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:
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 Sites List in 9hy5
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 Sites List in 9hy5
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 Sites List in 9hy5
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 Sites List in 9hy5
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
|