Sodium in PDB 9hae: Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder

The structure of Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder, PDB code: 9hae was solved by M.Pacesa, L.Nickel, B.E.Correia, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.93 / 2.22
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	55.71, 90.25, 63.41, 90, 93.02, 90
R / Rfree (%)	20.2 / 23.6

The binding sites of Sodium atom in the Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder (pdb code 9hae). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder, PDB code: 9hae:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:49.8 occ:1.00 OD1 A:ASP36 2.3 48.5 1.0 O A:VAL34 2.5 48.0 1.0 NZ A:LYS33 2.7 60.6 1.0 CE A:LYS33 2.8 55.0 1.0 N A:ILE59 3.0 34.1 1.0 N A:ASN58 3.2 51.0 1.0 N A:ASP36 3.5 44.0 1.0 CG A:ASP36 3.5 59.0 1.0 CA A:ASN58 3.7 41.9 1.0 CG1 A:ILE59 3.7 41.1 1.0 C A:PRO35 3.8 42.9 1.0 C A:VAL34 3.8 44.0 1.0 C A:ASN58 3.8 38.9 1.0 CB A:ILE59 3.8 35.8 1.0 CD A:LYS33 3.9 78.2 1.0 CA A:ILE59 3.9 35.1 1.0 CA A:ASP36 3.9 55.4 1.0 C A:ARG57 4.0 43.2 1.0 CA A:PRO35 4.2 43.6 1.0 CD1 A:ILE59 4.2 39.2 1.0 O A:ILE59 4.2 35.8 1.0 O A:PRO35 4.2 42.3 1.0 CA A:ARG57 4.3 55.9 1.0 CB A:ASP36 4.3 43.0 1.0 OD2 A:ASP36 4.4 64.6 1.0 N A:PRO35 4.4 49.8 1.0 C A:ILE59 4.5 41.2 1.0 N A:VAL34 4.7 44.7 1.0 CG A:LYS33 4.8 49.5 1.0 CA A:VAL34 4.8 48.9 1.0 O A:ARG57 4.8 43.5 1.0 O A:MET56 5.0 47.4 1.0 O A:ASN58 5.0 42.2 1.0

Sodium binding site 2 out of 3 in the Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:53.5 occ:1.00 OD1 C:ASP36 2.4 61.3 1.0 O C:VAL34 2.5 52.5 1.0 N C:ILE59 3.0 41.5 1.0 CE C:LYS33 3.3 73.7 1.0 N C:ASN58 3.3 43.9 1.0 N C:ASP36 3.4 50.0 1.0 CG C:ASP36 3.6 59.4 1.0 CG1 C:ILE59 3.6 43.3 1.0 C C:PRO35 3.6 55.2 1.0 C C:VAL34 3.7 46.8 1.0 CB C:ILE59 3.7 41.9 1.0 CA C:ASN58 3.8 37.2 1.0 CA C:ASP36 3.8 53.8 1.0 C C:ASN58 3.8 44.8 1.0 O C:HOH313 3.9 58.3 1.0 CA C:ILE59 3.9 40.6 1.0 NZ C:LYS33 3.9 86.9 1.0 O C:HOH348 3.9 60.2 1.0 CD1 C:ILE59 4.0 37.9 1.0 CA C:PRO35 4.0 45.6 1.0 C C:ARG57 4.1 53.1 1.0 O C:PRO35 4.2 46.5 1.0 O C:ILE59 4.2 44.3 1.0 CB C:ASP36 4.3 47.5 1.0 N C:PRO35 4.3 53.8 1.0 CA C:ARG57 4.4 49.1 1.0 CD C:LYS33 4.4 84.2 1.0 OD2 C:ASP36 4.5 66.9 1.0 C C:ILE59 4.5 45.3 1.0 CG C:LYS33 4.7 67.7 1.0 N C:VAL34 4.8 46.7 1.0 CA C:VAL34 4.8 50.2 1.0 O C:ARG57 5.0 40.8 1.0 O C:MET56 5.0 59.1 1.0

Sodium binding site 3 out of 3 in the Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Dust Mite Allergen Der F 7 with Computationally Designed DERF7_B2 Binder within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:59.1 occ:1.00 O C:ASN134 2.4 64.6 1.0 OG1 C:THR136 2.7 64.4 1.0 O C:HOH353 3.2 64.9 1.0 C C:ASN134 3.4 69.2 1.0 CD C:PRO130 3.6 66.2 1.0 CB C:THR136 3.8 47.1 1.0 CG C:PRO130 3.8 69.7 1.0 N C:THR136 3.9 52.0 1.0 C C:ILE135 3.9 54.6 1.0 N C:ASN134 4.0 81.9 1.0 O C:ILE135 4.1 53.5 1.0 CA C:ASN134 4.2 72.1 1.0 N C:ILE135 4.3 64.0 1.0 CA C:THR136 4.4 52.9 1.0 CB C:ASN134 4.5 83.0 1.0 O C:GLU128 4.5 51.3 1.0 CA C:ILE135 4.6 61.6 1.0

M.Pacesa, L.Nickel, J.Schmidt, E.Pyatova, C.Schellhaas, L.Kissling, A.Alcaraz-Serna, Y.Cho, K.H.Ghamary, L.Vinue, B.J.Yachnin, A.M.Wollacot, S.Buckley, S.Georgeon, C.A.Goverde, G.N.Hatzopoulos, P.Gonczy, Y.D.Muller, G.Schwank, S.Ovchinnikov, B.E.Correia. Bindcraft: One-Shot Design of Functional Protein Binders Biorxiv 2024.
ISSN: ISSN 2692-8205
DOI: 10.1101/2024.09.30.615802