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Chlorine in PDB 9hy5: Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0

Protein crystallography data

The structure of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0, PDB code: 9hy5 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) 56.06 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 64.731, 64.731, 160.99, 90, 90, 120
R / Rfree (%) 16.7 / 20

Other elements in 9hy5:

The structure of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0 also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0 (pdb code 9hy5). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0, PDB code: 9hy5:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 9hy5

Go back to Chlorine Binding Sites List in 9hy5
Chlorine binding site 1 out of 6 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0


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 9.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl301

b:44.0
occ:1.00
NH1 A:ARG199 3.4 36.8 1.0
N A:ARG199 3.5 35.2 1.0
CG A:ARG199 3.6 32.3 1.0
CB A:ARG199 3.7 33.3 1.0
CB A:PRO197 3.7 37.9 1.0
CD A:ARG199 3.9 37.7 1.0
N A:ALA198 3.9 37.7 1.0
CA A:ARG199 4.1 32.0 1.0
C A:ALA198 4.3 34.7 1.0
O A:HOH592 4.3 48.5 1.0
C A:PRO197 4.4 37.0 1.0
CZ A:ARG199 4.4 35.3 1.0
CA A:ALA198 4.4 36.6 1.0
O A:HOH746 4.5 69.6 1.0
CA A:PRO197 4.5 36.5 1.0
CB A:ALA198 4.5 46.0 1.0
NE A:ARG199 4.6 35.2 1.0
O A:HOH567 4.8 48.2 1.0
OE2 A:GLU217 4.8 53.7 1.0
O A:HOH510 4.9 48.6 1.0
CG A:PRO197 4.9 39.6 1.0

Chlorine binding site 2 out of 6 in 9hy5

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Chlorine binding site 2 out of 6 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0


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 9.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl306

b:40.4
occ:1.00
O A:HOH518 3.0 44.1 1.0
O A:HOH540 3.0 39.5 1.0
OG A:SER141 3.1 35.0 1.0
CA A:PRO142 3.7 29.5 1.0
CB A:SER141 3.9 29.4 1.0
CA A:SER141 4.0 27.8 1.0
NA A:NA311 4.1 37.1 0.8
O A:HOH661 4.3 46.3 1.0
N A:THR143 4.3 29.8 1.0
CB A:PRO142 4.4 30.5 1.0
C A:PRO142 4.4 30.7 1.0
N A:PRO142 4.5 27.5 1.0
O A:GLN140 4.7 31.9 1.0
C A:SER141 4.7 28.5 1.0
CG2 A:THR143 4.9 38.2 1.0
O A:HOH755 5.0 53.6 1.0

Chlorine binding site 3 out of 6 in 9hy5

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Chlorine binding site 3 out of 6 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0


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 9.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl307

b:35.1
occ:0.80
O A:HOH459 3.0 45.8 1.0
N A:GLY238 3.1 29.4 1.0
N A:GLN140 3.1 27.3 1.0
CA A:GLY238 3.6 28.6 1.0
O A:HOH639 3.7 57.9 1.0
CA A:THR139 3.9 27.4 1.0
CB A:GLN140 3.9 27.8 1.0
O A:HOH409 4.0 55.8 1.0
O A:LEU138 4.0 32.3 1.0
C A:THR139 4.0 28.1 1.0
CA A:GLN140 4.0 26.5 1.0
O A:GLN140 4.1 31.9 1.0
CG A:GLN140 4.3 29.9 1.0
C A:GLY237 4.3 30.7 1.0
O A:HOH678 4.4 57.7 1.0
C A:GLY238 4.4 30.9 1.0
CG2 A:THR139 4.5 33.6 1.0
C A:GLN140 4.5 28.1 1.0
O A:HOH666 4.6 51.1 1.0
CA A:GLY237 4.6 26.1 1.0
O A:HOH446 4.6 60.4 1.0
N A:GLY239 4.6 27.6 1.0
CG2 A:THR143 4.8 38.2 1.0
C A:LEU138 4.8 30.1 1.0
CB A:THR139 4.8 30.3 1.0
N A:THR139 4.8 28.0 1.0
CD A:GLN140 5.0 28.9 1.0

Chlorine binding site 4 out of 6 in 9hy5

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Chlorine binding site 4 out of 6 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0


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 9.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl308

b:48.9
occ:1.00
O A:HOH668 3.2 30.2 0.5
N A:TYR62 3.3 33.5 1.0
CA A:SER61 3.7 30.9 1.0
O A:HOH631 4.0 53.5 1.0
C A:SER61 4.0 31.6 1.0
CD2 A:TYR62 4.0 34.2 1.0
O A:TYR62 4.0 33.8 1.0
CB A:TYR62 4.1 32.5 1.0
CA A:TYR62 4.2 32.3 1.0
O A:THR60 4.4 36.4 1.0
O A:HOH668 4.4 30.9 0.5
CB A:SER61 4.5 36.7 1.0
CG A:TYR62 4.6 33.9 1.0
C A:TYR62 4.6 33.7 1.0
N A:SER61 4.7 30.9 1.0
O A:HOH481 4.8 50.2 1.0
C A:THR60 4.9 36.5 1.0
OG A:SER61 4.9 43.3 1.0

Chlorine binding site 5 out of 6 in 9hy5

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Chlorine binding site 5 out of 6 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl309

b:53.2
occ:1.00
O A:HOH414 3.0 48.9 1.0
O A:HOH626 3.1 39.1 1.0
N A:ALA32 3.2 35.5 1.0
CB A:ALA32 3.5 32.9 1.0
N A:PHE31 3.7 32.6 1.0
CB A:PHE31 3.8 31.6 1.0
CA A:ALA32 3.9 31.5 1.0
CG2 A:THR30 3.9 34.2 1.0
CA A:PHE31 4.1 31.5 1.0
C A:PHE31 4.1 33.5 1.0
C A:THR30 4.4 32.1 1.0
CD2 A:PHE31 4.6 32.9 1.0
O A:HOH749 4.6 54.9 1.0
CG A:PHE31 4.7 31.8 1.0
CA A:THR30 4.7 32.2 1.0
CG A:LYS76 4.9 47.2 1.0
CB A:THR30 5.0 34.7 1.0

Chlorine binding site 6 out of 6 in 9hy5

Go back to Chlorine Binding Sites List in 9hy5
Chlorine binding site 6 out of 6 in the Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Sc-4E (Scfv Derived From the Mab 4E1 Against CD93) Crystallized at pH 9.0 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl310

b:54.4
occ:1.00
N A:GLY167 3.1 38.6 1.0
N A:ASP166 3.6 36.8 1.0
CB A:ASP164 3.8 36.6 1.0
CA A:GLY167 3.8 45.5 1.0
O A:HOH620 3.9 47.6 1.0
C A:TYR165 3.9 36.6 1.0
N A:TYR165 4.0 32.0 1.0
CA A:TYR165 4.1 32.4 1.0
C A:ASP166 4.1 40.3 1.0
C A:ASP164 4.2 34.7 1.0
CA A:ASP166 4.3 39.8 1.0
O A:ASP164 4.5 35.6 1.0
CA A:ASP164 4.6 35.0 1.0
O A:TYR165 4.7 35.4 1.0
OD2 A:ASP164 4.7 42.2 1.0
C A:GLY167 4.8 43.4 1.0
CG A:ASP164 4.8 42.2 1.0
O A:HOH482 4.9 52.3 1.0
O A:HOH419 4.9 55.8 1.0
N A:ASP168 4.9 37.5 1.0

Reference:

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
Page generated: Sun Jul 13 17:03:05 2025

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