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Manganese in PDB 8e0v: 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: 8e0v 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) 49.65 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 210.193, 52.908, 150.481, 90, 115.71, 90
R / Rfree (%) 19.4 / 22.8

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 8e0v). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 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: 8e0v:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 8e0v

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Manganese binding site 1 out of 4 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:31.9
occ:0.36
 OE2 A:GLU302 2.4 32.3 1.0
NE2 A:HIS268 2.7 36.5 1.0
SG A:CYS61 2.8 27.7 1.0
OD2 A:ASP326 3.0 31.5 1.0
CD A:GLU302 3.2 30.4 1.0
CE1 A:HIS268 3.3 36.8 1.0
OE1 A:GLU302 3.4 32.8 1.0
CG A:ASP326 3.7 30.6 1.0
CB A:ASP326 3.7 29.4 1.0
CB A:CYS61 3.7 27.8 1.0
NH2 A:ARG92 3.8 28.7 1.0
CD2 A:HIS268 3.8 36.5 1.0
O A:HOH620 4.1 29.0 1.0
CA A:CYS61 4.3 27.2 1.0
CG A:GLU302 4.4 29.2 1.0
ND1 A:HIS268 4.6 35.9 1.0
CG A:LYS97 4.7 30.2 1.0
O A:HOH617 4.7 31.0 1.0
O A:HOH582 4.7 31.1 1.0
OD1 A:ASP326 4.7 29.1 1.0
CZ A:ARG92 4.8 28.4 1.0
CG A:HIS268 4.8 37.4 1.0
O A:CYS61 4.9 26.8 1.0
C A:CYS61 5.0 26.8 1.0

Manganese binding site 2 out of 4 in 8e0v

Go back to Manganese Binding Sites List in 8e0v
Manganese binding site 2 out of 4 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:32.7
occ:0.80
 OE2 B:GLU302 1.9 31.5 1.0
OD2 B:ASP326 2.1 31.8 1.0
NE2 B:HIS268 2.5 32.6 1.0
SG B:CYS61 2.7 31.0 1.0
CD B:GLU302 2.8 32.1 1.0
OE1 B:GLU302 3.0 33.3 1.0
CG B:ASP326 3.1 31.9 1.0
O B:HOH528 3.2 32.6 1.0
CD2 B:HIS268 3.2 32.8 1.0
CB B:ASP326 3.6 31.2 1.0
CE1 B:HIS268 3.6 32.6 1.0
CB B:CYS61 3.6 30.5 1.0
O2' B:PEP402 4.0 31.7 1.0
O B:HOH577 4.1 32.1 1.0
NZ B:LYS97 4.1 31.0 1.0
CG B:GLU302 4.2 31.3 1.0
OD1 B:ASP326 4.2 31.9 1.0
C1 B:PEP402 4.3 32.9 1.0
CA B:CYS61 4.3 30.4 1.0
NH2 B:ARG92 4.3 31.0 1.0
CG B:HIS268 4.4 33.2 1.0
C2 B:PEP402 4.5 32.6 1.0
ND1 B:HIS268 4.6 33.4 1.0
C3 B:PEP402 4.8 31.5 1.0
CA B:ASP326 4.8 31.0 1.0
N B:ASP326 4.8 30.9 1.0
O1 B:PEP402 4.8 32.4 1.0
O B:CYS61 4.9 31.2 1.0
CE B:LYS97 4.9 31.3 1.0
C B:CYS61 5.0 30.9 1.0

Manganese binding site 3 out of 4 in 8e0v

Go back to Manganese Binding Sites List in 8e0v
Manganese binding site 3 out of 4 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
C:Mn401

b:20.6
occ:0.48
 OE2 C:GLU302 1.7 20.8 1.0
O C:HOH531 2.0 21.0 1.0
OD2 C:ASP326 2.2 21.2 1.0
NE2 C:HIS268 2.4 21.6 1.0
CD C:GLU302 2.6 19.9 1.0
SG C:CYS61 2.8 18.4 1.0
OE1 C:GLU302 2.9 20.5 1.0
CG C:ASP326 3.2 20.8 1.0
CD2 C:HIS268 3.2 21.3 1.0
CB C:ASP326 3.5 19.4 1.0
CE1 C:HIS268 3.5 21.2 1.0
CB C:CYS61 3.7 18.6 1.0
O C:HOH713 3.9 24.4 1.0
O C:HOH570 3.9 22.3 1.0
CG C:GLU302 4.0 19.9 1.0
NZ C:LYS97 4.0 19.4 1.0
O2' C:PEP402 4.1 19.9 1.0
NH2 C:ARG92 4.2 18.4 1.0
OD1 C:ASP326 4.3 20.8 1.0
CA C:CYS61 4.3 17.9 1.0
C1 C:PEP402 4.4 20.9 1.0
CG C:HIS268 4.4 21.7 1.0
ND1 C:HIS268 4.5 21.6 1.0
C2 C:PEP402 4.7 21.0 1.0
CE C:LYS97 4.8 19.5 1.0
CA C:ASP326 4.8 19.6 1.0
O C:CYS61 4.8 17.8 1.0
N C:ASP326 4.9 18.3 1.0
O1 C:PEP402 4.9 19.6 1.0
C3 C:PEP402 5.0 20.6 1.0
C C:CYS61 5.0 17.6 1.0

Manganese binding site 4 out of 4 in 8e0v

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Manganese binding site 4 out of 4 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 4 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:38.5
occ:1.00
 OE2 D:GLU302 1.9 33.6 1.0
NE2 D:HIS268 2.7 37.2 1.0
OD2 D:ASP326 2.8 34.1 1.0
SG D:CYS61 3.0 30.5 1.0
CD D:GLU302 3.0 31.6 1.0
NH2 D:ARG92 3.4 31.6 1.0
OE1 D:GLU302 3.5 34.6 1.0
O D:HOH529 3.6 33.5 1.0
CD2 D:HIS268 3.6 38.2 1.0
CE1 D:HIS268 3.6 36.2 1.0
CG D:ASP326 3.7 34.7 1.0
CB D:CYS61 3.8 29.8 1.0
CB D:ASP326 3.9 32.5 1.0
O D:HOH557 4.0 35.1 1.0
O D:HOH532 4.1 32.5 1.0
CG D:GLU302 4.3 30.4 1.0
CA D:CYS61 4.4 29.7 1.0
CZ D:ARG92 4.4 30.0 1.0
ND1 D:HIS268 4.7 37.7 1.0
CG D:HIS268 4.7 37.8 1.0
OD1 D:ASP326 4.7 35.2 1.0
O D:HOH543 4.8 33.1 1.0
O D:CYS61 4.9 27.8 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 11:36:28 2024

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