Atomistry » Iodine » PDB 2axe-2fwh » 2bmk
Atomistry »
  Iodine »
    PDB 2axe-2fwh »
      2bmk »

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

Protein crystallography data

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

Iodine Binding Sites:

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 2bmk

Go back to Iodine Binding Sites List in 2bmk
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 2bmk

Go back to Iodine Binding Sites List in 2bmk
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 2bmk

Go back to Iodine Binding Sites List in 2bmk
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 2bmk

Go back to Iodine Binding Sites List in 2bmk
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 2bmk

Go back to Iodine Binding Sites List in 2bmk
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 2bmk

Go back to Iodine Binding Sites List in 2bmk
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

Reference:

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
Page generated: Fri Aug 8 12:53:40 2025

Last articles

Mg in 1J34
Mg in 1J3L
Mg in 1J2B
Mg in 1J2J
Mg in 1J1U
Mg in 1J1Y
Mg in 1J1C
Mg in 1J09
Mg in 1IZC
Mg in 1IYX
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy