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Magnesium in PDB 7kkg: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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, N84D 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, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kkg 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) 45.88 / 1.64
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.67, 225.73, 200.88, 90, 90, 90
R / Rfree (%) 13.8 / 16.9

Other elements in 7kkg:

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site also contains other interesting chemical elements:

Sodium (Na) 3 atoms

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 21;

Binding sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site (pdb code 7kkg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 21 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kkg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 21 in 7kkg

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Magnesium binding site 1 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:Mg301

b:8.6
occ:1.00
 O A:HOH403 3.1 17.6 1.0
O A:HOH654 3.2 25.9 1.0
O D:HOH493 3.2 17.4 1.0
N A:VAL107 3.3 7.2 1.0
N A:GLY82 3.3 8.1 1.0
O A:LEU105 3.6 9.3 1.0
CA A:GLY82 3.7 9.8 1.0
N A:ALA81 3.8 7.7 1.0
CB A:VAL107 3.8 7.6 1.0
CA A:SER106 3.9 7.2 1.0
C A:LEU105 3.9 7.2 1.0
C A:SER106 4.0 8.4 1.0
CG1 A:VAL107 4.1 10.3 1.0
N A:SER106 4.1 6.6 1.0
CA A:VAL107 4.1 8.2 1.0
CA A:GLY80 4.1 7.8 1.0
CG A:LEU105 4.2 7.4 1.0
CD2 A:LEU105 4.3 10.0 1.0
C A:GLY80 4.3 8.7 1.0
C A:ALA81 4.4 9.2 1.0
CD2 A:TYR137 4.4 13.5 1.0
O A:HOH404 4.5 18.0 1.0
CB A:LEU105 4.5 9.6 1.0
CA A:ALA81 4.7 7.5 1.0
CA A:GLY46 4.7 18.7 1.0
C A:GLY82 4.8 7.8 1.0
CA A:LEU105 4.9 6.0 1.0
O A:VAL45 4.9 19.4 1.0
CE2 A:TYR137 5.0 17.4 1.0

Magnesium binding site 2 out of 21 in 7kkg

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Magnesium binding site 2 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:Mg301

b:9.3
occ:1.00
 O B:HOH408 3.0 18.9 1.0
N B:VAL107 3.3 7.5 1.0
N B:GLY82 3.3 9.8 1.0
O E:HOH419 3.3 20.4 1.0
O B:HOH601 3.4 24.5 1.0
O B:LEU105 3.5 11.2 1.0
CA B:GLY82 3.7 11.1 1.0
N B:ALA81 3.8 8.1 1.0
CB B:VAL107 3.8 6.7 1.0
CA B:SER106 3.9 7.1 1.0
C B:LEU105 3.9 9.3 1.0
CG1 B:VAL107 4.0 10.0 1.0
C B:SER106 4.0 7.9 1.0
N B:SER106 4.1 7.4 1.0
CA B:GLY80 4.1 7.7 1.0
CA B:VAL107 4.1 7.9 1.0
CG B:LEU105 4.2 8.6 1.0
C B:GLY80 4.3 9.3 1.0
CD2 B:LEU105 4.3 12.0 1.0
C B:ALA81 4.4 9.7 1.0
CD2 B:TYR137 4.4 14.1 1.0
CB B:LEU105 4.5 6.1 1.0
O B:HOH404 4.5 19.4 1.0
CA B:ALA81 4.7 8.7 1.0
C B:GLY82 4.8 11.1 1.0
CA B:LEU105 4.9 6.4 1.0
CA B:GLY46 4.9 18.5 1.0
CE2 B:TYR137 4.9 16.5 1.0
O B:VAL45 5.0 17.9 1.0

Magnesium binding site 3 out of 21 in 7kkg

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Magnesium binding site 3 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:10.2
occ:1.00
 O B:HOH459 2.0 22.1 1.0
O B:HOH475 2.0 13.1 1.0
O B:HOH592 2.2 22.7 1.0
O B:HOH498 3.9 15.1 1.0
O B:THR73 4.1 13.8 1.0
OD1 B:ASP102 4.1 13.3 1.0
O B:HOH646 4.1 32.3 1.0
O B:VAL75 4.3 9.8 1.0
OD2 B:ASP102 4.3 10.1 1.0
O B:CYS70 4.6 10.6 1.0
O B:HOH513 4.6 16.0 1.0
CG B:ASP102 4.6 14.8 1.0
CD B:LYS76 4.9 22.0 1.0

Magnesium binding site 4 out of 21 in 7kkg

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Magnesium binding site 4 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:41.4
occ:1.00
 OE2 B:GLU68 2.3 28.3 1.0
O B:HOH562 2.7 24.4 1.0
NZ B:LYS71 2.8 49.3 1.0
CE B:LYS71 3.1 31.9 1.0
CD B:GLU68 3.4 37.3 1.0
CB B:GLU68 3.4 14.4 1.0
CA B:GLU68 3.4 11.7 1.0
CD B:LYS71 3.7 21.9 1.0
N B:GLU68 3.9 10.8 1.0
CG B:GLU68 4.0 28.6 1.0
O B:HOH434 4.3 25.0 1.0
CG1 B:VAL67 4.4 12.8 1.0
OE1 B:GLU68 4.4 43.3 1.0
C B:VAL67 4.5 12.6 1.0
CG B:LYS71 4.6 20.2 1.0
O B:VAL67 4.8 11.4 1.0
C B:GLU68 4.8 15.5 1.0
O B:GLU64 4.8 11.5 1.0

Magnesium binding site 5 out of 21 in 7kkg

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Magnesium binding site 5 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:22.7
occ:1.00
 O B:HOH688 2.0 24.7 1.0
O B:HOH686 2.1 22.7 1.0
O B:HOH419 3.9 27.7 1.0
O B:HOH653 4.0 27.2 1.0
O B:HOH717 4.1 35.6 1.0
O B:HOH544 4.3 25.4 1.0
O B:GLU36 4.3 14.4 1.0
CB B:GLU36 4.5 9.4 1.0
O B:HOH617 4.6 44.4 1.0

Magnesium binding site 6 out of 21 in 7kkg

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Magnesium binding site 6 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:Mg301

b:11.3
occ:1.00
 O C:HOH485 2.0 24.7 1.0
O C:HOH475 2.0 19.6 1.0
O C:HOH496 2.1 12.9 1.0
O C:HOH487 4.0 18.1 1.0
O C:HOH469 4.1 13.8 1.0
OD1 C:ASP102 4.2 13.3 1.0
O C:THR73 4.2 15.3 1.0
O C:VAL75 4.3 10.0 1.0
OD2 C:ASP102 4.4 11.6 1.0
O C:HOH631 4.5 30.4 1.0
O C:CYS70 4.6 10.9 1.0
CG C:ASP102 4.7 12.0 1.0
O C:HOH510 4.8 14.8 1.0

Magnesium binding site 7 out of 21 in 7kkg

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Magnesium binding site 7 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:37.0
occ:1.00
 O C:HOH516 3.0 27.1 1.0
N C:ASP131 3.1 13.0 1.0
OD1 C:ASP131 3.4 21.3 1.0
CG C:ASP131 3.5 27.1 1.0
CA C:VAL130 3.5 14.5 1.0
C C:VAL130 3.5 15.3 1.0
CB C:ASP131 3.8 19.6 1.0
CE C:LYS97 3.8 21.9 1.0
CG C:LYS97 3.8 19.5 1.0
OD2 C:ASP131 4.0 34.3 1.0
CA C:ASP131 4.0 12.9 1.0
CD C:LYS97 4.1 25.6 1.0
O C:SER129 4.1 16.4 1.0
CB C:VAL130 4.4 13.9 1.0
N C:VAL130 4.4 14.1 1.0
O C:VAL130 4.5 18.1 1.0
NZ C:LYS97 4.7 25.5 1.0
C C:SER129 4.7 18.3 1.0
CG1 C:VAL130 4.9 14.8 1.0
CB C:LYS97 4.9 11.1 1.0

Magnesium binding site 8 out of 21 in 7kkg

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Magnesium binding site 8 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:Mg303

b:43.3
occ:1.00
 OD1 C:ASN4 2.6 33.6 1.0
NZ C:LYS76 2.7 22.9 1.0
O C:HOH450 3.0 23.5 1.0
CE C:LYS76 3.2 23.1 1.0
O C:ILE5 3.4 15.4 1.0
CD C:LYS76 3.4 16.8 1.0
CG1 C:ILE6 3.5 12.0 1.0
CG C:ASN4 3.7 37.7 1.0
O C:HOH494 3.9 28.0 1.0
CD1 C:ILE6 4.0 23.4 1.0
ND2 C:ASN4 4.2 58.2 1.0
C C:ILE5 4.2 14.5 1.0
CB C:ASP102 4.3 10.5 1.0
O C:ASP102 4.3 11.8 1.0
CG C:LYS76 4.6 13.7 1.0
N C:ILE5 4.7 14.6 1.0
OD1 C:ASP102 4.7 13.3 1.0
CG C:PRO133 4.8 15.4 1.0
CB C:ILE6 4.9 12.3 1.0
N C:ILE6 4.9 11.2 1.0
C C:ASP102 4.9 12.2 1.0
CG C:ASP102 5.0 12.0 1.0
CA C:ILE6 5.0 9.1 1.0
CB C:ASN4 5.0 31.2 1.0

Magnesium binding site 9 out of 21 in 7kkg

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Magnesium binding site 9 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:Mg304

b:39.9
occ:1.00
 NE C:ARG142 2.9 12.8 0.8
O C:HOH740 3.0 28.5 1.0
O C:HOH645 3.3 27.6 1.0
CD C:ARG142 3.4 11.2 0.8
O C:HOH606 3.6 10.5 1.0
CD F:LYS113 3.8 19.2 1.0
CZ C:ARG142 4.0 13.9 0.8
CG C:ARG142 4.0 9.1 1.0
NZ F:LYS113 4.0 45.5 1.0
NE C:ARG142 4.1 11.5 0.2
CZ C:ARG142 4.2 14.1 0.2
NH2 C:ARG142 4.2 11.3 0.8
NH2 C:ARG142 4.3 15.1 0.2
CE F:LYS113 4.6 28.4 1.0
O C:HOH456 4.6 33.2 1.0
O C:GLY141 4.7 15.5 1.0
O C:HOH425 4.7 22.1 1.0
C C:GLY141 4.7 13.2 1.0
O C:HOH600 4.7 20.9 1.0
CD C:ARG142 4.7 10.5 0.2
NH1 C:ARG142 4.8 13.2 0.2
N C:ARG142 5.0 9.0 0.2
N C:ARG142 5.0 8.8 0.8

Magnesium binding site 10 out of 21 in 7kkg

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Magnesium binding site 10 out of 21 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D 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, N84D 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:Mg305

b:9.5
occ:1.00
 O C:HOH402 3.1 19.5 1.0
O C:HOH619 3.2 25.0 1.0
N C:VAL107 3.3 7.2 1.0
O F:HOH413 3.3 20.2 1.0
N C:GLY82 3.3 10.5 1.0
O C:LEU105 3.6 11.7 1.0
CA C:GLY82 3.7 12.5 1.0
N C:ALA81 3.8 8.7 1.0
CB C:VAL107 3.9 8.1 1.0
CA C:SER106 3.9 7.9 1.0
C C:LEU105 4.0 8.9 1.0
C C:SER106 4.0 8.6 1.0
CG1 C:VAL107 4.0 9.9 1.0
N C:SER106 4.1 6.9 1.0
CA C:GLY80 4.1 8.5 1.0
CA C:VAL107 4.1 7.4 1.0
CG C:LEU105 4.2 7.0 1.0
CD2 C:LEU105 4.3 10.9 1.0
C C:GLY80 4.3 10.3 1.0
C C:ALA81 4.4 8.9 1.0
O C:HOH408 4.5 22.0 1.0
CB C:LEU105 4.6 7.2 1.0
CD2 C:TYR137 4.6 14.3 1.0
CA C:ALA81 4.7 9.2 1.0
CA C:GLY46 4.7 17.3 1.0
C C:GLY82 4.8 9.7 1.0
O C:VAL45 4.9 23.5 1.0
CA C:LEU105 4.9 7.5 1.0
OH F:TYR111 5.0 14.7 1.0

Reference:

S.Saran, M.Majdi Yazd, D.R.J.Palmer, D.A.R.Sanders. A Tight Dimer Interface N84 Residue, Plays A Critical Role in the Transmission of the Allosteric Inhibition Signals in Cj.Dhdps To Be Published.
Page generated: Wed Oct 2 22:22:26 2024

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