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Magnesium in PDB 7kg2: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site:
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 and L-Histidine Bound at the Allosteric Site, PDB code: 7kg2 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) 49.63 / 1.89
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.78, 230.74, 202.2, 90, 90, 90
R / Rfree (%) 17 / 20.7

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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site (pdb code 7kg2). 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site, PDB code: 7kg2:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 14 in 7kg2

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Magnesium binding site 1 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg308

b:47.2
occ:1.00
 O A:HOH445 2.8 31.1 1.0
O A:HOH419 3.1 28.9 1.0
O A:HOH414 3.2 32.4 1.0
O A:THR73 3.6 26.0 1.0
O A:LYS74 4.1 28.6 1.0
CD A:LYS76 4.2 41.8 1.0
C A:LYS74 4.3 30.4 1.0
O A:VAL75 4.3 23.4 1.0
CE A:LYS76 4.5 49.2 1.0
CA A:LYS74 4.5 31.2 1.0
C A:THR73 4.7 23.4 1.0
OD1 A:ASP102 4.8 30.4 1.0
C A:VAL75 4.8 26.1 1.0
N A:VAL75 4.9 25.8 1.0

Magnesium binding site 2 out of 14 in 7kg2

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Magnesium binding site 2 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg309

b:57.0
occ:1.00
 CD1 A:LEU226 4.0 26.6 1.0
CG1 A:ILE7 4.2 22.3 1.0
CA A:GLY8 4.2 22.4 1.0
CD1 A:ILE7 4.4 26.1 1.0
N A:GLY8 4.5 23.0 1.0
OD2 A:ASP40 4.6 25.9 1.0
CG A:ASP40 4.7 30.5 1.0
C A:ILE7 4.8 25.7 1.0
O A:ILE7 4.8 23.0 1.0
OD1 A:ASP40 5.0 25.1 1.0

Magnesium binding site 3 out of 14 in 7kg2

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Magnesium binding site 3 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg310

b:33.2
occ:1.00
 O A:HOH475 2.0 39.5 1.0
OD2 A:ASP227 2.2 30.5 1.0
CG A:ASP227 3.1 32.8 1.0
OD1 A:ASP227 3.3 32.4 1.0
O A:HOH410 4.0 28.9 1.0
O A:HOH528 4.3 36.6 1.0
CB A:ASP227 4.4 24.4 1.0
O A:HOH522 4.7 36.3 1.0

Magnesium binding site 4 out of 14 in 7kg2

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Magnesium binding site 4 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg311

b:54.9
occ:1.00
 O C:GLY141 3.7 23.9 1.0
O2 A:EDO302 3.8 42.1 1.0
O C:PRO140 3.9 21.5 1.0
O A:PRO140 4.0 21.7 1.0
CA A:GLY144 4.0 21.1 1.0
C C:GLY141 4.2 26.6 1.0
O A:GLY141 4.3 22.8 1.0
CA C:GLY144 4.3 24.3 1.0
N A:GLY144 4.3 19.2 1.0
CA C:GLY141 4.3 21.3 1.0
N C:GLY144 4.6 23.9 1.0
C A:GLY141 4.7 26.0 1.0
CA A:GLY141 4.7 23.3 1.0
C C:PRO140 4.8 21.9 1.0
C A:PRO140 5.0 23.6 1.0

Magnesium binding site 5 out of 14 in 7kg2

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Magnesium binding site 5 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg312

b:56.9
occ:1.00
 O A:HOH454 2.6 37.5 1.0
OD2 A:ASP158 2.8 29.2 1.0
OD1 A:ASP158 3.3 33.1 1.0
CG A:ASP158 3.5 34.4 1.0
O4 A:PGE316 4.0 47.5 1.0
C6 A:PGE316 4.1 36.9 1.0
CG A:LYS154 4.4 34.5 1.0
OH A:TYR120 4.4 30.8 1.0
CD A:LYS154 4.6 36.7 1.0
CB A:LYS154 4.7 25.7 1.0
CE A:LYS154 4.8 37.7 1.0
CB A:ASP158 4.9 28.1 1.0

Magnesium binding site 6 out of 14 in 7kg2

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Magnesium binding site 6 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:28.1
occ:1.00
 O B:HOH445 2.1 32.9 1.0
OD2 B:ASP227 2.1 28.9 1.0
CG B:ASP227 3.0 32.9 1.0
OD1 B:ASP227 3.4 32.3 1.0
O B:HOH477 4.2 33.5 1.0
CB B:ASP227 4.4 23.3 1.0
O B:HOH500 4.7 35.9 1.0

Magnesium binding site 7 out of 14 in 7kg2

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Magnesium binding site 7 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg307

b:42.2
occ:1.00
 OD1 B:ASP102 2.6 30.2 1.0
O B:HOH440 2.9 28.3 1.0
O B:HOH409 3.1 34.0 1.0
CG B:ASP102 3.5 30.0 1.0
OD2 B:ASP102 3.7 25.7 1.0
O B:HOH406 4.1 34.1 1.0
O B:HOH470 4.5 31.7 1.0
CD B:LYS76 4.5 38.7 1.0
O B:HOH418 4.7 34.9 1.0
NZ B:LYS76 4.7 47.4 1.0
CE B:LYS76 4.8 44.4 1.0
CB B:ASP102 4.9 24.3 1.0

Magnesium binding site 8 out of 14 in 7kg2

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Magnesium binding site 8 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg307

b:52.4
occ:1.00
 OH C:TYR230 3.0 43.6 1.0
O C:SER200 3.3 22.9 1.0
N C:GLY202 3.9 21.9 1.0
O D:HOH526 4.1 38.0 1.0
CA C:GLY202 4.1 23.5 1.0
CZ C:TYR230 4.1 40.0 1.0
CD D:LYS234 4.2 23.2 1.0
C C:SER200 4.2 23.6 1.0
C C:ASN201 4.4 19.9 1.0
O C:LEU199 4.6 22.4 1.0
O C:HOH473 4.6 30.8 1.0
OH D:TYR196 4.6 26.3 1.0
CE2 C:TYR230 4.7 38.7 1.0
CE D:LYS234 4.8 25.5 1.0
CA C:SER200 4.9 25.2 1.0
N C:ASN201 4.9 23.1 1.0
CA C:ASN201 4.9 19.6 1.0

Magnesium binding site 9 out of 14 in 7kg2

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Magnesium binding site 9 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg310

b:41.1
occ:1.00
 OD1 D:ASP40 2.0 24.0 1.0
O D:HOH508 2.2 36.4 1.0
O D:HOH504 2.3 30.8 1.0
CG D:ASP40 3.3 29.1 1.0
O D:HOH516 3.9 42.9 1.0
O D:HOH492 4.0 43.4 1.0
OD2 D:ASP40 4.1 24.9 1.0
CB D:ASP40 4.1 26.6 1.0
NE2 D:HIS223 4.3 25.5 1.0
CA D:ASP40 4.3 26.0 1.0
C2 D:PG4317 4.4 48.0 1.0
O D:GLY38 4.4 21.9 1.0
CE1 D:HIS223 4.6 22.6 1.0
O D:ILE39 4.7 27.8 1.0
N D:ASP40 4.8 21.4 1.0
C D:ILE39 5.0 22.6 1.0

Magnesium binding site 10 out of 14 in 7kg2

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Magnesium binding site 10 out of 14 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine 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, H59K Mutant with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg311

b:41.7
occ:1.00
 N D:LEU273 2.9 31.0 1.0
C1 D:EDO308 3.3 43.1 1.0
CA D:ARG272 3.6 27.6 1.0
CB D:LEU273 3.7 26.6 1.0
CG D:ARG272 3.8 34.5 1.0
C D:ARG272 3.8 29.5 1.0
CG D:LEU273 3.9 32.3 1.0
CA D:LEU273 3.9 26.1 1.0
O D:HOH419 4.0 30.1 1.0
O D:PHE271 4.0 33.6 1.0
O1 D:EDO308 4.3 45.1 1.0
C2 D:EDO308 4.3 48.1 1.0
CD1 D:LEU273 4.3 34.2 1.0
CB D:ARG272 4.3 32.0 1.0
N D:ARG272 4.7 28.8 1.0
C D:PHE271 4.8 27.7 1.0
O D:LEU273 4.8 25.2 1.0
O D:HOH426 4.8 30.1 1.0
CD D:ARG272 4.9 38.6 1.0
C D:LEU273 4.9 20.9 1.0
O D:ARG272 5.0 25.7 1.0

Reference:

M.M.Majdi 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: Thu Aug 14 08:10:53 2025

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