
|
OD1
|
C:ASN92
|
3.9
|
24.5
|
1.0
|
CA
|
C:GLY119
|
4.0
|
18.8
|
1.0
|
O3
|
C:PO4501
|
4.1
|
61.0
|
1.0
|
C
|
C:THR120
|
4.3
|
22.1
|
1.0
|
N
|
C:GLY121
|
4.3
|
22.7
|
1.0
|
O
|
C:THR120
|
4.3
|
21.0
|
1.0
|
N
|
C:THR120
|
4.4
|
22.9
|
1.0
|
N
|
C:PRO122
|
4.5
|
20.4
|
1.0
|
CA
|
C:GLY121
|
4.5
|
21.7
|
1.0
|
CA
|
C:PRO122
|
4.6
|
18.9
|
1.0
|
O
|
C:HIS123
|
4.6
|
14.7
|
1.0
|
CB
|
C:ASP90
|
4.6
|
18.8
|
1.0
|
N
|
C:HIS123
|
4.7
|
15.8
|
1.0
|
CA
|
C:THR120
|
4.8
|
24.1
|
1.0
|
O
|
C:ILE91
|
4.8
|
16.2
|
1.0
|
N
|
C:ILE91
|
4.9
|
15.6
|
1.0
|
CD
|
C:ARG82
|
4.9
|
28.8
|
1.0
|
CB
|
C:ASN92
|
4.9
|
18.3
|
1.0
|
C
|
C:PRO122
|
4.9
|
19.2
|
1.0
|
CA
|
C:ASP90
|
4.9
|
17.1
|
1.0
|
NH1
|
C:ARG82
|
4.9
|
32.4
|
1.0
|
C
|
C:ILE91
|
5.0
|
15.6
|
1.0
|
C
|
C:ASP90
|
5.0
|
17.1
|
1.0
|
|
Sodium binding site 4 out
of 4 in 7p1r
Go back to
Sodium Binding Sites List in 7p1r
Sodium binding site 4 out
of 4 in the Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn
![](/pictures/NA/pdb/p1/7p1r-NA-sphere_04.jpg) Mono view
![](/pictures/NA/pdb/p1/7p1r-NA-sphere_04_stereo.jpg) Stereo pair view
|
A full contact list of Sodium with other atoms in the Na binding
site number 4 of Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro- Kdn within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:Na503
b:11.2
occ:1.00
|
OD1
|
D:ASP90
|
2.3
|
17.4
|
1.0
|
O
|
D:GLY119
|
2.3
|
17.1
|
1.0
|
O
|
D:HOH640
|
2.4
|
17.4
|
1.0
|
O
|
D:GLY121
|
2.4
|
21.8
|
1.0
|
O1
|
D:PO4501
|
2.4
|
37.8
|
1.0
|
OD1
|
D:ASN92
|
2.4
|
14.5
|
1.0
|
O3
|
D:PO4501
|
2.8
|
40.1
|
1.0
|
P
|
D:PO4501
|
3.2
|
41.2
|
1.0
|
CG
|
D:ASP90
|
3.3
|
20.8
|
1.0
|
C
|
D:GLY119
|
3.4
|
18.1
|
1.0
|
CG
|
D:ASN92
|
3.5
|
15.6
|
1.0
|
C
|
D:GLY121
|
3.6
|
20.7
|
1.0
|
OD2
|
D:ASP90
|
3.7
|
27.5
|
1.0
|
ND2
|
D:ASN92
|
3.8
|
17.0
|
1.0
|
CA
|
D:GLY119
|
4.0
|
18.9
|
1.0
|
O
|
D:HOH835
|
4.2
|
32.1
|
1.0
|
C
|
D:THR120
|
4.2
|
20.2
|
1.0
|
N
|
D:GLY121
|
4.2
|
21.1
|
1.0
|
O
|
D:THR120
|
4.3
|
20.1
|
1.0
|
O4
|
D:PO4501
|
4.3
|
39.9
|
1.0
|
O2
|
D:PO4501
|
4.3
|
42.0
|
1.0
|
N
|
D:THR120
|
4.4
|
19.6
|
1.0
|
CA
|
D:GLY121
|
4.5
|
21.1
|
1.0
|
N
|
D:PRO122
|
4.6
|
21.3
|
1.0
|
O
|
D:HIS123
|
4.6
|
14.9
|
1.0
|
CB
|
D:ASP90
|
4.7
|
18.5
|
1.0
|
CA
|
D:PRO122
|
4.7
|
20.1
|
1.0
|
CA
|
D:THR120
|
4.7
|
20.3
|
1.0
|
O
|
D:ILE91
|
4.8
|
14.1
|
1.0
|
CB
|
D:ASN92
|
4.8
|
15.3
|
1.0
|
N
|
D:ILE91
|
4.8
|
13.3
|
1.0
|
N
|
D:HIS123
|
4.9
|
16.3
|
1.0
|
C
|
D:ILE91
|
4.9
|
14.3
|
1.0
|
CA
|
D:ASP90
|
4.9
|
17.3
|
1.0
|
C
|
D:ASP90
|
5.0
|
15.1
|
1.0
|
|
Reference:
T.M.Gloster,
S.A.Mcmahon.
Structure of Trichophyton Rubrum Kdnase in Complex with 2,3-Difluoro-Kdn To Be Published.
Page generated: Fri Nov 5 16:05:15 2021
|