Magnesium in PDB 7km1: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site, PDB code: 7km1 was solved by S.Saran, M.Majdi Yazdi, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.56 / 1.84
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.01, 230.45, 200.64, 90, 90, 90
R / Rfree (%) 18.1 / 21.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site (pdb code 7km1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site, PDB code: 7km1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7km1

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Magnesium binding site 1 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:52.0
occ:1.00
 O A:HOH468 2.1 43.3 1.0
O A:HOH435 2.1 40.4 1.0
O D:HOH513 2.2 48.5 1.0
O A:HOH478 2.2 48.6 1.0
O A:HOH428 2.2 47.5 1.0
OD1 A:ASP150 4.1 35.8 1.0
O A:HOH510 4.1 30.4 1.0
O D:HOH421 4.2 37.6 1.0
OD2 A:ASP150 4.2 40.9 1.0
OD2 A:ASP177 4.2 29.1 1.0
OD1 A:ASP177 4.3 31.3 1.0
CG A:ASP150 4.5 37.6 1.0
CG A:ASP177 4.7 27.9 1.0

Magnesium binding site 2 out of 7 in 7km1

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Magnesium binding site 2 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:61.2
occ:1.00
 OD1 A:ASP150 3.5 35.8 1.0
CG2 A:ILE153 4.0 32.5 1.0
O A:ASP150 4.2 25.5 1.0
CA A:ASP150 4.2 27.2 1.0
CG A:ASP150 4.2 37.6 1.0
CB A:ILE153 4.3 26.1 1.0
CB A:ASP150 4.3 26.7 1.0
NH1 A:ARG157 4.4 33.1 1.0
CG A:LYS154 4.5 36.9 1.0
C A:ASP150 4.7 24.8 1.0
CD1 A:ILE153 4.8 27.0 1.0
N A:LYS154 5.0 26.4 1.0

Magnesium binding site 3 out of 7 in 7km1

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Magnesium binding site 3 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg308

b:49.2
occ:1.00
 O B:HOH449 2.0 34.4 1.0
O C:HOH436 2.1 37.8 1.0
O2 C:EDO305 4.1 42.2 1.0
OD1 B:ASP150 4.1 35.6 1.0
C1 C:EDO305 4.1 43.8 1.0
OD2 B:ASP150 4.1 35.7 1.0
O B:HOH505 4.2 30.8 1.0
OD2 B:ASP177 4.3 29.2 1.0
OD1 B:ASP177 4.3 28.8 1.0
CG B:ASP150 4.5 37.5 1.0
O1 C:EDO305 4.7 60.0 1.0
C2 C:EDO305 4.7 49.4 1.0
CG B:ASP177 4.7 32.0 1.0

Magnesium binding site 4 out of 7 in 7km1

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Magnesium binding site 4 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg309

b:30.5
occ:1.00
 O B:HOH446 2.0 41.8 1.0
OD2 B:ASP227 2.1 29.8 1.0
CG B:ASP227 3.0 36.1 1.0
OD1 B:ASP227 3.3 31.6 1.0
O B:HOH422 3.9 29.2 1.0
O B:HOH490 4.3 34.5 1.0
CB B:ASP227 4.4 29.2 1.0
O B:HOH506 4.4 36.6 1.0

Magnesium binding site 5 out of 7 in 7km1

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Magnesium binding site 5 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg309

b:30.0
occ:1.00
 O C:HOH458 2.0 35.5 1.0
OD2 C:ASP227 2.1 29.7 1.0
O C:HOH431 2.4 44.2 1.0
CG C:ASP227 3.0 32.4 1.0
OD1 C:ASP227 3.2 36.2 1.0
O C:HOH419 4.0 30.6 1.0
O C:HOH490 4.2 35.8 1.0
CB C:ASP227 4.3 28.7 1.0
O C:HOH508 4.5 31.9 1.0

Magnesium binding site 6 out of 7 in 7km1

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Magnesium binding site 6 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg305

b:52.0
occ:1.00
 O D:HOH440 2.0 40.2 1.0
O D:HOH451 2.3 38.7 1.0
OD1 D:ASP150 3.8 40.0 1.0
O A:HOH504 4.0 39.1 1.0
OD2 D:ASP150 4.1 46.0 1.0
OD2 D:ASP177 4.2 28.3 1.0
OD1 D:ASP177 4.3 29.0 1.0
O D:HOH486 4.3 33.7 1.0
CG D:ASP150 4.3 38.4 1.0
CG D:ASP177 4.7 30.9 1.0

Magnesium binding site 7 out of 7 in 7km1

Go back to Magnesium Binding Sites List in 7km1
Magnesium binding site 7 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg306

b:35.7
occ:1.00
 OD1 D:ASP40 2.0 26.9 1.0
O D:HOH502 2.1 36.0 1.0
O D:HOH477 2.3 33.8 1.0
CG D:ASP40 3.3 30.1 1.0
OD2 D:ASP40 4.1 25.9 1.0
CB D:ASP40 4.2 27.7 1.0
O D:HOH472 4.2 44.9 1.0
OXT D:ACT307 4.3 47.4 1.0
NE2 D:HIS223 4.3 28.5 1.0
O D:GLY38 4.3 26.8 1.0
CA D:ASP40 4.4 27.2 1.0
O D:ACT307 4.4 46.7 1.0
CE1 D:HIS223 4.5 26.1 1.0
O D:ILE39 4.7 28.9 1.0
C D:ACT307 4.8 48.3 1.0
N D:ASP40 4.9 22.9 1.0
C D:ILE39 5.0 24.8 1.0

Reference:

S.Saran, Y.Skovpen, M.Majdi Yazdi, D.R.J.Palmer, D.A.R.Sanders. H59 Plays the Most Vital Role in the Transmission of the Allosteric Inhibition Signals in Cj.Dhdps Enzyme To Be Published.
Page generated: Wed Oct 2 22:26:52 2024

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