Iodine in PDB 1wc7: Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine

The structure of Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine, PDB code: 1wc7 was solved by B.Golinelli-Pimpaneau, P.Christen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.33
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.476, 81.691, 79.330, 90.00, 89.98, 90.00
R / Rfree (%)	22.2 / 30.9

The binding sites of Iodine atom in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine (pdb code 1wc7). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 5 binding sites of Iodine where determined in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine, PDB code: 1wc7:
Jump to Iodine binding site number: 1; 2; 3; 4; 5;

Iodine binding site 1 out of 5 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ A:I1213 b:62.5 occ:1.00 OG1 H:THR68 3.3 48.4 1.0 ND2 H:ASN82A 3.4 46.2 1.0 NH1 A:ARG61 3.6 41.5 1.0 CG A:ARG61 3.7 19.2 1.0 N A:ARG61 3.7 32.8 1.0 CB A:ARG61 4.0 19.6 1.0 N A:ALA60 4.2 43.7 1.0 CB A:PRO59 4.4 30.1 1.0 CA A:ARG61 4.4 28.7 1.0 CB H:THR68 4.5 38.8 1.0 C A:ALA60 4.5 40.6 1.0 CD A:ARG61 4.6 22.4 1.0 CB A:ALA60 4.6 25.1 1.0 CA A:ALA60 4.7 35.2 1.0 CG H:ASN82A 4.7 35.5 1.0 C A:PRO59 4.8 45.5 1.0 CG H:GLN81 4.8 28.0 1.0 CZ A:ARG61 4.8 33.7 1.0 CA A:PRO59 4.8 35.4 1.0 CG2 H:THR68 4.9 33.0 1.0

Iodine binding site 2 out of 5 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ B:I1214 b:63.8 occ:1.00 NE1 B:TRP100E 2.8 31.3 1.0 CA B:GLY97 3.5 15.7 1.0 CD1 B:TRP100E 3.6 31.4 1.0 N B:GLY97 3.6 22.4 1.0 N B:ASN100A 3.7 44.9 1.0 CB B:ASN100A 3.8 47.0 1.0 O B:TYR99 3.8 64.2 1.0 C B:TYR99 3.9 58.8 1.0 C B:GLY97 3.9 21.6 1.0 N B:TYR99 3.9 59.0 1.0 CG B:ASN100A 3.9 47.5 1.0 CE2 B:TRP100E 4.0 30.3 1.0 CB B:TYR99 4.0 66.9 1.0 CE2 B:TYR32 4.0 43.1 1.0 CA B:ASN100A 4.1 45.7 1.0 CA B:TYR99 4.1 62.1 1.0 O B:GLY97 4.2 29.4 1.0 OD1 B:ASN100A 4.2 50.9 1.0 N B:GLY100 4.3 54.6 1.0 C B:ASN100A 4.3 41.6 1.0 O B:ASN100A 4.3 45.4 1.0 CD1 B:TYR99 4.4 69.1 1.0 ND2 B:ASN100A 4.4 47.3 1.0 N B:SER98 4.4 27.9 1.0 CD2 B:TYR32 4.4 42.9 1.0 CZ2 B:TRP100E 4.5 33.1 1.0 CG B:TYR99 4.6 69.0 1.0 C B:GLY100 4.7 45.7 1.0 C B:LYS96 4.7 16.1 1.0 CG B:TRP100E 4.8 29.9 1.0 CA B:GLY100 4.9 51.7 1.0

Iodine binding site 3 out of 5 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ H:I1214 b:93.4 occ:1.00 NE1 H:TRP100E 3.0 32.0 1.0 N H:ASN100A 3.0 45.6 1.0 CB H:ASN100A 3.5 47.9 1.0 CA H:ASN100A 3.6 46.4 1.0 O H:GLY97 3.7 28.4 1.0 C H:GLY97 3.7 21.0 1.0 C H:TYR99 3.7 58.9 1.0 N H:GLY100 3.7 54.7 1.0 CA H:GLY97 3.7 14.2 1.0 N H:TYR99 3.7 59.2 1.0 CE2 H:TRP100E 3.7 30.1 1.0 N H:GLY97 3.7 23.5 1.0 CZ2 H:TRP100E 3.8 31.4 1.0 OH H:TYR32 3.9 60.5 1.0 CB H:TYR99 3.9 66.8 1.0 C H:GLY100 4.0 45.5 1.0 C H:ASN100A 4.0 40.9 1.0 CA H:TYR99 4.0 62.1 1.0 CG H:ASN100A 4.0 47.8 1.0 O H:ASN100A 4.1 45.3 1.0 CD1 H:TRP100E 4.1 31.5 1.0 ND2 H:ASN100A 4.1 46.8 1.0 O H:TYR99 4.1 63.7 1.0 CE2 H:TYR32 4.2 43.4 1.0 CA H:GLY100 4.2 50.8 1.0 CD1 H:TYR99 4.2 69.5 1.0 CZ H:TYR32 4.3 46.5 1.0 N H:SER98 4.4 27.9 1.0 CG H:TYR99 4.5 68.9 1.0 N H:TYR100B 4.8 43.5 1.0 OD1 H:ASN100A 4.8 50.4 1.0 C H:LYS96 4.9 16.1 1.0 C H:SER98 4.9 52.1 1.0 O H:GLY100 5.0 42.8 1.0

Iodine binding site 4 out of 5 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ H:I1215 b:84.9 occ:1.00 OH H:TYR33 3.4 36.7 1.0 NE H:ARG52 3.6 21.5 1.0 CE2 H:TYR33 3.6 31.7 1.0 OH L:TYR94 3.6 28.7 1.0 NH2 H:ARG52 3.8 29.8 1.0 CZ H:TYR33 4.0 30.9 1.0 CZ H:ARG52 4.1 22.1 1.0 CE H:LYS96 4.4 25.0 1.0 CD H:LYS96 4.4 31.0 1.0 CD H:ARG52 4.5 22.4 1.0 CD2 H:TYR33 4.8 28.9 1.0 CZ L:TYR94 4.8 24.6 1.0

Iodine binding site 5 out of 5 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-L-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ L:I1213 b:81.1 occ:1.00 N L:ARG61 3.8 32.2 1.0 NH1 L:ARG61 3.9 41.5 1.0 CG L:ARG61 4.1 21.1 1.0 CB L:ARG61 4.2 21.2 1.0 N L:ALA60 4.2 42.7 1.0 CB L:ALA60 4.4 25.7 1.0 CD L:ARG61 4.4 24.0 1.0 C L:ALA60 4.4 40.4 1.0 CA L:ARG61 4.4 28.6 1.0 CA L:ALA60 4.6 36.3 1.0 CB L:PRO59 4.9 28.9 1.0 C L:PRO59 5.0 44.8 1.0

B.Golinelli-Pimpaneau, B.Golinelli-Pimpaneau, P.Christen. N/A N/A.
ISSN: ISSN 0907-4449
PubMed: 15805602
DOI: 10.1107/S0907444905003331