Chlorine 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:

Sodium

(Na)

2 atoms

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 5.5, PDB code: 9hy3:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl301 b:43.7 occ:1.00 N A:ARG199 3.4 34.5 1.0 NH1 A:ARG199 3.5 35.2 1.0 CB A:ARG199 3.6 32.3 1.0 CG A:ARG199 3.6 33.3 1.0 CB A:PRO197 3.7 35.2 1.0 CD A:ARG199 3.8 37.5 1.0 N A:ALA198 3.8 38.0 1.0 CA A:ARG199 4.1 31.7 1.0 O A:HOH530 4.2 50.2 1.0 C A:ALA198 4.3 35.5 1.0 C A:PRO197 4.4 37.0 1.0 CA A:ALA198 4.4 37.8 1.0 CZ A:ARG199 4.5 36.8 1.0 CA A:PRO197 4.5 34.8 1.0 NE A:ARG199 4.6 35.7 1.0 CB A:ALA198 4.6 46.0 1.0 OE2 A:GLU217 4.9 56.4 1.0 CG A:PRO197 5.0 42.0 1.0 O A:HOH513 5.0 51.5 1.0

Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl308 b:33.0 occ:0.80 O A:HOH527 3.0 45.4 1.0 N A:GLN140 3.1 24.1 1.0 N A:GLY238 3.1 28.3 1.0 O A:HOH684 3.4 62.0 1.0 CA A:GLY238 3.6 26.6 1.0 O A:HOH599 3.8 55.0 1.0 CA A:THR139 3.8 27.3 1.0 O A:LEU138 3.9 30.2 1.0 C A:THR139 4.0 25.7 1.0 O A:GLN140 4.0 28.6 1.0 CB A:GLN140 4.0 26.3 1.0 CA A:GLN140 4.0 25.1 1.0 O A:HOH444 4.1 54.3 1.0 CG A:GLN140 4.2 27.1 1.0 C A:GLY237 4.3 26.3 1.0 O A:HOH670 4.4 46.6 1.0 C A:GLY238 4.4 27.9 1.0 O A:HOH649 4.5 47.4 1.0 C A:GLN140 4.5 27.7 1.0 O A:HOH544 4.5 55.8 1.0 CG2 A:THR139 4.5 32.7 1.0 N A:GLY239 4.6 26.9 1.0 CA A:GLY237 4.6 24.4 1.0 C A:LEU138 4.8 28.3 1.0 CB A:THR139 4.8 30.8 1.0 N A:THR139 4.8 27.5 1.0 CG2 A:THR143 4.8 34.0 1.0 CD A:GLN140 5.0 28.6 1.0

Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl binding site number 3 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:Cl309 b:39.5 occ:1.00 O A:HOH492 3.0 39.1 1.0 O A:HOH515 3.1 47.2 1.0 OG A:SER141 3.1 34.2 1.0 CA A:PRO142 3.6 29.1 1.0 CB A:SER141 3.9 28.8 1.0 CA A:SER141 3.9 27.2 1.0 NA A:NA307 4.1 39.7 0.8 O A:HOH646 4.3 52.8 1.0 N A:THR143 4.3 30.2 1.0 C A:PRO142 4.3 30.6 1.0 N A:PRO142 4.4 26.4 1.0 CB A:PRO142 4.4 29.9 1.0 C A:SER141 4.6 27.4 1.0 O A:GLN140 4.7 28.6 1.0 CG2 A:THR143 4.9 34.0 1.0

Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl310 b:49.1 occ:1.00 N A:TYR62 3.2 32.4 1.0 O A:HOH481 3.3 33.7 0.5 CA A:SER61 3.8 30.8 1.0 CD1 A:TYR62 3.9 35.2 1.0 C A:SER61 4.0 30.6 1.0 O A:TYR62 4.1 32.7 1.0 O A:HOH430 4.1 47.8 1.0 CB A:TYR62 4.1 31.7 1.0 CA A:TYR62 4.2 32.0 1.0 O A:HOH650 4.2 51.8 1.0 O A:THR60 4.4 35.8 1.0 CG A:TYR62 4.5 32.7 1.0 CB A:SER61 4.5 36.3 1.0 C A:TYR62 4.6 32.3 1.0 O A:HOH481 4.7 29.8 0.5 N A:SER61 4.8 30.4 1.0 C A:THR60 4.9 34.5 1.0 OG A:SER61 4.9 48.8 1.0 CE1 A:TYR62 5.0 37.9 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