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Manganese in PDB 1vs1: Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep

Enzymatic activity of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep

All present enzymatic activity of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep:
2.5.1.54;

Protein crystallography data

The structure of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep, PDB code: 1vs1 was solved by I.A.Shumilin, L.Zhou, J.Wu, R.W.Woodard, R.Bauerle, R.H.Kretsinger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.30
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 54.768, 130.404, 78.362, 90.00, 110.61, 90.00
R / Rfree (%) 17.3 / 21.8

Manganese Binding Sites:

The binding sites of Manganese atom in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep (pdb code 1vs1). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 4 binding sites of Manganese where determined in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep, PDB code: 1vs1:
Jump to Manganese binding site number: 1; 2; 3; 4;

Manganese binding site 1 out of 4 in 1vs1

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Manganese binding site 1 out of 4 in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn301

b:42.5
occ:1.00
 OE2 A:GLU242 2.1 49.3 1.0
O A:HOH313 2.3 42.6 1.0
OD1 A:ASP253 2.4 47.4 1.0
NE2 A:HIS216 2.4 50.0 1.0
SG A:CYS46 2.6 33.5 1.0
CD A:GLU242 3.0 31.5 1.0
OE1 A:GLU242 3.1 30.2 1.0
CE1 A:HIS216 3.2 41.1 1.0
O1 A:PEP302 3.3 45.2 1.0
CB A:CYS46 3.4 31.4 1.0
CD2 A:HIS216 3.5 31.5 1.0
CG A:ASP253 3.6 52.4 1.0
C1 A:PEP302 4.0 47.5 1.0
NE2 A:GLN256 4.0 39.2 1.0
CA A:CYS46 4.1 32.0 1.0
CB A:ASP253 4.2 50.0 1.0
ND1 A:HIS216 4.3 40.9 1.0
CG A:GLU242 4.4 33.7 1.0
NZ A:LYS75 4.4 37.8 1.0
C3 A:PEP302 4.4 37.5 1.0
NH2 A:ARG70 4.5 36.4 1.0
OD2 A:ASP253 4.5 45.1 1.0
CG A:HIS216 4.5 35.9 1.0
C2 A:PEP302 4.7 52.2 1.0
O2' A:PEP302 4.7 40.5 1.0
C A:CYS46 5.0 32.0 1.0

Manganese binding site 2 out of 4 in 1vs1

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Manganese binding site 2 out of 4 in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn301

b:49.1
occ:1.00
 OE2 B:GLU242 2.1 50.1 1.0
O B:HOH304 2.4 48.8 1.0
NE2 B:HIS216 2.5 48.5 1.0
OD1 B:ASP253 2.6 47.9 1.0
SG B:CYS46 2.7 34.9 1.0
CD B:GLU242 3.0 37.3 1.0
CB B:CYS46 3.3 30.0 1.0
OE1 B:GLU242 3.3 35.6 1.0
CE1 B:HIS216 3.4 37.3 1.0
O1 B:PEP303 3.5 44.4 1.0
CD2 B:HIS216 3.5 30.5 1.0
CG B:ASP253 3.7 56.9 1.0
CA B:CYS46 4.1 32.1 1.0
C1 B:PEP303 4.2 46.4 1.0
NE2 B:GLN256 4.2 39.5 1.0
CB B:ASP253 4.3 48.7 1.0
NZ B:LYS75 4.3 32.4 1.0
CG B:GLU242 4.4 30.2 1.0
ND1 B:HIS216 4.5 43.0 1.0
CG B:HIS216 4.6 35.7 1.0
OD2 B:ASP253 4.6 54.2 1.0
NH2 B:ARG70 4.8 33.9 1.0
O2' B:PEP303 4.8 39.0 1.0
C3 B:PEP303 4.8 33.2 1.0
C2 B:PEP303 4.9 47.0 1.0
C B:CYS46 4.9 32.2 1.0
CE B:LYS75 4.9 33.5 1.0
O2 B:PEP303 4.9 45.6 1.0

Manganese binding site 3 out of 4 in 1vs1

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Manganese binding site 3 out of 4 in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn301

b:51.5
occ:1.00
 OE2 C:GLU242 2.0 50.0 1.0
O C:HOH340 2.2 69.8 1.0
NE2 C:HIS216 2.6 48.9 1.0
OD1 C:ASP253 2.6 55.0 1.0
SG C:CYS46 2.7 38.7 1.0
O1 C:PEP304 2.9 54.1 1.0
CD C:GLU242 3.2 36.2 1.0
CE1 C:HIS216 3.2 42.2 1.0
CB C:CYS46 3.4 30.1 1.0
CD2 C:HIS216 3.7 32.7 1.0
CG C:ASP253 3.7 56.0 1.0
OE1 C:GLU242 3.8 38.0 1.0
C1 C:PEP304 3.8 60.1 1.0
NZ C:LYS75 4.0 35.8 1.0
CA C:CYS46 4.1 32.1 1.0
CG C:GLU242 4.3 35.0 1.0
NE2 C:GLN256 4.3 41.2 1.0
ND1 C:HIS216 4.3 43.6 1.0
CB C:ASP253 4.4 49.6 1.0
O2' C:PEP304 4.5 41.3 1.0
OD2 C:ASP253 4.5 47.1 1.0
NH2 C:ARG70 4.5 29.3 1.0
CG C:HIS216 4.6 37.0 1.0
C2 C:PEP304 4.8 58.9 1.0
C3 C:PEP304 4.8 54.8 1.0
CE C:LYS75 4.8 38.8 1.0
C C:CYS46 4.8 32.5 1.0
NH1 C:ARG70 4.9 34.8 1.0
O C:CYS46 4.9 33.0 1.0

Manganese binding site 4 out of 4 in 1vs1

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Manganese binding site 4 out of 4 in the Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7- Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn301

b:45.6
occ:1.00
 OE2 D:GLU242 1.9 44.3 1.0
OD2 D:ASP253 2.3 49.6 1.0
SG D:CYS46 2.5 34.0 1.0
O D:HOH306 2.6 63.9 1.0
NE2 D:HIS216 2.6 48.9 1.0
O1 D:PEP305 3.0 50.7 1.0
CD D:GLU242 3.0 36.4 1.0
CB D:CYS46 3.3 30.2 1.0
CE1 D:HIS216 3.3 36.7 1.0
CG D:ASP253 3.4 57.0 1.0
OE1 D:GLU242 3.5 36.6 1.0
CD2 D:HIS216 3.6 35.2 1.0
C1 D:PEP305 4.0 52.7 1.0
CA D:CYS46 4.1 31.9 1.0
CB D:ASP253 4.1 49.7 1.0
NE2 D:GLN256 4.1 43.4 1.0
CG D:GLU242 4.3 34.5 1.0
OD1 D:ASP253 4.3 56.9 1.0
NZ D:LYS75 4.4 31.1 1.0
NH2 D:ARG70 4.4 26.9 1.0
ND1 D:HIS216 4.4 41.1 1.0
C3 D:PEP305 4.5 40.8 1.0
CG D:HIS216 4.6 37.4 1.0
O2' D:PEP305 4.8 52.4 1.0
C2 D:PEP305 4.9 48.2 1.0
C D:CYS46 4.9 32.3 1.0

Reference:

I.A.Shumilin, L.Zhou, J.Wu, R.W.Woodard, R.Bauerle, R.H.Kretsinger. Crystal Structure of 3-Deoxy-D-Arabino-Heptulosonate-7-Phosphate Synthase (Dahp Synthase) From Aeropyrum Pernix in Complex with MN2+ and Pep To Be Published.
Page generated: Sat Aug 16 09:18:20 2025

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