Magnesium in PDB 7kk1: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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, N84A 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, N84A Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kk1 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) 49.81 / 1.77
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.69, 231.98, 200.45, 90, 90, 90
R / Rfree (%) 16.8 / 19.9

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site (pdb code 7kk1). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 15 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kk1:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 15 in 7kk1

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Magnesium binding site 1 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:144.5
occ:1.00
 O A:HOH455 3.0 21.6 1.0
N A:VAL107 3.3 16.5 1.0
N A:GLY82 3.3 20.8 1.0
O D:HOH409 3.4 22.7 1.0
O A:LEU105 3.6 20.1 1.0
CA A:GLY82 3.7 21.4 1.0
CB A:VAL107 3.8 17.5 1.0
N A:ALA81 3.8 13.8 1.0
CG1 A:VAL107 3.9 18.7 1.0
CA A:SER106 4.0 19.4 1.0
C A:SER106 4.1 15.4 1.0
C A:LEU105 4.1 17.5 1.0
CA A:VAL107 4.1 15.4 1.0
CA A:GLY80 4.2 17.8 1.0
N A:SER106 4.2 13.9 1.0
C A:GLY80 4.4 17.1 1.0
C A:ALA81 4.4 19.1 1.0
CD2 A:TYR137 4.4 18.1 1.0
CG A:LEU105 4.5 18.8 1.0
CD2 A:LEU105 4.5 17.7 1.0
CA A:ALA81 4.7 18.6 1.0
O A:HOH431 4.7 22.8 1.0
CB A:LEU105 4.8 16.1 1.0
C A:GLY82 4.8 18.9 1.0
O A:VAL45 4.9 19.6 1.0
CA A:GLY46 4.9 20.8 1.0
CE2 A:TYR137 4.9 19.7 1.0
OH D:TYR111 5.0 18.9 1.0

Magnesium binding site 2 out of 15 in 7kk1

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Magnesium binding site 2 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:38.2
occ:1.00
 O A:HOH586 2.6 35.1 1.0
CG A:LYS71 4.0 24.7 1.0
O A:HOH466 4.0 28.6 1.0
CE A:LYS71 4.2 36.5 1.0
CD A:LYS71 4.4 31.4 1.0
O A:HOH476 4.5 21.6 1.0
CB A:LYS71 4.9 22.3 1.0

Magnesium binding site 3 out of 15 in 7kk1

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Magnesium binding site 3 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:15.3
occ:1.00
 O B:HOH408 3.2 21.4 1.0
N B:VAL107 3.2 15.8 1.0
N B:GLY82 3.4 17.5 1.0
O C:HOH411 3.4 20.4 1.0
O B:LEU105 3.6 19.0 1.0
CB B:VAL107 3.7 17.1 1.0
CA B:GLY82 3.8 19.4 1.0
N B:ALA81 3.8 17.8 1.0
CG1 B:VAL107 3.9 16.7 1.0
CA B:SER106 3.9 16.5 1.0
C B:SER106 4.0 15.8 1.0
C B:LEU105 4.1 18.7 1.0
CA B:VAL107 4.1 14.4 1.0
N B:SER106 4.2 15.7 1.0
CA B:GLY80 4.2 15.9 1.0
CD2 B:TYR137 4.4 18.8 1.0
C B:GLY80 4.4 16.9 1.0
CD2 B:LEU105 4.4 18.5 1.0
CG B:LEU105 4.4 19.6 1.0
C B:ALA81 4.5 19.8 1.0
CA B:ALA81 4.8 18.0 1.0
CB B:LEU105 4.8 19.2 1.0
O B:HOH460 4.8 22.4 1.0
C B:GLY82 4.8 18.3 1.0
CE2 B:TYR137 4.9 20.8 1.0
O B:VAL45 4.9 18.0 1.0
OH C:TYR111 5.0 19.1 1.0
CA B:GLY46 5.0 17.3 1.0

Magnesium binding site 4 out of 15 in 7kk1

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Magnesium binding site 4 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:26.3
occ:1.00
 O B:PRO109 2.7 17.1 1.0
N B:LYS113 2.8 17.4 1.0
O B:THR143 2.8 17.2 1.0
CA B:LYS113 3.1 17.6 1.0
N B:TYR111 3.4 13.8 1.0
CB B:CYS145 3.5 21.2 1.0
C B:TYR110 3.6 15.2 1.0
SG B:CYS145 3.7 20.4 1.0
CA B:TYR110 3.7 16.4 1.0
CD B:PRO114 3.7 16.2 1.0
C B:PRO109 3.7 16.5 1.0
N B:ASN112 3.8 18.3 1.0
C B:THR143 3.8 16.9 1.0
CG B:LYS113 3.9 30.4 1.0
N B:CYS145 3.9 18.2 1.0
C B:ASN112 4.0 18.7 1.0
C B:GLY144 4.0 19.7 1.0
CB B:LYS113 4.0 18.8 1.0
C B:TYR111 4.0 17.8 1.0
N B:TYR110 4.2 16.5 1.0
CA B:TYR111 4.2 15.9 1.0
C B:LYS113 4.2 15.6 1.0
OD1 B:ASN112 4.3 17.6 1.0
O B:GLY144 4.3 19.4 1.0
O B:TYR110 4.3 16.9 1.0
CA B:CYS145 4.3 18.4 1.0
N B:PRO114 4.4 16.0 1.0
CA B:GLY144 4.4 19.6 1.0
CB B:THR143 4.5 16.8 1.0
CA B:ASN112 4.5 16.5 1.0
N B:GLY144 4.6 14.9 1.0
O B:TYR111 4.6 17.0 1.0
CA B:THR143 4.7 16.4 1.0
OG1 B:THR143 4.7 16.4 1.0
CG B:PRO114 4.9 19.6 1.0

Magnesium binding site 5 out of 15 in 7kk1

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Magnesium binding site 5 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:20.0
occ:1.00
 OD2 B:ASP227 2.0 20.1 1.0
O B:HOH521 2.1 26.4 1.0
O B:HOH491 2.1 28.0 1.0
CG B:ASP227 3.0 24.6 1.0
OD1 B:ASP227 3.3 24.3 1.0
O B:HOH451 4.0 20.7 1.0
CB B:ASP227 4.3 18.0 1.0
O B:HOH542 4.3 23.4 1.0

Magnesium binding site 6 out of 15 in 7kk1

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Magnesium binding site 6 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:Mg305

b:20.1
occ:1.00
 O B:HOH468 1.9 25.2 1.0
O B:HOH463 1.9 30.8 1.0
O B:HOH441 2.2 19.3 1.0
O B:HOH448 4.1 21.8 1.0
O B:HOH483 4.1 20.1 1.0
OD1 B:ASP102 4.2 23.9 1.0
O B:THR73 4.2 21.6 1.0
O B:VAL75 4.3 19.6 1.0
OD2 B:ASP102 4.3 19.8 1.0
O B:HOH561 4.4 38.9 1.0
O B:CYS70 4.5 18.9 1.0
CG B:ASP102 4.7 22.1 1.0
O B:HOH443 4.7 23.3 1.0

Magnesium binding site 7 out of 15 in 7kk1

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Magnesium binding site 7 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:Mg306

b:50.7
occ:1.00
 O B:HOH495 4.2 25.1 1.0
CB B:ALA220 4.2 17.9 1.0
CE2 B:PHE224 4.9 22.0 1.0

Magnesium binding site 8 out of 15 in 7kk1

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Magnesium binding site 8 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:17.5
occ:1.00
 O C:HOH468 3.1 21.8 1.0
N C:VAL107 3.2 16.3 1.0
N C:GLY82 3.4 20.2 1.0
O B:HOH406 3.4 21.4 1.0
O C:LEU105 3.6 18.9 1.0
CA C:GLY82 3.7 20.0 1.0
CB C:VAL107 3.7 17.5 1.0
N C:ALA81 3.8 14.9 1.0
CG1 C:VAL107 3.9 19.0 1.0
CA C:SER106 3.9 17.0 1.0
C C:LEU105 4.0 17.3 1.0
C C:SER106 4.0 17.1 1.0
CA C:VAL107 4.1 15.8 1.0
N C:SER106 4.1 16.1 1.0
CA C:GLY80 4.2 19.6 1.0
CD2 C:TYR137 4.4 18.1 1.0
CD2 C:LEU105 4.4 19.0 1.0
CG C:LEU105 4.4 17.2 1.0
C C:ALA81 4.4 17.8 1.0
C C:GLY80 4.4 17.2 1.0
CB C:LEU105 4.7 16.9 1.0
CA C:ALA81 4.7 16.5 1.0
C C:GLY82 4.8 18.8 1.0
CE2 C:TYR137 4.9 18.8 1.0
O C:HOH456 4.9 21.6 1.0
O C:VAL45 4.9 18.9 1.0
CA C:GLY46 5.0 19.2 1.0

Magnesium binding site 9 out of 15 in 7kk1

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Magnesium binding site 9 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:41.4
occ:1.00
 N C:GLU281 2.9 25.5 1.0
CB C:GLU281 3.0 34.0 1.0
CA C:GLU281 3.5 29.3 1.0
N C:LYS280 3.7 30.5 1.0
C C:LYS280 3.8 27.1 1.0
CB C:SER279 3.9 27.3 1.0
OG C:SER279 3.9 27.5 1.0
O C:HOH415 4.0 32.9 1.0
CB C:LYS280 4.0 32.2 1.0
CA C:LYS280 4.0 33.2 1.0
C C:SER279 4.3 28.1 1.0
OE1 C:GLU281 4.3 56.0 1.0
CG C:GLU281 4.4 43.5 1.0
CA C:SER279 4.6 26.2 1.0
C C:GLU281 4.8 30.1 1.0
CD C:GLU281 4.9 55.7 1.0
O C:LYS280 4.9 25.8 1.0
N C:ASN282 5.0 25.1 1.0

Magnesium binding site 10 out of 15 in 7kk1

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Magnesium binding site 10 out of 15 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A 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, N84A 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:17.2
occ:1.00
 O D:HOH472 2.9 22.9 1.0
N D:VAL107 3.2 17.7 1.0
N D:GLY82 3.3 20.4 1.0
O A:HOH407 3.6 22.6 1.0
O D:LEU105 3.6 21.8 1.0
CA D:GLY82 3.7 19.1 1.0
N D:ALA81 3.8 18.5 1.0
CB D:VAL107 3.8 18.1 1.0
CG1 D:VAL107 3.9 19.4 1.0
CA D:SER106 3.9 15.7 1.0
C D:LEU105 4.0 18.0 1.0
C D:SER106 4.0 15.8 1.0
CA D:VAL107 4.1 16.9 1.0
N D:SER106 4.1 15.1 1.0
CA D:GLY80 4.2 18.1 1.0
CG D:LEU105 4.3 18.5 1.0
C D:ALA81 4.3 21.7 1.0
CD2 D:LEU105 4.3 16.7 1.0
C D:GLY80 4.4 17.8 1.0
CD2 D:TYR137 4.4 17.9 1.0
CA D:ALA81 4.7 20.9 1.0
CB D:LEU105 4.7 19.5 1.0
C D:GLY82 4.8 20.4 1.0
CE2 D:TYR137 4.9 21.1 1.0
O D:HOH471 4.9 21.9 1.0
O D:VAL45 5.0 20.0 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: Fri Nov 5 15:14:55 2021

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