Magnesium in PDB 7ko3: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D 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, E88D 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, E88D 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, E88D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7ko3 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) 43.82 / 2.22
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.32, 232.26, 200.37, 90, 90, 90
R / Rfree (%) 15.7 / 20.6

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site (pdb code 7ko3). 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, E88D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7ko3:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7ko3

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Magnesium binding site 1 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D 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, E88D 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:39.5
occ:1.00
O A:HOH451 2.1 39.1 1.0
OD2 A:ASP227 2.2 35.5 1.0
O A:HOH406 2.2 28.4 1.0
O A:HOH423 2.3 33.0 1.0
CG A:ASP227 2.9 32.7 1.0
OD1 A:ASP227 3.0 40.4 1.0
CB A:ASP227 4.2 25.1 1.0
O A:HOH440 4.3 35.8 1.0
O A:HOH435 4.5 27.8 1.0
O A:HOH489 4.6 32.2 1.0

Magnesium binding site 2 out of 7 in 7ko3

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Magnesium binding site 2 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D 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, E88D 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:51.3
occ:1.00
ND2 A:ASN252 3.3 19.7 1.0
NE A:ARG142 3.4 62.1 1.0
CB A:ASN252 4.0 20.9 1.0
CZ A:ARG142 4.0 35.0 1.0
CG A:ASN252 4.1 24.4 1.0
NH2 A:ARG142 4.1 37.8 1.0
CE2 A:PHE248 4.1 26.8 1.0
CD A:ARG142 4.1 40.8 1.0
CG2 A:THR47 4.4 35.8 1.0
C1 A:KPI166 4.4 32.0 1.0
CB A:THR47 4.6 39.6 1.0
OH A:TYR137 4.6 31.1 1.0
CZ A:PHE248 4.8 26.0 1.0
O2 A:KPI166 5.0 32.0 1.0
O A:HOH516 5.0 27.6 1.0

Magnesium binding site 3 out of 7 in 7ko3

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Magnesium binding site 3 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D 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, E88D 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:47.8
occ:1.00
OG1 A:THR55 2.7 31.5 1.0
CB A:GLU57 3.6 38.3 1.0
CB A:THR55 3.6 34.8 1.0
CG2 A:THR55 3.8 28.4 1.0
CG A:GLU58 3.9 31.2 1.0
CG A:GLU57 4.0 59.9 1.0
CD A:GLU58 4.1 40.3 1.0
O A:HOH476 4.2 36.0 1.0
OE2 A:GLU58 4.3 37.0 1.0
N A:GLU58 4.4 24.9 1.0
CA A:GLU57 4.6 29.1 1.0
OE1 A:GLU58 4.6 31.4 1.0
C A:GLU57 4.8 34.5 1.0
N A:GLU57 4.8 31.4 1.0
O A:HOH468 4.9 43.3 1.0
CB A:GLU58 4.9 30.0 1.0

Magnesium binding site 4 out of 7 in 7ko3

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Magnesium binding site 4 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D 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, E88D 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:41.8
occ:1.00
OD2 B:ASP227 2.1 34.8 1.0
CG B:ASP227 3.2 24.6 1.0
OD1 B:ASP227 3.6 39.8 1.0
O B:HOH473 4.3 28.3 1.0
CB B:ASP227 4.4 26.4 1.0
O B:HOH522 4.5 34.9 1.0

Magnesium binding site 5 out of 7 in 7ko3

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Magnesium binding site 5 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D 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, E88D 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:48.3
occ:1.00
NE B:ARG142 3.2 55.5 1.0
ND2 B:ASN252 3.3 20.1 1.0
CD B:ARG142 3.9 42.1 1.0
CZ B:ARG142 3.9 48.4 1.0
CG2 B:THR47 4.0 32.6 1.0
NH2 B:ARG142 4.0 44.3 1.0
CB B:ASN252 4.1 20.0 1.0
CG B:ASN252 4.2 24.9 1.0
CE2 B:PHE248 4.3 29.0 1.0
CB B:THR47 4.3 35.6 1.0
OH B:TYR137 4.4 32.1 1.0
C1 B:KPI166 4.6 28.9 1.0
OG1 B:THR47 4.8 35.7 1.0
O B:HOH498 4.8 26.4 1.0
O1 B:KPI166 4.9 32.7 1.0
NH1 B:ARG142 5.0 22.1 1.0

Magnesium binding site 6 out of 7 in 7ko3

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Magnesium binding site 6 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D 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, E88D 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:Mg302

b:49.6
occ:1.00
NE D:ARG142 3.3 41.0 1.0
NH2 D:ARG142 3.3 37.6 1.0
ND2 D:ASN252 3.4 21.0 1.0
CZ D:ARG142 3.7 31.1 1.0
CB D:ASN252 4.1 20.3 1.0
CE2 D:PHE248 4.1 35.5 1.0
CG D:ASN252 4.2 25.4 1.0
CD D:ARG142 4.4 35.6 1.0
CG2 D:THR47 4.4 29.7 1.0
OH D:TYR137 4.5 35.6 1.0
C1 D:KPI166 4.5 28.9 1.0
CB D:THR47 4.6 35.7 1.0
O D:HOH475 4.7 27.8 1.0
CZ D:PHE248 4.8 30.8 1.0
NH1 D:ARG142 5.0 23.2 1.0
O2 D:KPI166 5.0 34.0 1.0

Magnesium binding site 7 out of 7 in 7ko3

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Magnesium binding site 7 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, E88D 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, E88D 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:Mg302

b:26.9
occ:1.00
O F:HOH441 3.0 30.9 1.0
N F:VAL107 3.2 22.8 1.0
N F:GLY82 3.3 28.0 1.0
O D:HOH440 3.3 35.1 1.0
O F:LEU105 3.4 30.9 1.0
CA F:GLY82 3.7 30.7 1.0
N F:ALA81 3.8 26.5 1.0
CB F:VAL107 3.8 22.9 1.0
C F:LEU105 3.8 27.3 1.0
CA F:SER106 3.9 27.3 1.0
CG1 F:VAL107 3.9 25.2 1.0
C F:SER106 4.0 22.4 1.0
N F:SER106 4.1 21.2 1.0
CA F:VAL107 4.1 24.8 1.0
CA F:GLY80 4.1 27.1 1.0
CG F:LEU105 4.3 21.9 1.0
C F:GLY80 4.3 33.9 1.0
C F:ALA81 4.3 27.4 1.0
CD2 F:TYR137 4.4 24.7 1.0
CD2 F:LEU105 4.4 22.8 1.0
CB F:LEU105 4.6 28.3 1.0
CA F:ALA81 4.7 26.6 1.0
C F:GLY82 4.7 23.7 1.0
CE2 F:TYR137 4.8 23.3 1.0
CA F:LEU105 4.9 25.7 1.0
O F:VAL45 5.0 31.0 1.0
CA F:GLY46 5.0 29.8 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: Thu Nov 25 10:02:10 2021

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