Chlorine in PDB 5k3v: Apo-PDX1.3 (Arabidopsis)

All present enzymatic activity of Apo-PDX1.3 (Arabidopsis):
4.3.3.6;

The structure of Apo-PDX1.3 (Arabidopsis), PDB code: 5k3v was solved by G.C.Robinson, M.Kaufmann, C.Roux, T.B.Fitzpatrick, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	92.95 / 1.90
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	178.220, 178.220, 116.430, 90.00, 90.00, 120.00
R / Rfree (%)	17.7 / 20.3

The binding sites of Chlorine atom in the Apo-PDX1.3 (Arabidopsis) (pdb code 5k3v). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Apo-PDX1.3 (Arabidopsis), PDB code: 5k3v:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in the Apo-PDX1.3 (Arabidopsis)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Apo-PDX1.3 (Arabidopsis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl404 b:47.1 occ:1.00 ND2 A:ASN295 3.4 45.4 1.0 N C:LEU125 3.6 20.6 0.5 N C:LEU125 3.6 18.5 0.5 O C:HOH613 3.7 43.6 1.0 O C:HOH569 3.7 32.4 1.0 CB C:LEU125 4.0 18.3 0.5 CB C:LEU125 4.1 25.0 0.5 CG C:LEU125 4.1 28.0 0.5 OD1 A:ASN295 4.2 48.1 1.0 CA C:THR124 4.2 20.2 1.0 CG2 C:THR124 4.3 22.2 1.0 CG A:ASN295 4.3 49.4 1.0 CD1 C:LEU125 4.4 29.2 0.5 C C:THR124 4.4 21.1 1.0 CA C:LEU125 4.5 18.4 0.5 CA C:LEU125 4.5 22.1 0.5 CB C:THR124 4.8 21.8 1.0 O C:LEU123 4.9 19.2 1.0

Chlorine binding site 2 out of 5 in the Apo-PDX1.3 (Arabidopsis)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Apo-PDX1.3 (Arabidopsis) within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl405 b:55.8 occ:1.00 O A:HOH576 3.6 29.0 1.0 O A:HOH626 3.7 42.5 1.0 N A:LEU125 3.7 18.2 1.0 CB A:LEU125 4.1 25.1 1.0 CG2 A:THR124 4.1 22.1 1.0 CA A:THR124 4.3 20.9 1.0 O A:HOH612 4.5 46.3 1.0 C A:THR124 4.5 19.3 1.0 CA A:LEU125 4.6 20.4 1.0 CB A:THR124 4.8 21.0 1.0

Chlorine binding site 3 out of 5 in the Apo-PDX1.3 (Arabidopsis)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Apo-PDX1.3 (Arabidopsis) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl403 b:63.7 occ:1.00 O D:HOH584 2.7 50.8 1.0 CB D:PRO208 3.4 27.2 1.0 N D:TYR209 3.6 26.3 1.0 N D:ASP210 3.7 27.5 1.0 CA D:PRO208 3.8 26.1 1.0 C D:PRO208 3.8 26.0 1.0 OD2 D:ASP210 4.0 56.3 1.0 CG D:ASP210 4.1 45.8 1.0 CB D:ASP210 4.2 35.1 1.0 CA D:TYR209 4.4 27.1 1.0 CA D:ASP210 4.6 29.9 1.0 C D:TYR209 4.6 26.6 1.0 CB D:TYR209 4.6 28.6 1.0 O D:PRO208 4.7 24.1 1.0 OD1 D:ASP210 4.7 51.5 1.0 CG D:PRO208 4.8 27.6 1.0 O D:HOH562 4.8 34.3 1.0

Chlorine binding site 4 out of 5 in the Apo-PDX1.3 (Arabidopsis)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Apo-PDX1.3 (Arabidopsis) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl404 b:52.1 occ:1.00 ND2 D:ASN295 3.4 60.4 1.0 OD1 D:ASN295 4.1 52.2 1.0 CG D:ASN295 4.2 58.9 1.0 O D:HOH608 4.7 49.4 1.0

Chlorine binding site 5 out of 5 in the Apo-PDX1.3 (Arabidopsis)


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Apo-PDX1.3 (Arabidopsis) within 5.0Å range: probe atom residue distance (Å) B Occ D:Cl405 b:52.3 occ:1.00 ND2 B:ASN295 3.5 65.2 1.0 N D:LEU125 3.6 20.1 1.0 O D:HOH565 3.7 28.9 1.0 CB D:LEU125 4.0 22.4 1.0 OD1 B:ASN295 4.1 56.9 1.0 CA D:THR124 4.2 22.0 1.0 CG2 D:THR124 4.2 24.6 1.0 CG B:ASN295 4.3 58.1 1.0 C D:THR124 4.4 21.5 1.0 CA D:LEU125 4.5 19.7 1.0 CB D:THR124 4.8 23.6 1.0 O D:LEU123 4.9 20.0 1.0

G.C.Robinson, M.Kaufmann, C.Roux, T.B.Fitzpatrick. Structural Definition of the Lysine Swing in Arabidopsis Thaliana PDX1: Intermediate Channeling Facilitating Vitamin B6 Biosynthesis. Proc.Natl.Acad.Sci.Usa V. 113 E5821 2016.
ISSN: ESSN 1091-6490
PubMed: 27647886
DOI: 10.1073/PNAS.1608125113