Sodium in PDB 9hy1: Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 7.5 (Dimeric State From Gel Filtration)

The structure of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 7.5 (Dimeric State From Gel Filtration), PDB code: 9hy1 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)	55.75 / 1.81
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.369, 64.369, 159.88, 90, 90, 120
R / Rfree (%)	16.9 / 19.6

The structure of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 7.5 (Dimeric State From Gel Filtration) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 7.5 (Dimeric State From Gel Filtration) (pdb code 9hy1). 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 7.5 (Dimeric State From Gel Filtration), PDB code: 9hy1:
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 7.5 (Dimeric State From Gel Filtration)


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 7.5 (Dimeric State From Gel Filtration) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na306 b:51.6 occ:1.00 O A:HOH568 2.4 55.3 1.0 O A:HOH578 2.4 60.1 1.0 O A:HOH584 2.4 50.5 1.0 OG A:SER79 2.4 47.7 1.0 O A:HOH628 2.4 57.0 1.0 O A:HOH508 2.5 46.0 1.0 CB A:SER79 3.3 44.6 1.0 O A:TYR29 3.9 40.1 1.0 O A:HOH425 4.0 62.6 1.0 O A:HOH572 4.3 51.8 1.0 O A:HOH554 4.3 54.9 1.0 CB A:PHE31 4.4 39.9 1.0 O A:THR26 4.4 43.2 1.0 N A:PHE31 4.5 43.5 1.0 CA A:SER79 4.6 44.5 1.0 OG1 A:THR26 4.7 40.8 1.0 CA A:SER27 5.0 43.7 1.0

Sodium binding site 2 out of 2 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 7.5 (Dimeric State From Gel Filtration)


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 7.5 (Dimeric State From Gel Filtration) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na307 b:54.5 occ:1.00 O A:TYR104 2.4 39.3 1.0 O A:HOH604 2.5 50.2 1.0 C A:TYR104 3.6 36.4 1.0 CA A:TYR104 4.0 36.7 1.0 CB A:TYR104 4.1 39.4 1.0 O A:HOH614 4.2 49.5 1.0 O A:HOH445 4.3 42.1 1.0 O A:HOH551 4.5 68.3 1.0 CD1 A:PHE105 4.6 38.3 1.0 O A:HOH420 4.6 57.7 1.0 N A:PHE105 4.7 34.8 1.0 CE1 A:PHE105 5.0 40.5 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