Chlorine in PDB 8yyz: Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals

The structure of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals, PDB code: 8yyz was solved by J.M.M.Caaveiro, A.Senoo, I.Kaneda, K.Tsumoto, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.04 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	69.51, 84.08, 126.04, 90, 90, 90
R / Rfree (%)	18.4 / 22.2

The structure of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals also contains other interesting chemical elements:

Iodine

(I)

2 atoms

The binding sites of Chlorine atom in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals (pdb code 8yyz). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals, PDB code: 8yyz:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl201 b:38.6 occ:1.00 OG A:SER151 3.0 20.8 1.0 CB A:SER151 3.8 20.4 1.0 N A:ASP152 3.8 22.0 1.0 CB A:ASP152 3.9 25.4 1.0 C A:SER151 3.9 21.2 1.0 CA A:ASP152 3.9 23.8 1.0 O A:SER151 4.0 22.0 1.0 O A:GLY119 4.1 28.8 1.0 O A:HOH416 4.3 40.5 1.0 CA A:SER151 4.5 19.4 1.0 O A:HOH418 4.7 23.7 0.6 CA A:VAL120 4.9 24.1 1.0

Chlorine binding site 2 out of 5 in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl303 b:47.5 occ:1.00 O H:HOH521 2.8 39.0 1.0 N H:SER88 3.3 33.9 1.0 CA H:THR87 3.9 33.5 1.0 CB H:SER88 4.0 35.0 1.0 C H:THR87 4.0 32.3 1.0 CB H:PRO14 4.1 39.2 1.0 CB H:THR87 4.1 35.1 1.0 OG H:SER88 4.2 37.9 1.0 CA H:SER88 4.2 33.9 1.0 CG H:PRO14 4.2 39.1 1.0 CG2 H:THR87 5.0 36.5 1.0 CG1 H:VAL117 5.0 26.6 1.0

Chlorine binding site 3 out of 5 in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl302 b:45.2 occ:1.00 N L:VAL115 3.3 24.8 1.0 CA L:SER114 3.8 27.8 1.0 CE L:LYS207 4.0 34.8 1.0 O L:VAL115 4.0 25.1 1.0 NZ L:LYS207 4.0 36.6 1.0 C L:SER114 4.1 25.8 1.0 CA L:VAL115 4.3 24.3 1.0 CB L:SER114 4.3 30.2 1.0 CB L:VAL115 4.3 23.8 1.0 O L:PRO113 4.4 25.5 1.0 CG1 L:VAL205 4.6 34.4 1.0 CG2 L:VAL115 4.6 23.5 1.0 C L:VAL115 4.6 25.1 1.0 N L:SER114 4.9 26.0 1.0

Chlorine binding site 4 out of 5 in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl303 b:48.8 occ:1.00 OG L:SER114 2.9 35.7 1.0 ND2 L:ASN137 3.5 33.4 1.0 CB L:SER114 3.9 30.2 1.0 CG2 H:THR189 4.2 34.9 1.0 CB L:ASN137 4.2 28.0 1.0 CG L:ASN137 4.3 30.8 1.0 CE2 L:PHE116 4.5 27.3 1.0 ND2 L:ASN138 4.5 37.4 1.0 CZ L:PHE116 4.5 28.6 1.0 O L:HOH501 4.6 37.4 1.0 CB H:THR189 4.7 36.0 1.0 CG2 H:THR141 4.7 46.0 1.0 OG1 H:THR189 4.8 35.4 1.0 O L:ASN137 4.9 26.9 1.0 CB H:THR141 4.9 48.2 1.0

Chlorine binding site 5 out of 5 in the Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Crystal Structure of Sonic Hedgehog in Complex with Antibody 5E1 Mutant H-R102A in the Absence of Metals within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl304 b:49.3 occ:1.00 O L:HOH427 3.5 23.8 1.0 O L:THR197 3.7 23.9 1.0 C L:THR197 4.1 24.6 1.0 CA L:HIS198 4.2 24.1 1.0 CG2 L:THR197 4.3 28.4 1.0 N L:LYS145 4.3 30.9 1.0 CA L:ALA144 4.3 29.4 1.0 O L:GLU143 4.3 29.8 1.0 N L:HIS198 4.4 24.2 1.0 C L:ALA144 4.5 29.9 1.0 N L:ALA144 4.6 28.8 1.0 C L:GLU143 4.6 31.5 1.0 N L:GLN199 4.6 27.3 1.0 CB L:THR197 4.6 26.6 1.0 C L:HIS198 4.7 25.9 1.0 CB L:LYS145 4.9 34.8 1.0

I.Kaneda, R.Matsunaga, S.Nagatoishi, A.Senoo, J.M.M.Caaveiro, D.Kuroda, K.Tsumoto. Biophysical Insights to Improve Affinity of Antibodies to Fluctuated Epitope of Antigen: A Case of Anti-Shh Antibody 5E1 Against Shh Antigen. To Be Published.