Sodium in PDB 9hy3: Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5

The structure of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5, PDB code: 9hy3 was solved by L.Raucci, M.Orlandini, C.Pozzi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.78 / 1.62
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.531, 64.531, 160.509, 90, 90, 120
R / Rfree (%)	17.5 / 20.7

The structure of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5 also contains other interesting chemical elements:

Chlorine

(Cl)

4 atoms

The binding sites of Sodium atom in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5 (pdb code 9hy3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5, PDB code: 9hy3:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:41.2 occ:1.00 O A:HOH639 2.4 50.9 1.0 O A:HOH611 2.4 48.5 1.0 OG A:SER79 2.4 38.5 1.0 O A:HOH661 2.4 50.5 1.0 O A:HOH629 2.4 39.6 1.0 O A:HOH521 2.5 33.2 1.0 CB A:SER79 3.2 35.9 1.0 O A:TYR29 3.9 30.6 1.0 O A:HOH705 4.0 58.6 1.0 O A:HOH448 4.2 53.5 1.0 O A:HOH545 4.2 44.8 1.0 CB A:PHE31 4.3 30.1 1.0 O A:HOH583 4.4 37.0 1.0 O A:THR26 4.4 30.0 1.0 N A:PHE31 4.6 30.8 1.0 CA A:SER79 4.6 31.9 1.0 OG1 A:THR26 4.6 29.2 1.0 CA A:SER27 4.9 32.3 1.0

Sodium binding site 2 out of 2 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:39.7 occ:0.80 O A:HOH418 2.4 45.7 1.0 OG A:SER141 2.4 34.2 1.0 O A:HOH646 2.4 52.8 1.0 CB A:SER141 3.4 28.8 1.0 CL A:CL309 4.1 39.5 1.0 O A:HOH591 4.3 40.4 1.0 O A:HOH434 4.4 48.5 1.0 O A:HOH713 4.5 34.1 1.0 CA A:SER141 4.7 27.2 1.0 O2 A:EDO303 4.8 59.7 1.0 O A:HOH515 4.9 47.2 1.0

L.Raucci, C.D.Perrone, S.Barbera, L.J.De Boer, G.M.Tosi, J.Brunetti, L.Bracci, C.Pozzi, F.Galvagni, M.Orlandini. Structural and Antigen-Binding Surface Definition of An Anti-CD93 Monoclonal Antibody For the Treatment of Degenerative Vascular Eye Diseases. Int.J.Biol.Macromol. V. 309 43118 2025.
ISSN: ISSN 0141-8130
PubMed: 40228767
DOI: 10.1016/J.IJBIOMAC.2025.143118