Iodine in PDB 2bmk: Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-Alanine

The structure of Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-Alanine, PDB code: 2bmk 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)	40.00 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	63.152, 81.152, 79.331, 90.00, 90.35, 90.00
R / Rfree (%)	21 / 27.3

The binding sites of Iodine atom in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-Alanine (pdb code 2bmk). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 6 binding sites of Iodine where determined in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-Alanine, PDB code: 2bmk:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6;

Iodine binding site 1 out of 6 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-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-D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ B:I1215 b:47.8 occ:1.00 CA B:GLY97 3.3 31.4 1.0 NE1 B:TRP100E 3.4 17.9 1.0 CE2 B:TYR32 3.5 26.7 1.0 N B:GLY97 3.5 27.9 1.0 C B:GLY97 3.5 34.6 1.0 O B:HOH2048 3.6 33.3 1.0 N B:TYR99 3.6 47.8 1.0 OH B:TYR32 3.6 32.7 1.0 CB B:TYR99 3.7 52.2 1.0 O B:GLY97 3.9 35.6 1.0 CZ B:TYR32 3.9 28.8 1.0 CB B:ASN100A 4.0 43.8 1.0 CA B:TYR99 4.0 50.5 1.0 CD1 B:TYR99 4.0 57.1 1.0 ND2 B:ASN100A 4.0 47.9 1.0 N B:SER98 4.1 37.7 1.0 CD1 B:TRP100E 4.1 16.8 1.0 C B:TYR99 4.2 50.2 1.0 N B:ASN100A 4.2 43.7 1.0 CG B:TYR99 4.3 55.5 1.0 O B:ASN100A 4.4 37.2 1.0 O B:TYR99 4.4 51.4 1.0 CD2 B:TYR32 4.4 22.6 1.0 CE2 B:TRP100E 4.5 17.7 1.0 CA B:ASN100A 4.5 41.9 1.0 CG B:ASN100A 4.6 46.4 1.0 C B:ASN100A 4.7 39.9 1.0 C B:SER98 4.7 44.0 1.0 N B:GLY100 4.7 49.5 1.0 C B:LYS96 4.7 27.5 1.0 CZ2 B:TRP100E 4.9 17.9 1.0 CA B:SER98 5.0 41.0 1.0

Iodine binding site 2 out of 6 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-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-D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ B:I1216 b:99.2 occ:1.00 ND2 B:ASN53 3.5 18.7 1.0 ND2 B:ASN52A 3.5 22.4 1.0 OG B:SER98 3.7 44.8 1.0 CA B:SER98 3.8 41.0 1.0 CB B:SER98 4.1 41.3 1.0 OD1 B:ASN52A 4.3 21.6 1.0 O B:GLY97 4.3 35.6 1.0 CG B:ASN52A 4.4 22.5 1.0 N B:SER98 4.4 37.7 1.0 C B:GLY97 4.6 34.6 1.0 CB B:ALA52C 4.6 20.2 1.0 CE1 B:TYR33 4.7 13.5 1.0 CG B:ASN53 4.7 20.3 1.0 O B:HOH2046 4.8 49.1 1.0 C B:SER98 4.9 44.0 1.0

Iodine binding site 3 out of 6 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-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-D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ B:I1218 b:66.2 occ:1.00 OG1 B:THR68 3.5 25.5 1.0 ND2 B:ASN82A 4.1 29.4 1.0 O B:HOH2031 4.3 36.2 1.0 CB B:THR68 4.4 23.9 1.0 O H:HOH2005 4.8 39.0 1.0 CG B:GLN81 4.8 36.7 1.0 CG2 B:THR68 4.9 21.8 1.0

Iodine binding site 4 out of 6 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-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-D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ H:I1215 b:38.2 occ:1.00 O H:HOH2041 3.4 23.9 1.0 ND2 H:ASN82A 3.6 31.5 1.0 OG1 H:THR68 3.6 24.4 1.0 CB H:THR68 4.4 23.3 1.0 CG H:GLN81 4.5 22.4 1.0 CG H:ASN82A 4.7 30.9 1.0 CG2 H:THR68 5.0 19.9 1.0 OD1 H:ASN82A 5.0 31.3 1.0

Iodine binding site 5 out of 6 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-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-D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ H:I1216 b:73.4 occ:1.00 NE1 H:TRP100E 3.5 21.6 1.0 CA H:GLY97 3.6 31.4 1.0 ND2 H:ASN100A 3.6 55.6 1.0 CB H:TYR99 3.6 56.0 1.0 N H:TYR99 3.7 50.0 1.0 N H:GLY97 3.9 27.0 1.0 C H:GLY97 3.9 34.3 1.0 CA H:TYR99 4.0 54.2 1.0 N H:ASN100A 4.1 55.1 1.0 OH H:TYR32 4.1 27.3 1.0 CB H:ASN100A 4.1 55.1 1.0 C H:TYR99 4.1 55.4 1.0 CD1 H:TYR99 4.1 58.6 1.0 N H:SER98 4.2 37.9 1.0 O H:ASN100A 4.2 53.4 1.0 CE2 H:TYR32 4.3 21.3 1.0 CD1 H:TRP100E 4.3 22.2 1.0 CG H:ASN100A 4.3 56.0 1.0 CG H:TYR99 4.3 58.1 1.0 O H:GLY97 4.4 33.6 1.0 O H:TYR99 4.4 56.6 1.0 CZ H:TYR32 4.5 22.7 1.0 CA H:ASN100A 4.5 54.6 1.0 CE2 H:TRP100E 4.5 22.2 1.0 N H:GLY100 4.5 55.8 1.0 C H:ASN100A 4.6 53.4 1.0 C H:SER98 4.8 45.2 1.0 CZ2 H:TRP100E 4.9 21.8 1.0

Iodine binding site 6 out of 6 in the Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-Alanine


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of Fab Fragment of Plp-Dependent Catalytic Antibody 15A9 in Complex with Phosphopyridoxyl-D-Alanine within 5.0Å range: probe atom residue distance (Å) B Occ H:I1217 b:86.4 occ:1.00 N H:PHE27 3.3 18.8 1.0 C H:GLY26 3.5 18.8 1.0 CA H:PHE27 3.7 21.0 1.0 O H:GLY26 3.9 19.8 1.0 CA H:GLY26 3.9 19.7 1.0 C H:PHE27 4.0 21.4 1.0 O H:PHE27 4.1 23.0 1.0 N H:GLY26 4.1 20.4 1.0 N H:THR28 4.6 22.7 1.0

B.Golinelli-Pimpaneau, C.Luthi, P.Christen. Structural Basis For D-Amino Acid Transamination By the Pyridoxal 5'-Phosphate-Dependent Catalytic Antibody 15A9. J. Biol. Chem. V. 281 23969 2006.
ISSN: ISSN 0021-9258
PubMed: 16790434
DOI: 10.1074/JBC.M602184200