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Magnesium in PDB 7kg9: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kg9 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) 49.04 / 2.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.83, 225.17, 200.7, 90, 90, 90
R / Rfree (%) 27.5 / 33.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site (pdb code 7kg9). 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kg9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7kg9

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Magnesium binding site 1 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:20.1
occ:1.00
 O B:HOH427 1.9 20.8 1.0
O B:HOH420 2.3 27.5 1.0
OD2 B:ASP102 3.8 21.8 1.0
O B:VAL75 4.1 27.0 1.0
O B:HOH405 4.2 19.8 1.0
OD1 B:ASP102 4.3 21.0 1.0
O B:THR73 4.3 20.2 1.0
CG B:ASP102 4.5 21.9 1.0
O B:CYS70 4.5 24.6 1.0

Magnesium binding site 2 out of 7 in 7kg9

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Magnesium binding site 2 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:26.9
occ:1.00
 OD2 B:ASP227 2.6 25.5 1.0
CG B:ASP227 3.5 26.1 1.0
OD1 B:ASP227 4.0 26.8 1.0
O B:HOH439 4.2 20.0 1.0
CB B:ASP227 4.7 21.6 1.0

Magnesium binding site 3 out of 7 in 7kg9

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Magnesium binding site 3 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:32.1
occ:1.00
 O C:HOH508 2.0 24.3 1.0
O C:HOH418 2.4 23.0 1.0
OD2 C:ASP177 3.2 17.3 1.0
OD1 C:ASP177 3.9 22.6 1.0
CG C:ASP177 3.9 18.0 1.0
O C:HOH468 4.0 25.9 1.0
OD1 C:ASP150 4.2 31.4 1.0
O E:HOH443 4.5 21.7 1.0
O C:HOH404 4.7 23.0 1.0
O E:HOH526 4.8 18.3 1.0
CB C:THR149 4.9 18.3 1.0
CG C:ASP150 4.9 25.2 1.0
OD2 C:ASP150 4.9 31.2 1.0

Magnesium binding site 4 out of 7 in 7kg9

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Magnesium binding site 4 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg304

b:24.4
occ:1.00
 O D:LEU105 2.9 20.9 1.0
N D:VAL107 2.9 21.5 1.0
N D:GLY82 3.2 23.3 1.0
O D:HOH469 3.2 19.4 1.0
CA D:GLY82 3.3 22.4 1.0
CB D:VAL107 3.5 26.2 1.0
C D:LEU105 3.5 21.3 1.0
CG1 D:VAL107 3.6 20.5 1.0
CA D:SER106 3.6 23.4 1.0
C D:SER106 3.7 19.2 1.0
CA D:VAL107 3.7 20.7 1.0
N D:SER106 3.8 19.6 1.0
N D:ALA81 4.0 14.3 1.0
C D:ALA81 4.3 18.0 1.0
CG D:LEU105 4.3 19.5 1.0
CD2 D:TYR137 4.4 25.6 1.0
C D:GLY82 4.5 23.2 1.0
CA D:GLY80 4.5 17.5 1.0
CB D:LEU105 4.6 17.6 1.0
C D:GLY80 4.6 18.0 1.0
CA D:LEU105 4.7 21.5 1.0
CD2 D:LEU105 4.7 20.2 1.0
O D:SER106 4.8 20.4 1.0
CA D:ALA81 4.8 16.6 1.0
CG2 D:VAL107 4.8 19.4 1.0
O D:GLY82 4.9 19.6 1.0

Magnesium binding site 5 out of 7 in 7kg9

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Magnesium binding site 5 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg305

b:39.5
occ:1.00
 O D:HOH428 2.4 21.9 1.0
O D:HOH539 2.9 26.6 1.0
O D:HOH519 3.0 28.1 1.0
OD1 D:ASP150 4.0 27.4 1.0
OD2 D:ASP177 4.4 19.0 1.0
OD2 D:ASP150 4.6 36.8 1.0
OD1 D:ASP177 4.6 25.0 1.0
CG D:ASP150 4.7 29.8 1.0
CG D:ASP177 5.0 21.7 1.0

Magnesium binding site 6 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 6 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg306

b:31.4
occ:1.00
 O F:HOH485 2.1 19.4 1.0
O F:HOH501 2.5 23.7 1.0
OD1 F:ASP150 2.7 34.0 1.0
O F:HOH492 2.9 22.4 1.0
CG F:ASP150 3.7 32.2 1.0
OD1 F:ASP177 3.9 29.1 1.0
OD2 F:ASP150 4.1 29.3 1.0
O F:HOH470 4.1 26.0 1.0
OD2 F:ASP177 4.2 20.8 1.0
NE2 F:HIS181 4.3 22.9 1.0
CE1 F:HIS181 4.3 19.6 1.0
ND1 F:HIS181 4.4 19.6 1.0
CD2 F:HIS181 4.4 28.0 1.0
CG F:HIS181 4.4 24.2 1.0
CG F:ASP177 4.5 21.1 1.0
CG2 F:THR149 4.6 19.7 1.0

Magnesium binding site 7 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 7 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg307

b:29.8
occ:1.00
 O F:HOH464 2.3 27.4 1.0
ND1 F:HIS223 2.9 31.7 1.0
OG F:SER219 3.2 29.4 1.0
CE1 F:HIS223 3.7 28.9 1.0
O F:SER219 3.8 21.4 1.0
CA F:ALA220 3.9 19.1 1.0
N F:ALA220 3.9 18.1 1.0
C F:SER219 3.9 18.4 1.0
CG F:HIS223 4.0 26.9 1.0
CB F:SER219 4.2 20.2 1.0
CB F:HIS223 4.2 23.6 1.0
CB F:ALA220 4.5 19.6 1.0
CA F:SER219 4.7 21.4 1.0
O F:GLY38 4.8 27.2 1.0
NE2 F:HIS223 4.9 28.1 1.0
CA F:GLY38 5.0 28.0 1.0

Reference:

M.Majdi Yazd, K.Reddy Annadi, S.Saran, A.Bhagwat, D.A.R.Sanders, D.R.J.Palmer. Fluorescence-Based Assay Development For Screening Novel Inhibitors of Dihydrodipicolinate Synthase From Campylobacter Jejuni To Be Published.
Page generated: Thu Aug 14 08:11:06 2025

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