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:

Fluorine (F) 4 atoms

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


Mono view


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


Mono view


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


Mono view


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


Mono view


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

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