Chlorine in PDB 3m8o: Human IGA1 Fab Fragment

The structure of Human IGA1 Fab Fragment, PDB code: 3m8o was solved by A.Buschiazzo, F.Trajtenberg, A.Correa, P.Oppezzo, O.Pritsch, G.Dighiero, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.29 / 1.55
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	43.780, 76.300, 55.850, 90.00, 105.48, 90.00
R / Rfree (%)	15.3 / 18.2

The binding sites of Chlorine atom in the Human IGA1 Fab Fragment (pdb code 3m8o). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Human IGA1 Fab Fragment, PDB code: 3m8o:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Human IGA1 Fab Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Human IGA1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl220 b:23.0 occ:1.00 CB L:THR114 3.5 9.1 1.0 N L:VAL115 3.6 7.8 1.0 CA L:THR114 3.7 7.7 1.0 CG2 L:THR114 3.7 9.4 1.0 C L:THR114 4.2 9.0 1.0 CG2 L:VAL115 4.5 10.3 1.0 CB L:VAL115 4.6 8.1 1.0 CA L:VAL115 4.7 7.1 1.0 OG1 L:THR114 4.8 9.8 1.0

Chlorine binding site 2 out of 5 in the Human IGA1 Fab Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Human IGA1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl221 b:17.0 occ:1.00 OD1 L:ASN96 2.8 13.0 0.5 O L:HOH416 2.9 19.5 1.0 OE2 L:GLU39 3.0 13.4 0.4 N L:LEU55 3.0 8.1 1.0 CG L:GLU39 3.2 6.5 0.4 O L:HOH497 3.3 18.3 0.6 ND2 L:ASN96 3.4 8.6 0.5 CG L:ASN96 3.4 11.0 0.5 CD L:GLU39 3.6 11.0 0.4 N L:LEU38 3.6 7.0 1.0 ND2 L:ASN96 3.7 15.2 0.5 CA L:LEU55 3.7 5.3 1.0 O L:LEU38 3.8 7.5 1.0 CB L:TYR54 3.9 7.6 1.0 C L:ASP37 4.0 7.3 1.0 CB L:ASN96 4.0 8.2 0.5 CA L:ASP37 4.0 8.4 1.0 C L:LEU38 4.0 6.9 1.0 O H:HOH658 4.1 42.6 1.0 C L:TYR54 4.1 6.7 1.0 CG L:ASN96 4.1 8.2 0.5 O L:ASN36 4.2 8.7 1.0 CA L:TYR54 4.2 6.5 1.0 CG L:LEU55 4.4 11.8 1.0 CA L:LEU38 4.4 6.2 1.0 CB L:GLU39 4.5 7.6 0.6 CD2 L:LEU55 4.5 11.9 1.0 N L:GLU39 4.6 6.8 0.6 N L:GLU39 4.6 7.0 0.4 CB L:GLU39 4.6 7.1 0.4 CB L:ASN96 4.7 10.3 0.5 OE1 L:GLU39 4.7 10.3 0.6 CB L:LEU55 4.7 7.3 1.0 O L:ASP37 4.7 7.8 1.0 O L:HOH395 4.7 32.9 1.0 OD1 L:ASP37 4.8 11.3 1.0 C L:LEU55 4.8 6.0 1.0 OE1 L:GLU39 4.8 11.0 0.4 CB L:ASP37 4.9 9.3 1.0 N L:GLY56 4.9 7.6 1.0 CA L:GLU39 4.9 7.9 0.6 CA L:GLU39 5.0 7.6 0.4 O L:HOH264 5.0 24.7 1.0

Chlorine binding site 3 out of 5 in the Human IGA1 Fab Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Human IGA1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ L:Cl222 b:18.2 occ:1.00 O L:HOH277 3.2 25.5 1.0 O L:HOH236 3.3 25.2 1.0 N L:ARG66 3.4 9.1 1.0 NH1 L:ARG66 3.4 16.8 1.0 CB L:ARG66 3.6 8.8 1.0 CG L:ARG66 3.7 11.6 1.0 N L:ASP65 3.8 10.8 1.0 CB L:PRO64 3.8 16.4 1.0 CD L:ARG66 4.0 14.8 1.0 CA L:ARG66 4.0 8.8 1.0 C L:ASP65 4.2 10.8 1.0 CB L:ASP65 4.2 9.9 1.0 CA L:ASP65 4.3 11.6 1.0 C L:PRO64 4.4 11.4 1.0 CZ L:ARG66 4.5 16.4 1.0 CA L:PRO64 4.5 12.4 1.0 NE L:ARG66 4.7 12.5 1.0 OE2 L:GLU84 4.7 25.0 1.0 O L:HOH391 4.9 34.9 1.0

Chlorine binding site 4 out of 5 in the Human IGA1 Fab Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Human IGA1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl222 b:18.9 occ:1.00 O H:HOH422 3.1 22.8 1.0 OE2 L:GLU39 3.1 11.9 0.6 NH1 H:ARG101 3.2 24.0 1.0 NE1 H:TRP109 3.2 15.7 1.0 NH1 H:ARG107 3.5 18.0 1.0 CG H:ARG107 3.5 21.7 1.0 OH L:TYR41 3.6 21.2 1.0 NH2 H:ARG101 3.7 22.5 1.0 CD1 H:TRP109 3.7 14.2 1.0 CD H:ARG107 3.7 22.1 1.0 CG L:PRO51 3.9 17.1 1.0 OE1 L:GLU39 3.9 10.3 0.6 CD L:GLU39 3.9 9.8 0.6 CZ H:ARG101 3.9 21.0 1.0 OE1 L:GLU39 4.0 11.0 0.4 CE1 L:TYR41 4.0 13.1 1.0 CG2 H:VAL99 4.2 11.2 0.5 CZ L:TYR41 4.3 16.8 1.0 CB L:PRO51 4.4 14.2 1.0 CZ H:ARG107 4.4 21.6 1.0 CG1 H:VAL99 4.4 13.1 0.5 CE2 H:TRP109 4.5 12.7 1.0 NE H:ARG107 4.5 20.9 1.0 O H:ILE100 4.9 21.6 1.0 O H:HOH243 4.9 26.6 1.0 CD L:GLU39 4.9 11.0 0.4 CB H:ARG107 4.9 16.5 1.0

Chlorine binding site 5 out of 5 in the Human IGA1 Fab Fragment


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Human IGA1 Fab Fragment within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl223 b:21.9 occ:1.00 O H:HOH427 2.7 19.6 1.0 O H:HOH633 2.9 42.2 1.0 N H:SER41 3.0 19.7 1.0 O H:HOH279 3.1 25.6 1.0 CA H:ALA94 3.6 9.4 1.0 CB H:SER41 3.6 22.9 1.0 CA H:ALA40 3.7 10.3 1.0 CD1 H:LEU114 3.8 11.1 1.0 C H:ALA40 3.8 16.2 1.0 CA H:SER41 3.8 21.0 1.0 CG2 H:THR93 3.9 11.8 1.0 N H:ALA94 3.9 10.5 1.0 O H:THR93 4.1 12.3 1.0 C H:THR93 4.2 12.2 1.0 O H:HOH380 4.3 27.0 1.0 C H:ALA94 4.3 8.3 1.0 CB H:ALA40 4.3 12.0 1.0 O H:HOH449 4.4 31.0 1.0 O H:GLN39 4.4 10.8 1.0 N H:MET95 4.4 8.6 0.4 N H:MET95 4.4 8.6 0.6 O H:HOH426 4.6 27.9 1.0 O H:HOH291 4.7 14.2 1.0 CB H:ALA94 4.8 10.3 1.0 O H:HOH359 4.8 22.9 1.0 N H:ALA40 4.9 9.2 1.0 OG H:SER41 4.9 24.7 1.0 CB H:THR93 5.0 11.7 1.0 O H:ALA40 5.0 16.6 1.0

A.Correa, F.Trajtenberg, G.Obal, O.Pritsch, G.Dighiero, P.Oppezzo, A.Buschiazzo. Structure of A Human IGA1 Fab Fragment at 1.55 Angstrom Resolution: Potential Effect of the Constant Domains on Antigen-Affinity Modulation Acta Crystallogr.,Sect.D V. 69 388 2013.
ISSN: ISSN 0907-4449
PubMed: 23519414
DOI: 10.1107/S0907444912048664