Chlorine in PDB 8p89: X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5

The structure of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5, PDB code: 8p89 was solved by L.Broggini, S.Ricagno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	124.95 / 3.19
Space group	I 41 2 2
Cell size a, b, c (Å), α, β, γ (°)	145.215, 145.215, 245.184, 90, 90, 90
R / Rfree (%)	22.9 / 27.6

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Chlorine atom in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 (pdb code 8p89). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 15 binding sites of Chlorine where determined in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5, PDB code: 8p89:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl301 b:53.9 occ:1.00 O C:HOH310 3.2 11.9 1.0 CG2 A:THR167 3.4 67.0 1.0 OG1 A:THR167 4.1 86.7 1.0 OG B:SER169 4.2 89.8 1.0 N C:GLY42 4.3 58.8 1.0 CB A:THR167 4.3 79.4 1.0 CA C:GLY42 4.5 58.6 1.0 N B:LYS170 4.9 65.1 1.0

Chlorine binding site 2 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl302 b:63.5 occ:1.00 OG A:SER64 3.9 104.9 1.0 O A:ASN53 4.2 65.1 1.0 CB A:SER64 4.3 59.6 1.0 O A:GLY65 4.5 86.4 1.0 CB A:ASN53 4.5 77.5 1.0 N A:GLY65 4.7 59.7 1.0 CA A:SER64 4.8 68.3 1.0

Chlorine binding site 3 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl303 b:60.0 occ:1.00 CE1 A:HIS192 3.8 114.7 1.0 NE2 A:GLN188 4.2 93.6 1.0 NE2 A:HIS192 4.2 115.5 1.0 CG A:GLN188 4.7 89.1 1.0 CD A:GLN188 5.0 94.9 1.0

Chlorine binding site 4 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl304 b:37.9 occ:1.00 OH A:TYR176 2.9 78.8 1.0 NZ A:LYS170 3.4 51.1 1.0 CE2 A:TYR176 3.5 77.2 1.0 CZ A:TYR176 3.6 80.1 1.0 CE A:LYS170 4.0 68.5 1.0 CD2 A:TYR176 4.7 71.7 1.0 CD A:LYS170 4.8 80.0 1.0 CE1 A:TYR176 5.0 80.2 1.0

Chlorine binding site 5 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl201 b:61.4 occ:1.00 ND2 A:ASN97 4.6 89.4 1.0 N C:TYR60 4.6 70.3 1.0 O C:THR58 4.7 81.4 1.0 CA C:TYR59 4.9 59.1 1.0 O C:TYR60 5.0 71.4 1.0

Chlorine binding site 6 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl202 b:47.4 occ:1.00 OD1 C:ASN77 3.6 73.6 1.0 O C:ASN74 3.8 52.6 1.0 OD1 C:ASN30 4.2 60.9 1.0 CG C:ASN77 4.4 61.4 1.0 ND2 C:ASN77 4.4 62.1 1.0 CG C:ASN30 4.6 57.9 1.0 ND2 C:ASN30 4.8 72.8 1.0 C C:ASN74 4.9 47.1 1.0

Chlorine binding site 7 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl203 b:60.5 occ:1.00 CB C:PHE27 3.6 58.1 1.0 CG2 C:VAL2 4.0 57.8 1.0 O C:GLY26 4.2 70.2 1.0 CA C:PHE27 4.5 59.6 1.0 OH C:TYR32 4.5 85.7 1.0 NZ C:LYS98 4.7 66.4 1.0 CG C:PHE27 4.8 59.7 1.0

Chlorine binding site 8 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ C:Cl204 b:51.6 occ:1.00 OH C:TYR110 3.7 75.1 1.0 N C:VAL2 4.0 70.3 1.0 CZ C:TYR110 4.1 74.9 1.0 CG2 C:VAL2 4.1 57.8 1.0 CE1 C:TYR110 4.2 72.1 1.0 CB C:GLN1 4.2 57.2 1.0 CA C:GLN1 4.5 53.9 1.0 CB C:VAL2 4.5 39.8 1.0 C C:GLN1 4.8 62.8 1.0 CA C:VAL2 4.9 54.0 1.0 CE2 C:TYR110 5.0 74.7 1.0

Chlorine binding site 9 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl301 b:87.4 occ:1.00 O B:VAL3 3.0 84.9 1.0 C B:VAL3 3.9 83.8 1.0 CD2 B:LEU4 4.3 76.8 1.0 N B:VAL3 4.4 66.8 1.0 N B:SER25 4.5 103.5 1.0 CA B:LEU4 4.6 80.1 1.0 N B:LEU4 4.7 86.8 1.0 CA B:GLY24 4.7 94.6 1.0 CA B:VAL3 4.7 75.0 1.0 CB B:SER25 4.9 117.0 1.0

Chlorine binding site 10 out of 15 in the X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of X-Ray Structure of Cardiotoxic Light Chain H3 in Complex to Neutralizing Nanobody B5 within 5.0Å range: probe atom residue distance (Å) B Occ B:Cl302 b:63.6 occ:1.00 O B:VAL119 3.8 90.7 1.0 N B:VAL119 4.1 68.5 1.0 CA B:SER118 4.3 72.2 1.0 C B:SER118 4.5 73.3 1.0 CB B:SER118 4.5 77.6 1.0 C B:VAL119 4.6 82.1 1.0 OG B:SER118 4.9 80.2 1.0 OG1 B:THR120 4.9 80.7 1.0 CA B:VAL119 5.0 77.6 1.0

L.Broggini, M.M.Barzago, V.Speranzini, T.Schulte, F.Sonzini, M.Giono, M.Romeo, P.Milani, S.Caminito, G.Mazzini, P.Rognoni, G.Merlini, C.Pappone, L.Anastasia, M.Nuvolone, G.Palladini, L.Diomede, S.Ricagno. Nanobodies Counteract the Toxicity of An Amyloidogenic Light Chain By Stabilizing A Partially Open Dimeric Conformation J.Mol.Biol. 2023.
ISSN: ESSN 1089-8638
DOI: 10.1016/J.JMB.2023.168320