Sodium in PDB 7agb: Protease SAPP1P From Candida Parapsilosis in Complex with KB70

Enzymatic activity of Protease SAPP1P From Candida Parapsilosis in Complex with KB70

All present enzymatic activity of Protease SAPP1P From Candida Parapsilosis in Complex with KB70:
3.4.23.24;

Protein crystallography data

The structure of Protease SAPP1P From Candida Parapsilosis in Complex with KB70, PDB code: 7agb was solved by J.Dostal, O.Heidingsfeld, J.Brynda, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 34.58 / 1.70
Space group P 62 2 2
Cell size a, b, c (Å), α, β, γ (°) 172.021, 172.021, 252.692, 90, 90, 120
R / Rfree (%) 17.9 / 19.7

Sodium Binding Sites:

The binding sites of Sodium atom in the Protease SAPP1P From Candida Parapsilosis in Complex with KB70 (pdb code 7agb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Protease SAPP1P From Candida Parapsilosis in Complex with KB70, PDB code: 7agb:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in 7agb

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Sodium binding site 1 out of 6 in the Protease SAPP1P From Candida Parapsilosis in Complex with KB70


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Protease SAPP1P From Candida Parapsilosis in Complex with KB70 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na401

b:42.4
occ:1.00
 O A:GLY79 2.4 29.8 1.0
O4 A:PGE402 2.6 49.8 1.0
O3 A:PGE402 2.7 46.4 1.0
O2 A:PGE402 2.7 43.2 1.0
O1 A:PGE402 2.9 54.8 1.0
C A:GLY79 3.5 28.9 1.0
C3 A:PGE402 3.5 44.0 1.0
C2 A:PGE402 3.5 45.1 1.0
C4 A:PGE402 3.6 43.1 1.0
C6 A:PGE402 3.6 46.2 1.0
C5 A:PGE402 3.7 45.5 1.0
C1 A:PGE402 3.7 49.5 1.0
CA A:GLY79 4.1 28.0 1.0
O A:HOH591 4.3 34.7 1.0
O A:HOH597 4.5 54.4 1.0
N A:ASP80 4.6 28.4 1.0
CA A:ASP80 4.9 29.4 1.0

Sodium binding site 2 out of 6 in 7agb

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Sodium binding site 2 out of 6 in the Protease SAPP1P From Candida Parapsilosis in Complex with KB70


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Protease SAPP1P From Candida Parapsilosis in Complex with KB70 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:45.0
occ:1.00
 O B:GLY79 2.4 26.7 1.0
O3 B:PGE404 2.7 47.3 1.0
O1 B:PGE404 2.8 52.7 1.0
O4 B:PGE404 3.0 56.6 1.0
O2 B:PGE404 3.0 46.2 1.0
C2 B:PGE404 3.5 45.3 1.0
C1 B:PGE404 3.6 46.3 1.0
C B:GLY79 3.6 25.8 1.0
C5 B:PGE404 3.6 50.1 1.0
C6 B:PGE404 3.6 50.8 1.0
C3 B:PGE404 3.6 47.6 1.0
C4 B:PGE404 3.7 47.5 1.0
CA B:GLY79 4.2 25.6 1.0
N B:ASP80 4.6 26.0 1.0
CA B:ASP80 4.9 27.4 1.0

Sodium binding site 3 out of 6 in 7agb

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Sodium binding site 3 out of 6 in the Protease SAPP1P From Candida Parapsilosis in Complex with KB70


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Protease SAPP1P From Candida Parapsilosis in Complex with KB70 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na401

b:72.3
occ:1.00
 O4 C:PGE404 3.1 55.5 1.0
O C:GLY79 3.2 47.4 1.0
O1 C:PGE404 3.4 59.8 1.0
C C:GLY79 4.4 44.2 1.0
C6 C:PGE404 4.4 54.2 1.0
C C:ASP80 4.5 45.9 1.0
N C:GLY81 4.5 45.9 1.0
CA C:ASP80 4.7 45.8 1.0
O C:ASP80 4.7 46.0 1.0
C1 C:PGE404 4.8 60.1 1.0
O3 C:PGE404 4.9 55.8 1.0
CA C:GLY81 5.0 46.3 1.0

Sodium binding site 4 out of 6 in 7agb

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Sodium binding site 4 out of 6 in the Protease SAPP1P From Candida Parapsilosis in Complex with KB70


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Protease SAPP1P From Candida Parapsilosis in Complex with KB70 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na401

b:60.3
occ:1.00
 O1 D:PGE405 3.3 63.3 1.0
O2 D:PGE405 3.5 53.2 1.0
N L:ALA7 3.5 42.5 1.0
CD1 D:TYR129 3.8 47.5 1.0
C4 D:PGE405 4.0 47.1 1.0
O3 D:PGE405 4.0 48.6 1.0
CB D:TYR129 4.1 45.3 1.0
C1 D:PGE405 4.1 57.2 1.0
C6 D:PGE405 4.1 45.3 1.0
CG D:TYR129 4.1 46.5 1.0
C5 D:PGE405 4.3 45.2 1.0
C3 D:PGE405 4.3 47.7 1.0
C2 D:PGE405 4.3 53.8 1.0
O4 D:PGE405 4.3 42.3 1.0
CE1 D:TYR129 4.6 49.0 1.0
O D:HOH570 4.7 33.3 1.0
C L:PSA6 4.9 43.7 1.0

Sodium binding site 5 out of 6 in 7agb

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Sodium binding site 5 out of 6 in the Protease SAPP1P From Candida Parapsilosis in Complex with KB70


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Protease SAPP1P From Candida Parapsilosis in Complex with KB70 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na402

b:59.8
occ:1.00
 O D:GLY79 2.5 34.2 1.0
O1 D:PGE404 2.7 62.8 1.0
O2 D:PGE404 2.9 58.3 1.0
O4 D:PGE404 2.9 63.5 1.0
O3 D:PGE404 3.2 57.5 1.0
C D:GLY79 3.6 32.5 1.0
C6 D:PGE404 3.7 62.8 1.0
C5 D:PGE404 3.7 58.5 1.0
C4 D:PGE404 3.8 53.1 1.0
C1 D:PGE404 3.8 60.4 1.0
C2 D:PGE404 3.8 60.9 1.0
O D:HOH636 3.8 50.5 1.0
C3 D:PGE404 3.9 51.7 1.0
CA D:GLY79 4.3 31.7 1.0
O D:HOH509 4.4 44.6 1.0
N D:ASP80 4.7 31.7 1.0
CA D:ASP80 4.9 33.4 1.0

Sodium binding site 6 out of 6 in 7agb

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Sodium binding site 6 out of 6 in the Protease SAPP1P From Candida Parapsilosis in Complex with KB70


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Protease SAPP1P From Candida Parapsilosis in Complex with KB70 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na403

b:56.5
occ:1.00
 O1 D:PGE406 2.9 52.7 1.0
O3 D:PGE406 3.1 56.2 1.0
O2 D:PGE406 3.1 56.3 1.0
C3 D:PGE406 3.7 58.5 1.0
O4 D:PGE406 3.8 57.4 1.0
C6 D:PGE406 3.8 55.1 1.0
CB D:SER65 3.8 35.8 1.0
C2 D:PGE406 3.9 54.0 1.0
C4 D:PGE406 3.9 56.6 1.0
C1 D:PGE406 3.9 52.8 1.0
C5 D:PGE406 3.9 56.1 1.0
CA D:SER65 4.7 35.0 1.0
OG D:SER65 4.9 37.6 1.0

Reference:

J.Dostal, J.Brynda, L.Vankova, S.R.Zia, I.Pichova, O.Heidingsfeld, M.Lepsik. Structural Determinants For Subnanomolar Inhibition of the Secreted Aspartic Protease SAPP1P From Candida Parapsilosis . J Enzyme Inhib Med Chem V. 36 914 2021.
ISSN: ESSN 1475-6374
PubMed: 33843395
DOI: 10.1080/14756366.2021.1906664
Page generated: Mon Jul 12 15:54:52 2021

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