Chlorine in PDB 8e0z: Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations

Enzymatic activity of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations

All present enzymatic activity of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations:
2.5.1.54;

Protein crystallography data

The structure of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations, PDB code: 8e0z was solved by P.J.Berti, M.S.Junop, R.Grainger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.37 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.719, 53.13, 150.2, 90, 115.46, 90
R / Rfree (%) 17.9 / 21.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations (pdb code 8e0z). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations, PDB code: 8e0z:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 8e0z

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Chlorine binding site 1 out of 4 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl401

b:26.4
occ:1.00
 O A:HOH716 3.0 14.3 1.0
NE2 A:HIS304 3.2 7.9 1.0
N A:ASP65 3.2 10.2 1.0
N A:HIS64 3.3 9.2 1.0
O A:ASP65 3.6 10.6 1.0
CE1 A:HIS304 3.7 9.3 1.0
ND1 A:HIS64 3.8 13.4 1.0
CA A:ASP65 4.0 8.5 1.0
CA A:ILE63 4.0 9.1 1.0
CE1 A:HIS64 4.0 14.1 1.0
C A:HIS64 4.1 12.9 1.0
CB A:ASP65 4.1 8.5 1.0
CA A:HIS64 4.1 11.9 1.0
CG A:HIS64 4.2 11.5 1.0
C A:ILE63 4.2 11.9 1.0
C A:ASP65 4.2 8.4 1.0
CG2 A:ILE63 4.2 8.1 1.0
CB A:ALA68 4.3 9.8 1.0
CD2 A:HIS304 4.4 7.5 1.0
N A:ALA69 4.5 3.5 1.0
O A:SER62 4.5 9.4 1.0
NE2 A:HIS64 4.5 12.0 1.0
CD1 A:ILE63 4.6 7.7 1.0
CD2 A:HIS64 4.6 11.2 1.0
CB A:HIS64 4.7 9.5 1.0
O A:HOH523 4.7 12.2 1.0
CB A:ILE63 4.7 13.5 1.0
CB A:ALA69 4.8 6.4 1.0
O A:HOH584 4.9 13.2 1.0
CA A:ALA69 4.9 5.1 1.0
ND1 A:HIS304 5.0 6.4 1.0

Chlorine binding site 2 out of 4 in 8e0z

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Chlorine binding site 2 out of 4 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl401

b:46.1
occ:1.00
 NE2 B:HIS304 3.2 33.9 1.0
N B:ASP65 3.2 39.5 1.0
N B:HIS64 3.3 37.1 1.0
O B:HOH571 3.4 39.5 1.0
O B:ASP65 3.5 32.0 1.0
CE1 B:HIS304 3.8 32.5 1.0
CD2 B:HIS64 3.8 49.3 1.0
CA B:ASP65 4.0 34.9 1.0
CA B:ILE63 4.1 31.4 1.0
C B:ASP65 4.1 31.1 1.0
C B:HIS64 4.1 40.5 1.0
CA B:HIS64 4.1 41.9 1.0
CB B:ASP65 4.1 39.8 1.0
C B:ILE63 4.2 37.0 1.0
N B:ALA69 4.3 28.0 1.0
CG B:HIS64 4.3 46.3 1.0
CD2 B:HIS304 4.3 31.0 1.0
O B:SER62 4.3 39.4 1.0
CB B:ALA68 4.4 31.5 1.0
CG2 B:ILE63 4.5 28.2 1.0
CB B:HIS64 4.5 46.4 1.0
CB B:ALA69 4.6 26.3 1.0
NE2 B:HIS64 4.6 57.1 1.0
CA B:ALA69 4.7 27.8 1.0
CD1 B:ILE63 4.7 28.1 1.0
C B:ALA68 4.8 27.7 1.0
CG B:PRO60 4.8 28.1 1.0
CB B:ILE63 4.9 29.8 1.0
CB B:PRO60 4.9 25.8 1.0

Chlorine binding site 3 out of 4 in 8e0z

Go back to Chlorine Binding Sites List in 8e0z
Chlorine binding site 3 out of 4 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl401

b:30.2
occ:1.00
 O C:HOH598 3.0 20.6 1.0
NE2 C:HIS304 3.3 16.5 1.0
N C:ASP65 3.3 19.4 1.0
N C:HIS64 3.3 19.7 1.0
ND1 C:HIS64 3.5 21.5 1.0
O C:ASP65 3.6 15.7 1.0
CE1 C:HIS64 3.8 20.1 1.0
CE1 C:HIS304 3.8 13.6 1.0
CA C:ILE63 3.9 15.4 1.0
CG2 C:ILE63 4.0 10.8 1.0
CA C:ASP65 4.0 15.1 1.0
CB C:ASP65 4.0 15.4 1.0
C C:ILE63 4.1 16.8 1.0
CG C:HIS64 4.1 20.7 1.0
C C:HIS64 4.2 14.9 1.0
C C:ASP65 4.2 13.5 1.0
CA C:HIS64 4.2 18.6 1.0
CB C:ALA68 4.2 13.0 1.0
O C:SER62 4.4 26.4 1.0
NE2 C:HIS64 4.4 19.4 1.0
CD1 C:ILE63 4.5 11.1 1.0
CB C:ILE63 4.5 12.7 1.0
CD2 C:HIS304 4.5 13.9 1.0
N C:ALA69 4.5 14.5 1.0
CD2 C:HIS64 4.6 17.6 1.0
CB C:HIS64 4.7 18.8 1.0
CB C:ALA69 4.9 11.3 1.0
N C:ILE63 5.0 16.6 1.0

Chlorine binding site 4 out of 4 in 8e0z

Go back to Chlorine Binding Sites List in 8e0z
Chlorine binding site 4 out of 4 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Unbound:(Bound)2:Unbound Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl401

b:36.8
occ:1.00
 N D:HIS64 3.1 31.1 1.0
N D:ASP65 3.1 26.4 1.0
O D:HOH553 3.1 35.3 1.0
CD2 D:HIS64 3.3 40.3 1.0
NE2 D:HIS304 3.4 34.6 1.0
NE2 D:HIS64 3.6 43.5 1.0
CG D:HIS64 3.6 36.3 1.0
O D:ASP65 3.8 29.9 1.0
CB D:ASP65 3.8 27.1 1.0
CA D:ASP65 3.9 22.9 1.0
C D:HIS64 3.9 25.4 1.0
CA D:ILE63 3.9 31.9 1.0
CA D:HIS64 3.9 31.7 1.0
CE1 D:HIS304 3.9 31.0 1.0
C D:ILE63 4.0 34.8 1.0
CE1 D:HIS64 4.1 41.3 1.0
ND1 D:HIS64 4.2 37.9 1.0
C D:ASP65 4.2 26.7 1.0
CG2 D:ILE63 4.2 23.6 1.0
O D:SER62 4.3 35.1 1.0
CB D:HIS64 4.3 29.8 1.0
CD2 D:HIS304 4.6 29.5 1.0
CB D:ALA68 4.6 25.8 1.0
CB D:ILE63 4.7 24.7 1.0
CD1 D:ILE63 4.8 29.1 1.0
N D:ILE63 5.0 32.1 1.0
N D:ALA69 5.0 30.6 1.0

Reference:

N.Balachandran, R.A.Grainger, T.Rob, P.Liuni, D.J.Wilson, M.S.Junop, P.J.Berti. Role of Half-of-Sites Reactivity and Inter-Subunit Communications in Dahp Synthase Catalysis and Regulation. Biochemistry V. 61 2229 2022.
ISSN: ISSN 0006-2960
PubMed: 36197914
DOI: 10.1021/ACS.BIOCHEM.2C00465
Page generated: Tue Apr 4 22:48:41 2023

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