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Magnesium in PDB 7kpc: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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, E88Q 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, E88Q Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kpc 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) 43.70 / 1.76
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.35, 231.61, 199.85, 90, 90, 90
R / Rfree (%) 14.2 / 16.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 14;

Binding sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site (pdb code 7kpc). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 14 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kpc:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 7kpc

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Magnesium binding site 1 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg302

b:23.2
occ:1.00
 O A:HOH470 1.9 30.4 1.0
OD2 A:ASP227 2.0 26.3 1.0
O A:HOH437 2.1 25.2 1.0
CG A:ASP227 3.0 28.6 1.0
OD1 A:ASP227 3.3 30.5 1.0
O A:HOH442 4.1 20.3 1.0
O A:HOH491 4.2 34.6 1.0
CB A:ASP227 4.3 19.8 1.0
O A:HOH576 4.5 28.1 1.0

Magnesium binding site 2 out of 14 in 7kpc

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Magnesium binding site 2 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg303

b:15.5
occ:1.00
 O A:HOH427 3.1 26.1 1.0
N A:VAL107 3.2 16.1 1.0
N A:GLY82 3.2 21.6 1.0
O D:HOH405 3.4 27.8 1.0
O A:LEU105 3.6 20.5 1.0
CA A:GLY82 3.6 20.9 1.0
CB A:VAL107 3.7 16.1 1.0
N A:ALA81 3.8 17.2 1.0
CA A:SER106 3.8 15.7 1.0
C A:LEU105 3.9 17.5 1.0
CG1 A:VAL107 3.9 18.0 1.0
C A:SER106 4.0 16.5 1.0
N A:SER106 4.0 15.0 1.0
CA A:VAL107 4.1 14.9 1.0
CA A:GLY80 4.2 18.3 1.0
CG A:LEU105 4.2 18.8 1.0
CD2 A:LEU105 4.3 16.6 1.0
C A:GLY80 4.3 19.0 1.0
CD2 A:TYR137 4.4 19.1 1.0
C A:ALA81 4.4 21.4 1.0
CB A:LEU105 4.4 16.2 1.0
O A:HOH453 4.6 31.9 1.0
CA A:ALA81 4.7 16.8 1.0
C A:GLY82 4.7 21.2 1.0
CA A:LEU105 4.8 14.4 1.0
CE2 A:TYR137 4.9 21.9 1.0
O A:VAL45 4.9 21.9 1.0

Magnesium binding site 3 out of 14 in 7kpc

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Magnesium binding site 3 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg304

b:38.3
occ:1.00
 OE2 A:GLU58 2.7 29.6 1.0
N A:VAL22 2.8 24.5 1.0
O A:HOH569 3.1 31.3 1.0
CB A:LYS21 3.5 31.2 1.0
O A:HOH490 3.5 39.2 1.0
CD A:GLU58 3.5 31.6 1.0
CA A:LYS21 3.5 27.6 1.0
CG A:GLU58 3.6 24.9 1.0
C A:LYS21 3.7 24.5 1.0
CB A:VAL22 3.7 24.9 1.0
CG2 A:VAL22 3.8 22.1 1.0
CA A:VAL22 3.8 23.3 1.0
O A:HOH448 4.1 41.5 1.0
CG A:LYS21 4.2 33.7 1.0
NH2 A:ARG272 4.2 28.6 1.0
O A:VAL22 4.3 25.1 1.0
C A:VAL22 4.6 25.0 1.0
OE1 A:GLU58 4.7 25.1 1.0
CB A:GLU58 4.8 21.2 1.0
O A:HOH480 4.8 29.7 1.0
O A:LYS21 4.9 23.7 1.0
O A:HOH530 4.9 39.2 1.0
N A:LYS21 5.0 29.5 1.0

Magnesium binding site 4 out of 14 in 7kpc

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Magnesium binding site 4 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg305

b:71.8
occ:1.00
 O B:HOH593 3.1 22.2 1.0
O A:HOH594 3.1 47.3 1.0
O B:HOH590 3.2 47.9 1.0
O A:HOH515 3.6 47.1 1.0
CA A:GLY170 3.8 24.9 1.0
CB B:ASP173 3.8 18.2 1.0
O B:HOH433 3.8 22.1 1.0
O A:HOH402 3.9 35.0 1.0
CG B:ASP173 4.4 20.4 1.0
OD2 B:ASP173 4.5 21.1 1.0
OD1 B:ASN171 4.5 22.2 1.0
OE2 A:GLU191 4.6 31.8 1.0
O A:GLY170 4.7 30.7 1.0
C A:GLY170 4.7 28.2 1.0
OE1 A:GLU191 4.8 22.1 1.0
N A:GLY170 4.8 20.1 1.0
CD A:GLU191 4.9 31.6 1.0

Magnesium binding site 5 out of 14 in 7kpc

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Magnesium binding site 5 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg306

b:37.0
occ:1.00
 O A:HOH430 2.9 40.4 1.0
N A:LYS231 2.9 21.1 1.0
N A:TYR230 3.1 21.4 1.0
CB A:LYS231 3.6 27.1 1.0
C A:TYR230 3.7 21.0 1.0
CA A:TYR230 3.7 21.3 1.0
C A:ASN229 3.8 19.7 1.0
CA A:LYS231 3.8 23.2 1.0
C2 A:EDO312 3.9 61.4 1.0
O A:GLU228 4.0 24.2 1.0
CA A:ASN229 4.0 18.6 1.0
CB A:TYR230 4.0 22.6 1.0
OE2 A:GLU232 4.2 32.4 1.0
OE1 B:GLU228 4.3 48.5 1.0
O1 B:PEG311 4.4 63.9 1.0
O A:ASN229 4.6 20.4 1.0
C1 B:PEG311 4.8 60.5 1.0
O2 A:EDO312 4.8 63.3 1.0
C A:GLU228 4.8 21.8 1.0
N A:GLU232 4.9 19.5 1.0
O A:TYR230 4.9 23.7 1.0
N A:ASN229 4.9 18.9 1.0
C A:LYS231 5.0 23.6 1.0

Magnesium binding site 6 out of 14 in 7kpc

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Magnesium binding site 6 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg307

b:72.8
occ:1.00
 CB A:PRO140 3.7 22.1 1.0
OE1 A:GLU146 3.8 27.3 0.6
OE2 A:GLU146 3.8 30.6 0.5
O A:HOH449 4.0 46.1 1.0
O A:HOH605 4.0 49.7 1.0
CG A:PRO140 4.0 30.3 1.0
CB A:GLU146 4.3 24.0 0.5
CD A:GLU146 4.3 26.1 0.6
CB A:GLU146 4.3 24.4 0.6
CD A:GLU146 4.5 31.6 0.5
O A:HOH410 4.5 31.0 1.0
CG A:GLU146 4.8 30.5 0.6
OE2 A:GLU146 4.9 15.4 0.6
CG A:GLU146 5.0 30.6 0.5

Magnesium binding site 7 out of 14 in 7kpc

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Magnesium binding site 7 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg302

b:22.9
occ:1.00
 O B:HOH494 2.1 27.1 1.0
OD2 B:ASP227 2.1 27.6 1.0
O B:HOH509 2.1 27.6 1.0
CG B:ASP227 3.0 29.3 1.0
OD1 B:ASP227 3.4 31.0 1.0
O B:HOH454 4.0 21.0 1.0
O B:HOH624 4.3 30.4 1.0
CB B:ASP227 4.3 23.2 1.0
O B:HOH555 4.4 26.6 1.0

Magnesium binding site 8 out of 14 in 7kpc

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Magnesium binding site 8 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg303

b:16.7
occ:1.00
 O B:HOH409 3.2 29.1 1.0
N B:VAL107 3.2 17.2 1.0
N B:GLY82 3.2 18.9 1.0
O C:HOH409 3.5 29.9 1.0
O B:LEU105 3.5 18.1 1.0
CA B:GLY82 3.6 18.5 1.0
CB B:VAL107 3.7 14.4 1.0
N B:ALA81 3.8 17.5 1.0
CA B:SER106 3.8 17.5 1.0
C B:LEU105 3.9 18.9 1.0
N B:SER106 4.0 15.8 1.0
C B:SER106 4.0 18.1 1.0
CG1 B:VAL107 4.0 17.2 1.0
CA B:VAL107 4.0 16.2 1.0
CG B:LEU105 4.1 16.5 1.0
CA B:GLY80 4.2 18.2 1.0
CD2 B:LEU105 4.2 18.9 1.0
CD2 B:TYR137 4.3 18.2 1.0
C B:ALA81 4.4 17.0 1.0
C B:GLY80 4.4 16.2 1.0
CB B:LEU105 4.4 16.8 1.0
O B:HOH476 4.6 30.4 1.0
CA B:ALA81 4.7 17.7 1.0
C B:GLY82 4.7 18.7 1.0
CA B:LEU105 4.8 17.1 1.0
CE2 B:TYR137 4.8 20.8 1.0
O B:VAL45 5.0 18.1 1.0

Magnesium binding site 9 out of 14 in 7kpc

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Magnesium binding site 9 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg304

b:73.8
occ:1.00
 O C:HOH638 3.0 50.9 1.0
O B:HOH655 3.5 47.0 1.0
CA B:HIS87 3.9 21.8 1.0
N B:HIS87 3.9 18.5 1.0
CG2 B:THR86 4.0 18.0 1.0
CB B:HIS87 4.2 24.9 1.0
C B:THR86 4.2 19.9 1.0
CB B:THR86 4.3 20.3 1.0
O B:THR86 4.4 20.4 1.0
O C:HOH471 4.6 23.8 1.0
CG2 B:VAL90 4.7 20.2 1.0
O C:HOH561 4.8 26.6 1.0
CD1 C:LEU273 4.9 25.3 1.0
CA B:THR86 4.9 19.8 1.0

Magnesium binding site 10 out of 14 in 7kpc

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Magnesium binding site 10 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88Q 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, E88Q 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:Mg302

b:16.3
occ:1.00
 O C:HOH413 3.1 29.9 1.0
N C:VAL107 3.2 16.6 1.0
N C:GLY82 3.3 18.6 1.0
O B:HOH406 3.4 27.2 1.0
O C:LEU105 3.6 18.5 1.0
CA C:GLY82 3.6 20.1 1.0
CB C:VAL107 3.8 17.3 1.0
N C:ALA81 3.8 17.3 1.0
CA C:SER106 3.8 16.6 1.0
C C:LEU105 3.9 16.8 1.0
CG1 C:VAL107 3.9 17.7 1.0
N C:SER106 4.0 16.8 1.0
C C:SER106 4.0 17.9 1.0
CA C:VAL107 4.1 18.1 1.0
CG C:LEU105 4.1 17.5 1.0
CA C:GLY80 4.2 21.2 1.0
CD2 C:LEU105 4.2 17.1 1.0
CD2 C:TYR137 4.3 19.5 1.0
C C:GLY80 4.4 18.4 1.0
C C:ALA81 4.4 20.0 1.0
CB C:LEU105 4.4 18.2 1.0
O C:HOH475 4.6 32.3 1.0
CA C:ALA81 4.7 20.1 1.0
C C:GLY82 4.7 19.0 1.0
CA C:LEU105 4.8 18.1 1.0
CE2 C:TYR137 4.8 19.5 1.0
O C:VAL45 4.9 21.3 1.0

Reference:

S.Saran, M.Majdi Yazdi, I.Chung, D.A.R.Sanders. The Allosteric Site Residue, E88 Interacts with the Inhibitors to Transmit the Allosteric Inhibition Signals in Cj.Dhdps By Forming A Hydrogen Bond. To Be Published.
Page generated: Wed Oct 2 22:33:20 2024

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