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Manganese in PDB 8e0x: Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations

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

All present enzymatic activity of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, 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 Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations, PDB code: 8e0x 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) 43.48 / 1.97
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.717, 53.181, 150.366, 90, 115.8, 90
R / Rfree (%) 18.8 / 21.4

Manganese Binding Sites:

The binding sites of Manganese atom in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations (pdb code 8e0x). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 3 binding sites of Manganese where determined in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations, PDB code: 8e0x:
Jump to Manganese binding site number: 1; 2; 3;

Manganese binding site 1 out of 3 in 8e0x

Go back to Manganese Binding Sites List in 8e0x
Manganese binding site 1 out of 3 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn401

b:50.5
occ:0.34
 OE2 A:GLU302 2.1 54.4 1.0
OD2 A:ASP326 2.3 55.9 1.0
NE2 A:HIS268 2.7 52.3 1.0
CD A:GLU302 2.9 47.3 1.0
OE1 A:GLU302 3.0 54.1 1.0
SG A:CYS61 3.0 47.3 1.0
CG A:ASP326 3.1 56.5 1.0
CB A:ASP326 3.2 53.7 1.0
CD2 A:HIS268 3.3 54.6 1.0
CB A:CYS61 3.7 48.9 1.0
CE1 A:HIS268 3.7 48.3 1.0
O A:HOH650 3.7 54.1 1.0
NH2 A:ARG92 4.0 47.7 1.0
CG A:GLU302 4.3 47.4 1.0
OD1 A:ASP326 4.3 61.8 1.0
CG A:HIS268 4.4 52.8 1.0
NZ A:LYS97 4.5 46.4 1.0
CA A:CYS61 4.5 46.1 1.0
ND1 A:HIS268 4.6 51.2 1.0
CA A:ASP326 4.6 54.8 1.0
O1 A:PEP402 4.6 47.7 1.0
C1 A:PEP402 4.8 47.6 1.0
N A:ASP326 4.9 52.9 1.0

Manganese binding site 2 out of 3 in 8e0x

Go back to Manganese Binding Sites List in 8e0x
Manganese binding site 2 out of 3 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn401

b:28.1
occ:0.23
 O B:HOH520 1.9 34.7 1.0
OE2 B:GLU302 2.1 29.2 1.0
OD2 B:ASP326 2.2 30.9 1.0
NE2 B:HIS268 2.6 27.2 1.0
SG B:CYS61 2.9 25.4 1.0
CD B:GLU302 3.2 23.6 1.0
CG B:ASP326 3.2 29.5 1.0
CD2 B:HIS268 3.4 26.7 1.0
CE1 B:HIS268 3.6 27.8 1.0
O2' B:PEP402 3.6 29.0 1.0
OE1 B:GLU302 3.7 20.5 1.0
NZ B:LYS97 3.7 27.8 1.0
CB B:ASP326 3.8 24.9 1.0
CB B:CYS61 3.9 21.2 1.0
C1 B:PEP402 4.0 28.3 1.0
OD1 B:ASP326 4.1 31.1 1.0
NH2 B:ARG92 4.1 21.8 1.0
C2 B:PEP402 4.3 31.1 1.0
CG B:GLU302 4.4 20.5 1.0
CE B:LYS97 4.4 30.3 1.0
CA B:CYS61 4.5 18.6 1.0
C3 B:PEP402 4.5 31.4 1.0
O B:HOH652 4.6 27.2 1.0
CG B:HIS268 4.6 26.0 1.0
ND1 B:HIS268 4.6 22.9 1.0
O1 B:PEP402 4.7 25.3 1.0
O B:CYS61 4.8 20.6 1.0
C B:CYS61 5.0 22.6 1.0

Manganese binding site 3 out of 3 in 8e0x

Go back to Manganese Binding Sites List in 8e0x
Manganese binding site 3 out of 3 in the Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Dahp (3-Deoxy-D-Arabinoheptulosonate-7-Phosphate) Synthase Complexed with Mn(II), Pep, and Pi in Unbound:(Bound)2:Other Conformations within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn401

b:36.9
occ:0.29
 O D:HOH566 1.8 44.1 1.0
OE2 D:GLU302 2.1 39.0 1.0
OD2 D:ASP326 2.2 39.6 1.0
SG D:CYS61 2.7 36.4 1.0
NE2 D:HIS268 2.8 44.4 1.0
CD D:GLU302 3.0 36.0 1.0
CG D:ASP326 3.1 40.2 1.0
OE1 D:GLU302 3.2 40.0 1.0
CB D:ASP326 3.4 34.1 1.0
CD2 D:HIS268 3.4 43.1 1.0
CB D:CYS61 3.5 34.4 1.0
NH2 D:ARG92 3.8 37.6 1.0
CE1 D:HIS268 3.9 45.3 1.0
O D:HOH562 4.0 46.1 1.0
OD1 D:ASP326 4.3 39.9 1.0
CA D:CYS61 4.3 29.8 1.0
O1 D:PEP402 4.3 47.1 1.0
O D:HOH502 4.4 40.3 1.0
CG D:GLU302 4.4 32.9 1.0
CG D:HIS268 4.7 45.4 1.0
CA D:ASP326 4.7 32.2 1.0
C1 D:PEP402 4.8 46.5 1.0
N D:ASP326 4.9 30.4 1.0
CZ D:ARG92 4.9 35.1 1.0
ND1 D:HIS268 4.9 45.1 1.0
O D:CYS61 4.9 31.2 1.0
C D:CYS61 5.0 31.3 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: Sun Oct 6 11:36:30 2024

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