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Sodium in PDB 4m4n: Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase)

Enzymatic activity of Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase)

All present enzymatic activity of Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase):
3.2.1.18;

Protein crystallography data

The structure of Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase), PDB code: 4m4n was solved by J.C.Telford, G.L.Taylor, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 12.39 / 1.84
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 75.910, 58.070, 94.440, 90.00, 99.91, 90.00
R / Rfree (%) 17.3 / 22.4

Sodium Binding Sites:

The binding sites of Sodium atom in the Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase) (pdb code 4m4n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase), PDB code: 4m4n:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 4m4n

Go back to Sodium Binding Sites List in 4m4n
Sodium binding site 1 out of 2 in the Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na501

b:8.3
occ:1.00
OD1 A:ASP87 2.3 8.8 1.0
O A:HOH628 2.4 9.5 1.0
O A:GLY118 2.4 9.8 1.0
O A:GLY116 2.5 7.5 1.0
OD1 A:ASN89 2.5 7.0 1.0
O A:HOH1178 2.6 7.6 1.0
CG A:ASP87 3.4 8.5 1.0
C A:GLY116 3.4 8.1 1.0
CG A:ASN89 3.5 5.9 1.0
C A:GLY118 3.5 10.0 1.0
OD2 A:ASP87 3.8 11.3 1.0
ND2 A:ASN89 3.8 6.3 1.0
O A:HOH1126 4.0 33.6 1.0
O A:SER117 4.0 10.0 1.0
CA A:GLY116 4.0 6.9 1.0
C A:SER117 4.2 9.9 1.0
CA A:ALA119 4.3 9.0 1.0
N A:ALA119 4.3 9.6 1.0
N A:SER117 4.4 8.9 1.0
N A:GLY118 4.4 10.2 1.0
CA A:GLY118 4.5 10.1 1.0
O A:GLY120 4.6 4.7 1.0
O A:ILE88 4.6 4.8 1.0
CB A:ASP87 4.7 5.6 1.0
N A:ILE88 4.7 4.3 1.0
CA A:SER117 4.8 9.9 1.0
CB A:ASN89 4.8 5.3 1.0
C A:ILE88 4.8 4.8 1.0
C A:ALA119 4.9 8.7 1.0
CA A:ASP87 4.9 5.3 1.0

Sodium binding site 2 out of 2 in 4m4n

Go back to Sodium Binding Sites List in 4m4n
Sodium binding site 2 out of 2 in the Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Evaluation the Y358H Mutant of the Aspergillus Fumigatus Kdnase (Sialidase) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:13.0
occ:1.00
OD1 B:ASN89 2.3 11.9 1.0
O B:HOH1114 2.3 20.9 1.0
OD1 B:ASP87 2.4 12.1 1.0
O B:GLY118 2.5 16.5 1.0
O B:GLY116 2.5 14.0 1.0
CG B:ASN89 3.3 9.9 1.0
CG B:ASP87 3.5 9.9 1.0
C B:GLY116 3.5 13.6 1.0
ND2 B:ASN89 3.7 12.2 1.0
C B:GLY118 3.7 16.1 1.0
OD2 B:ASP87 3.8 11.2 1.0
CA B:GLY116 4.1 12.1 1.0
O B:SER117 4.3 16.7 1.0
O B:HOH1065 4.4 17.3 1.0
CA B:ALA119 4.4 14.9 1.0
C B:SER117 4.4 16.4 1.0
N B:ALA119 4.5 15.3 1.0
N B:GLY118 4.5 16.6 1.0
O B:ILE88 4.5 5.1 1.0
O B:HOH1039 4.5 29.9 1.0
O B:GLY120 4.6 12.2 1.0
N B:SER117 4.6 15.0 1.0
CB B:ASN89 4.7 7.2 1.0
CA B:GLY118 4.7 16.1 1.0
C B:ILE88 4.8 5.8 1.0
N B:ILE88 4.8 5.8 1.0
CB B:ASP87 4.8 7.4 1.0
C B:ALA119 4.9 14.7 1.0
N B:ASN89 4.9 6.2 1.0
CA B:SER117 5.0 16.2 1.0
CA B:ASP87 5.0 6.8 1.0

Reference:

J.Y.Yeung, J.C.Telford, F.S.Shidmoossavee, A.J.Bennet, G.L.Taylor, M.M.Moore. Active Site Mutants of A Fungal Kdnase To Be Published.
Page generated: Tue Dec 15 06:53:07 2020

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