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Praseodymium in PDB 8e0y: Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations

Enzymatic activity of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations

All present enzymatic activity of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations:
2.5.1.54;

Protein crystallography data

The structure of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations, PDB code: 8e0y 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) 46.47 / 2.01
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 209.851, 53.254, 150.543, 90, 115.59, 90
R / Rfree (%) 20.2 / 21.9

Praseodymium Binding Sites:

The binding sites of Praseodymium atom in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations (pdb code 8e0y). This binding sites where shown within 5.0 Angstroms radius around Praseodymium atom.
In total 8 binding sites of Praseodymium where determined in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations, PDB code: 8e0y:
Jump to Praseodymium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Praseodymium binding site 1 out of 8 in 8e0y

Go back to Praseodymium Binding Sites List in 8e0y
Praseodymium binding site 1 out of 8 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 1 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr401

b:54.4
occ:0.19
 OE2 A:GLU302 2.1 48.1 1.0
OD2 A:ASP326 2.8 40.8 1.0
NE2 A:HIS268 2.8 48.2 1.0
CD A:GLU302 3.0 39.0 1.0
SG A:CYS61 3.0 29.2 1.0
OE1 A:GLU302 3.1 37.7 1.0
CG A:ASP326 3.5 38.9 1.0
CD2 A:HIS268 3.6 47.8 1.0
CB A:ASP326 3.7 31.4 1.0
CE1 A:HIS268 3.9 47.3 1.0
CD A:LYS97 3.9 39.6 1.0
NH2 A:ARG92 3.9 31.8 1.0
CB A:CYS61 4.0 27.6 1.0
O A:HOH605 4.1 29.9 1.0
CG A:GLU302 4.4 33.2 1.0
CA A:CYS61 4.6 25.6 1.0
OD1 A:ASP326 4.6 35.1 1.0
O A:HOH529 4.7 37.1 1.0
O A:HOH530 4.8 37.4 1.0
CG A:HIS268 4.8 50.2 1.0
ND1 A:HIS268 4.9 50.3 1.0
CZ A:ARG92 4.9 29.7 1.0

Praseodymium binding site 2 out of 8 in 8e0y

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Praseodymium binding site 2 out of 8 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 2 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Pr402

b:42.2
occ:1.00
 O A:HOH606 2.3 47.6 1.0
O A:HOH578 2.5 46.5 1.0
HG1 A:FLC403 2.7 50.2 1.0
O A:HOH640 2.7 42.2 1.0
OD1 A:ASP121 2.7 28.1 1.0
OD2 A:ASP121 2.7 30.2 1.0
CBC A:FLC403 2.9 38.8 1.0
OA2 A:FLC403 2.9 46.4 1.0
O A:HOH645 3.0 48.5 1.0
OB2 A:FLC403 3.0 65.2 1.0
CAC A:FLC403 3.0 48.8 1.0
CG A:ASP121 3.1 29.8 1.0
OB1 A:FLC403 3.2 44.9 1.0
OA1 A:FLC403 3.3 67.3 1.0
CB A:FLC403 3.5 45.5 1.0
CG A:FLC403 3.5 41.9 1.0
CA A:FLC403 3.8 48.0 1.0
HG2 A:FLC403 4.1 50.2 1.0
HA1 A:FLC403 4.4 57.6 1.0
CB A:ASP121 4.6 25.1 1.0
CGC A:FLC403 4.6 32.9 1.0
OG2 A:FLC403 4.6 32.8 1.0
HA2 A:FLC403 4.6 57.6 1.0
NH1 A:ARG124 4.7 31.2 1.0
OHB A:FLC403 4.8 59.8 1.0
OE1 A:GLN118 4.9 49.1 1.0
HOB A:FLC403 4.9 71.8 1.0

Praseodymium binding site 3 out of 8 in 8e0y

Go back to Praseodymium Binding Sites List in 8e0y
Praseodymium binding site 3 out of 8 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 3 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pr401

b:57.0
occ:0.32
 OE2 B:GLU302 2.2 59.6 1.0
OD2 B:ASP326 2.2 52.9 1.0
NE2 B:HIS268 2.5 53.8 1.0
OE1 B:GLU302 2.7 59.6 1.0
CD B:GLU302 2.7 53.9 1.0
SG B:CYS61 2.8 47.8 1.0
CG B:ASP326 3.1 52.4 1.0
O B:HOH567 3.2 60.9 1.0
CB B:ASP326 3.3 52.4 1.0
CD2 B:HIS268 3.4 54.7 1.0
CE1 B:HIS268 3.5 55.2 1.0
CB B:CYS61 3.5 48.1 1.0
O B:HOH578 3.5 56.9 1.0
NH2 B:ARG92 4.1 49.4 1.0
NZ B:LYS97 4.2 51.9 1.0
CA B:CYS61 4.2 51.8 1.0
O B:HOH542 4.2 60.5 1.0
CG B:GLU302 4.2 55.3 1.0
OD1 B:ASP326 4.3 49.5 1.0
ND1 B:HIS268 4.5 58.1 1.0
CG B:HIS268 4.6 57.5 1.0
CA B:ASP326 4.6 51.4 1.0
O B:CYS61 4.8 45.4 1.0
N B:ASP326 4.8 49.2 1.0
CE B:LYS97 5.0 48.4 1.0
C B:CYS61 5.0 46.5 1.0

Praseodymium binding site 4 out of 8 in 8e0y

Go back to Praseodymium Binding Sites List in 8e0y
Praseodymium binding site 4 out of 8 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 4 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Pr402

b:56.4
occ:1.00
 OD2 B:ASP121 2.5 50.7 1.0
OXT B:ACT405 2.5 58.3 1.0
O B:ACT405 2.6 65.5 1.0
O B:HOH574 2.6 58.9 1.0
OD1 B:ASP121 2.6 47.6 1.0
HA2 B:FLC404 2.7 62.6 1.0
O B:HOH501 2.7 63.6 1.0
OA1 B:FLC404 2.8 57.3 1.0
OB1 B:FLC404 2.8 51.5 1.0
CG B:ASP121 2.9 48.9 1.0
C B:ACT405 2.9 62.8 1.0
CAC B:FLC404 3.2 66.6 1.0
CA B:FLC404 3.2 52.1 1.0
HG2 B:FLC404 3.2 66.0 1.0
O B:HOH544 3.3 62.5 1.0
CBC B:FLC404 3.5 52.5 1.0
CB B:FLC404 3.6 51.2 1.0
CG B:FLC404 3.8 55.0 1.0
HG1 B:FLC404 4.0 66.0 1.0
OA2 B:FLC404 4.2 64.9 1.0
NH1 B:ARG124 4.2 48.7 1.0
HA1 B:FLC404 4.2 62.6 1.0
CB B:ASP121 4.4 39.5 1.0
CH3 B:ACT405 4.4 57.7 1.0
OB2 B:FLC404 4.7 56.0 1.0
H1 B:ACT405 4.8 69.3 1.0
H3 B:ACT405 4.9 69.3 1.0
OHB B:FLC404 4.9 65.6 1.0
H2 B:ACT405 5.0 69.3 1.0

Praseodymium binding site 5 out of 8 in 8e0y

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Praseodymium binding site 5 out of 8 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 5 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pr402

b:24.3
occ:0.28
 OE2 C:GLU302 1.8 27.2 1.0
OD2 C:ASP326 1.9 32.1 1.0
O3 C:52L401 2.2 24.9 0.6
NE2 C:HIS268 2.5 28.4 1.0
SG C:CYS61 2.7 23.9 1.0
CG C:ASP326 2.8 29.1 1.0
CD C:GLU302 2.8 20.8 1.0
OE1 C:GLU302 3.1 20.7 1.0
C3 C:52L401 3.2 30.0 0.6
CD2 C:HIS268 3.2 25.7 1.0
CB C:ASP326 3.4 23.6 1.0
O29 C:52L401 3.5 26.8 0.6
CB C:CYS61 3.6 18.0 1.0
CE1 C:HIS268 3.7 26.8 1.0
OD1 C:ASP326 3.7 26.7 1.0
C17 C:52L401 3.9 25.9 0.6
C1 C:52L401 3.9 30.6 0.6
NZ C:LYS97 4.0 24.7 1.0
C2 C:52L401 4.1 30.9 0.6
O5 C:52L401 4.1 29.8 0.6
CG C:GLU302 4.2 17.0 1.0
CA C:CYS61 4.3 18.6 1.0
NH2 C:ARG92 4.3 20.7 1.0
O C:HOH637 4.3 25.5 1.0
C4 C:52L401 4.4 31.4 0.6
CG C:HIS268 4.5 25.2 1.0
N1 C:52L401 4.5 28.6 0.6
C5 C:52L401 4.5 34.9 0.6
ND1 C:HIS268 4.7 24.0 1.0
CA C:ASP326 4.7 23.7 1.0
O30 C:52L401 4.7 23.9 0.6
CE C:LYS97 4.8 26.7 1.0
O C:CYS61 4.9 18.4 1.0
N C:ASP326 4.9 20.2 1.0
C C:CYS61 5.0 19.2 1.0
O4 C:52L401 5.0 27.7 0.6

Praseodymium binding site 6 out of 8 in 8e0y

Go back to Praseodymium Binding Sites List in 8e0y
Praseodymium binding site 6 out of 8 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 6 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Pr403

b:46.2
occ:1.00
 OD1 C:ASP121 2.6 28.9 1.0
OB2 C:FLC404 2.6 37.9 1.0
O C:HOH721 2.7 47.0 1.0
O C:HOH683 2.7 47.3 1.0
OD2 C:ASP121 2.8 27.2 1.0
OHB C:FLC404 2.8 38.1 1.0
OG2 C:FLC404 2.9 40.2 1.0
O C:HOH723 2.9 40.6 1.0
O C:HOH743 2.9 43.5 1.0
CG C:ASP121 3.0 26.0 1.0
CBC C:FLC404 3.4 39.1 1.0
CB C:FLC404 3.5 38.9 1.0
HOB C:FLC404 3.6 45.7 1.0
CGC C:FLC404 3.6 50.1 1.0
CG C:FLC404 4.1 47.2 1.0
NH1 C:ARG124 4.2 30.1 1.0
HG2 C:FLC404 4.5 56.6 1.0
CB C:ASP121 4.5 23.6 1.0
OG1 C:FLC404 4.5 58.7 1.0
OB1 C:FLC404 4.6 45.5 1.0
OA2 C:FLC404 4.7 34.2 1.0
O C:HOH725 4.8 49.8 1.0
CA C:FLC404 4.9 36.9 1.0

Praseodymium binding site 7 out of 8 in 8e0y

Go back to Praseodymium Binding Sites List in 8e0y
Praseodymium binding site 7 out of 8 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 7 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pr401

b:64.1
occ:0.34
 OD2 D:ASP326 1.9 60.8 1.0
OE2 D:GLU302 2.1 54.7 1.0
NE2 D:HIS268 2.7 57.4 1.0
SG D:CYS61 2.9 49.6 1.0
CD D:GLU302 3.0 50.9 1.0
O D:HOH527 3.0 54.5 1.0
CG D:ASP326 3.0 57.0 1.0
OE1 D:GLU302 3.2 54.2 1.0
NH2 D:ARG92 3.3 52.5 1.0
CD2 D:HIS268 3.5 55.1 1.0
CB D:ASP326 3.5 48.0 1.0
CE1 D:HIS268 3.7 53.7 1.0
CB D:CYS61 3.8 48.7 1.0
OD1 D:ASP326 4.1 52.9 1.0
NZ D:LYS97 4.3 45.1 1.0
CG D:GLU302 4.4 48.4 1.0
CA D:CYS61 4.4 48.4 1.0
CZ D:ARG92 4.5 49.2 1.0
O D:HOH601 4.6 56.0 1.0
CG D:HIS268 4.7 55.8 1.0
ND1 D:HIS268 4.7 55.5 1.0
O D:HOH588 4.8 53.2 1.0
CE D:LYS97 4.8 48.5 1.0
CA D:ASP326 4.9 50.5 1.0
O D:CYS61 4.9 44.4 1.0

Praseodymium binding site 8 out of 8 in 8e0y

Go back to Praseodymium Binding Sites List in 8e0y
Praseodymium binding site 8 out of 8 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Praseodymium with other atoms in the Pr binding site number 8 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Dahp Oxime, Pr(III), and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Pr402

b:57.0
occ:1.00
 O D:HOH519 2.5 65.8 1.0
O D:HOH593 2.6 59.6 1.0
HA2 D:FLC403 2.6 56.9 1.0
OD1 D:ASP121 2.7 41.2 1.0
OB1 D:FLC403 2.8 48.1 1.0
O D:HOH602 2.8 55.0 1.0
O D:HOH605 2.9 56.6 1.0
OD2 D:ASP121 2.9 50.9 1.0
O D:HOH596 2.9 57.1 1.0
CAC D:FLC403 2.9 62.9 1.0
CA D:FLC403 3.1 47.4 1.0
CG D:ASP121 3.1 45.8 1.0
OA2 D:FLC403 3.3 57.5 1.0
HG2 D:FLC403 3.3 58.0 1.0
OA1 D:FLC403 3.3 61.6 1.0
CBC D:FLC403 3.6 47.0 1.0
CB D:FLC403 3.6 46.6 1.0
CG D:FLC403 3.9 48.3 1.0
HA1 D:FLC403 4.1 56.9 1.0
HG1 D:FLC403 4.3 58.0 1.0
NH1 D:ARG124 4.4 47.2 1.0
CB D:ASP121 4.6 40.6 1.0
OB2 D:FLC403 4.8 56.1 1.0
OHB D:FLC403 5.0 58.3 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: Fri Apr 7 19:47:45 2023

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