Magnesium in PDB 7kly: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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, H59N 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, H59N 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, H59N Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kly was solved by S.Saran, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.14 / 1.67
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.52, 231.49, 201.25, 90, 90, 90
R / Rfree (%) 16.3 / 19.2

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 L-Lysine Bound at the Allosteric Site (pdb code 7kly). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kly:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 7kly

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Magnesium binding site 1 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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, H59N 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
A:Mg310

b:47.0
occ:1.00
 N A:GLU267 2.9 26.5 1.0
OG A:SER26 2.9 27.8 1.0
CB A:SER26 3.3 25.4 1.0
O A:HOH443 3.4 40.8 1.0
CA A:ILE266 3.5 28.8 1.0
OD2 A:ASP23 3.6 29.2 1.0
CG A:GLU267 3.6 56.9 1.0
CB A:GLU267 3.7 36.2 1.0
CB A:ILE266 3.7 25.8 1.0
C A:ILE266 3.7 27.3 1.0
CA A:GLU267 3.9 31.4 1.0
O A:HOH419 4.0 34.1 1.0
CB A:PRO16 4.2 23.8 1.0
CG2 A:ILE266 4.2 27.2 1.0
CD A:GLU267 4.3 70.5 1.0
CG A:ASP23 4.4 29.2 1.0
N A:SER268 4.6 33.3 1.0
OE1 A:GLU267 4.6 65.5 1.0
CA A:SER26 4.7 27.2 1.0
CB A:ASP23 4.8 27.2 1.0
O A:LEU265 4.8 27.5 1.0
C A:GLU267 4.8 29.6 1.0
N A:ILE266 4.9 26.1 1.0
CG A:PRO16 4.9 24.1 1.0
O A:ILE266 4.9 25.6 1.0
OE2 A:GLU267 5.0 61.5 1.0

Magnesium binding site 2 out of 10 in 7kly

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Magnesium binding site 2 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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, H59N 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
A:Mg311

b:52.9
occ:1.00
 OD2 A:ASP158 2.9 22.4 1.0
O A:HOH497 3.0 30.9 1.0
CG A:ASP158 3.7 22.1 1.0
OD1 A:ASP158 3.7 24.6 1.0
C1 A:PG4302 3.8 44.9 1.0
CE A:LYS154 3.9 42.5 1.0
CG A:LYS154 3.9 23.8 1.0
O1 A:PG4302 3.9 50.1 1.0
CD A:LYS154 4.1 24.3 1.0
CB A:LYS154 4.2 19.2 1.0
NZ A:LYS154 4.7 40.5 1.0
OH A:TYR120 4.7 24.9 1.0
CA A:LYS154 4.9 18.3 1.0

Magnesium binding site 3 out of 10 in 7kly

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Magnesium binding site 3 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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, H59N 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:Mg308

b:53.5
occ:1.00
 N B:SER277 2.8 19.3 1.0
O C:HOH426 3.1 29.1 1.0
OG B:SER277 3.2 36.3 1.0
CB B:SER277 3.4 25.1 1.0
O B:HOH499 3.5 25.2 1.0
CB B:CYS276 3.5 15.7 1.0
CA B:CYS276 3.6 15.6 1.0
O C:HOH406 3.6 37.5 1.0
C B:CYS276 3.6 21.1 1.0
CA B:SER277 3.7 23.0 1.0
O B:HOH491 3.9 23.0 1.0
CD1 B:PHE271 4.7 19.5 1.0
O B:CYS276 4.8 21.8 1.0
C B:SER277 4.9 23.4 1.0
SG B:CYS276 5.0 20.9 1.0
N B:CYS276 5.0 19.5 1.0

Magnesium binding site 4 out of 10 in 7kly

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Magnesium binding site 4 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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, H59N 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:Mg309

b:20.6
occ:1.00
 O B:HOH469 1.9 27.1 1.0
O B:HOH452 2.1 19.6 1.0
O B:HOH471 3.8 22.0 1.0
OD1 B:ASP102 4.1 24.0 1.0
O B:THR73 4.1 22.3 1.0
O B:HOH472 4.1 21.8 1.0
O B:HOH543 4.2 37.5 1.0
O B:VAL75 4.3 19.1 1.0
OD2 B:ASP102 4.3 18.3 1.0
O B:CYS70 4.6 18.1 1.0
O B:HOH451 4.7 25.9 1.0
CG B:ASP102 4.7 19.0 1.0

Magnesium binding site 5 out of 10 in 7kly

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Magnesium binding site 5 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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, H59N 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:Mg310

b:19.8
occ:1.00
 O B:HOH422 1.9 35.5 1.0
O B:HOH508 2.0 26.8 1.0
OD2 B:ASP227 2.0 20.1 1.0
O B:HOH482 2.2 37.9 1.0
CG B:ASP227 3.0 24.5 1.0
OD1 B:ASP227 3.3 26.2 1.0
O B:HOH453 4.1 21.3 1.0
O B:HOH555 4.3 32.0 1.0
CB B:ASP227 4.3 16.6 1.0
O B:HOH533 4.4 25.0 1.0

Magnesium binding site 6 out of 10 in 7kly

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Magnesium binding site 6 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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, H59N 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:Mg311

b:51.8
occ:1.00
 O C:HOH562 3.9 40.8 1.0
N B:HIS87 4.1 16.9 1.0
CA B:HIS87 4.1 21.2 1.0
CG2 B:THR86 4.1 19.5 1.0
CB B:HIS87 4.3 18.9 1.0
O C:HOH440 4.3 20.9 1.0
C B:THR86 4.3 21.2 1.0
CB B:THR86 4.4 17.9 1.0
O B:THR86 4.6 19.5 1.0
O C:HOH509 4.7 24.4 1.0
CG2 B:VAL90 4.9 18.2 1.0

Magnesium binding site 7 out of 10 in 7kly

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Magnesium binding site 7 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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, H59N 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:Mg312

b:58.3
occ:1.00
 OD1 B:ASP102 3.9 24.0 1.0
O B:HOH415 4.1 24.2 1.0
O B:ALA101 4.3 22.6 1.0
O B:GLY100 4.3 21.8 1.0
CG B:ASP102 4.8 19.0 1.0
CA B:ASP102 4.8 20.1 1.0
C B:GLY100 4.9 21.7 1.0
C B:ALA101 4.9 16.2 1.0

Magnesium binding site 8 out of 10 in 7kly

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Magnesium binding site 8 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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 8 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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:Mg313

b:51.2
occ:1.00
 O B:HOH433 2.0 38.6 1.0
O B:HOH505 2.2 40.4 1.0
OD1 B:ASP150 4.1 33.4 1.0
O A:HOH522 4.2 40.2 1.0
OD1 B:ASP177 4.2 21.7 1.0
OD2 B:ASP177 4.2 23.0 1.0
O B:HOH540 4.3 24.5 1.0
OD2 B:ASP150 4.3 36.9 1.0
CG B:ASP150 4.5 32.4 1.0
CG B:ASP177 4.7 18.7 1.0

Magnesium binding site 9 out of 10 in 7kly

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Magnesium binding site 9 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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 9 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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:Mg316

b:53.8
occ:1.00
 O C:HOH436 2.0 43.8 1.0
O C:HOH448 2.0 40.9 1.0
O C:HOH518 3.2 45.6 1.0
OD1 C:ASP150 4.2 32.2 1.0
OD2 C:ASP150 4.3 32.6 1.0
O C:HOH529 4.3 26.0 1.0
O D:HOH515 4.3 45.0 1.0
OD2 C:ASP177 4.3 23.6 1.0
OD1 C:ASP177 4.4 23.2 1.0
CG C:ASP150 4.6 29.7 1.0
CG C:ASP177 4.8 19.1 1.0

Magnesium binding site 10 out of 10 in 7kly

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Magnesium binding site 10 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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 10 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59N 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:Mg313

b:33.5
occ:1.00
 O D:HOH459 1.9 30.1 1.0
OD1 D:ASP40 2.0 22.6 1.0
O D:HOH467 2.1 30.4 1.0
O D:HOH528 2.2 31.8 1.0
CG D:ASP40 3.2 26.6 1.0
CE D:LYS74 3.7 46.5 1.0
OD2 D:ASP40 4.0 17.8 1.0
CB D:ASP40 4.2 19.1 1.0
CD D:LYS74 4.2 44.3 1.0
NE2 D:HIS223 4.3 19.9 1.0
O D:HOH477 4.3 35.4 1.0
O D:GLY38 4.3 19.9 1.0
CA D:ASP40 4.4 17.2 1.0
CE1 D:HIS223 4.4 16.3 1.0
CG D:LYS74 4.8 42.2 1.0
O D:ILE39 4.8 23.3 1.0
NZ D:LYS74 4.8 28.8 1.0
N D:ASP40 4.9 18.1 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: Fri Nov 5 15:14:52 2021

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