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Magnesium in PDB 7lbd: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group, PDB code: 7lbd was solved by S.Saran, M.M.Yazdi, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.94 / 1.99
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.12, 232.14, 201.81, 90, 90, 90
R / Rfree (%) 19.1 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group (pdb code 7lbd). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group, PDB code: 7lbd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7lbd

Go back to Magnesium Binding Sites List in 7lbd
Magnesium binding site 1 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group


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, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:40.9
occ:1.00
 OD2 A:ASP227 2.2 35.0 1.0
CG A:ASP227 3.2 35.9 1.0
OD1 A:ASP227 3.5 35.8 1.0
O A:HOH475 4.3 37.4 1.0
CB A:ASP227 4.4 33.8 1.0
O A:HOH508 4.8 36.1 1.0

Magnesium binding site 2 out of 6 in 7lbd

Go back to Magnesium Binding Sites List in 7lbd
Magnesium binding site 2 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group


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, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:41.0
occ:1.00
 O A:HOH518 1.9 39.9 1.0
O A:HOH451 2.3 29.3 1.0
O A:HOH422 2.3 34.0 1.0
NZ A:LYS76 3.7 58.1 1.0
CE A:LYS76 3.8 55.9 1.0
OD1 A:ASP102 4.1 35.7 1.0
O A:THR73 4.3 37.7 1.0
OD2 A:ASP102 4.4 32.2 1.0
O A:HOH435 4.4 36.7 1.0
O A:VAL75 4.4 28.1 1.0
CD A:LYS76 4.6 48.7 1.0
CG A:ASP102 4.6 33.8 1.0
O A:CYS70 4.8 35.6 1.0

Magnesium binding site 3 out of 6 in 7lbd

Go back to Magnesium Binding Sites List in 7lbd
Magnesium binding site 3 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group


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, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:53.6
occ:1.00
 OD2 B:ASP177 3.2 28.3 1.0
O B:HOH491 3.4 39.3 1.0
OD1 B:ASP177 3.9 26.1 1.0
CG B:ASP177 4.0 24.4 1.0
OD1 B:ASP150 4.0 38.7 1.0
OD2 B:ASP150 4.1 39.8 1.0
CG B:ASP150 4.2 37.9 1.0
CB B:THR149 4.3 25.6 1.0
CG2 B:THR149 4.5 23.2 1.0
O B:HOH405 4.8 35.9 1.0
O A:HOH472 5.0 62.0 1.0
N B:ASP150 5.0 27.7 1.0

Magnesium binding site 4 out of 6 in 7lbd

Go back to Magnesium Binding Sites List in 7lbd
Magnesium binding site 4 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group


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, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:48.0
occ:1.00
 CG1 B:ILE7 4.1 28.3 1.0
CD1 B:ILE7 4.2 26.9 1.0
CA B:GLY8 4.3 23.9 1.0
CD1 B:LEU226 4.4 33.5 1.0
N B:GLY8 4.6 28.2 1.0
OD2 B:ASP40 4.7 30.6 1.0
C B:ILE7 4.8 31.5 1.0
NE2 B:HIS223 4.9 33.9 1.0
CG B:ASP40 4.9 31.8 1.0
O B:ILE7 4.9 31.1 1.0

Magnesium binding site 5 out of 6 in 7lbd

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Magnesium binding site 5 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group


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, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:66.6
occ:1.00
 O C:HOH517 2.0 63.9 1.0
O C:HOH495 2.4 57.2 1.0
OD1 C:ASP177 3.1 29.4 1.0
O D:HOH513 3.2 44.7 1.0
OD2 C:ASP177 3.4 29.0 1.0
CG C:ASP177 3.6 25.4 1.0
CE1 C:HIS181 3.7 28.7 1.0
ND1 C:HIS181 4.1 27.5 1.0
NE2 C:HIS181 4.2 27.4 1.0
O D:HOH473 4.2 42.2 1.0
CE2 D:TYR241 4.5 27.9 1.0
OD1 C:ASP150 4.6 37.7 1.0
CG C:HIS181 4.8 28.1 1.0
CD2 C:HIS181 4.8 27.9 1.0
CG2 C:THR149 4.8 30.7 1.0

Magnesium binding site 6 out of 6 in 7lbd

Go back to Magnesium Binding Sites List in 7lbd
Magnesium binding site 6 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group


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, H59K Mutant with Pyruvate Bound in the Active Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:59.5
occ:1.00
 CD1 F:LEU226 4.2 41.9 1.0
CA F:GLY8 4.7 33.0 1.0
OD1 F:ASP40 4.7 39.4 1.0
OD2 F:ASP40 4.7 38.3 1.0
CG F:ASP40 4.8 38.3 1.0
CG1 F:ILE7 4.8 41.1 1.0
CD1 F:ILE7 4.9 42.4 1.0

Reference:

M.M.Yazdi, S.Saran, D.A.R.Sanders, D.R.J.Palmer. Reversing the Roles of A Crucial Hydrogen-Bonding Pair: A Lysine-Insensitive Mutant of Campylobacter Jejuni Dihydrodipicolinate Synthase, H59K, Binds Histidine in Its Allosteric Site To Be Published.
Page generated: Wed Oct 2 23:19:32 2024

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