Magnesium in PDB 7kr8: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site, PDB code: 7kr8 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) 43.74 / 2.12
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.93, 231.65, 200.17, 90, 90, 90
R / Rfree (%) 17.3 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site (pdb code 7kr8). 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, H56A Mutant with Pyruvate Bound in the Active Site, PDB code: 7kr8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7kr8

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Magnesium binding site 1 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:42.8
occ:1.00
 OD1 B:ASN171 3.1 25.6 1.0
N B:ASP173 3.2 26.2 1.0
CB B:ASP173 3.4 23.6 1.0
N B:ILE172 3.5 28.1 1.0
CA B:ASN171 3.9 29.5 1.0
C B:ASN171 3.9 28.7 1.0
CA B:ASP173 3.9 26.3 1.0
CG2 B:ILE172 4.0 27.1 1.0
CG B:ASN171 4.1 25.2 1.0
C B:ILE172 4.2 26.5 1.0
CA B:ILE172 4.3 26.9 1.0
CB B:ASN171 4.6 28.0 1.0
O B:GLY170 4.6 40.0 1.0
CB B:ILE172 4.8 25.4 1.0
CG B:ASP173 4.8 28.9 1.0
O B:ASN171 4.8 24.7 1.0
N B:ASN171 5.0 29.2 1.0

Magnesium binding site 2 out of 7 in 7kr8

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Magnesium binding site 2 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:54.5
occ:1.00
 CB C:ALA220 4.1 26.3 1.0
O C:HOH519 4.3 42.5 1.0
CE2 C:PHE224 4.5 25.9 1.0
CZ C:PHE224 4.6 20.5 1.0
O C:HOH534 4.9 48.6 1.0

Magnesium binding site 3 out of 7 in 7kr8

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Magnesium binding site 3 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:36.5
occ:1.00
 O D:PRO109 2.7 27.7 1.0
O D:THR143 2.8 26.7 1.0
N D:LYS113 2.8 24.2 1.0
CA D:LYS113 3.0 25.8 1.0
N D:TYR111 3.2 28.3 1.0
CB D:CYS145 3.4 36.2 1.0
C D:TYR110 3.5 30.0 1.0
CA D:TYR110 3.6 27.8 1.0
C D:PRO109 3.7 24.3 1.0
C D:THR143 3.7 27.3 1.0
CG D:LYS113 3.8 41.6 1.0
N D:ASN112 3.8 27.1 1.0
CB D:LYS113 3.8 26.8 1.0
CD D:PRO114 3.8 28.0 1.0
N D:CYS145 3.9 27.4 1.0
C D:TYR111 3.9 28.2 1.0
SG D:CYS145 3.9 44.4 1.0
C D:ASN112 4.0 24.9 1.0
C D:GLY144 4.0 30.4 1.0
CA D:TYR111 4.1 27.7 1.0
N D:TYR110 4.1 25.3 1.0
O D:TYR110 4.1 27.4 1.0
CA D:CYS145 4.2 28.8 1.0
C D:LYS113 4.2 26.3 1.0
OD1 D:ASN112 4.3 29.2 1.0
CB D:THR143 4.4 26.9 1.0
N D:PRO114 4.4 27.8 1.0
CA D:GLY144 4.4 27.4 1.0
O D:GLY144 4.4 30.9 1.0
O D:TYR111 4.5 26.2 1.0
N D:GLY144 4.5 26.8 1.0
CA D:ASN112 4.5 27.0 1.0
CA D:THR143 4.6 25.5 1.0
CD D:LYS113 4.7 51.4 1.0
OG1 D:THR143 4.8 27.4 1.0
CA D:PRO109 4.9 21.5 1.0

Magnesium binding site 4 out of 7 in 7kr8

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Magnesium binding site 4 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:38.3
occ:1.00
 O D:HOH443 2.3 35.1 1.0
O D:HOH461 2.3 27.0 1.0
O D:HOH459 3.8 36.4 1.0
OD1 D:ASP102 4.0 34.5 1.0
OD2 D:ASP102 4.3 29.0 1.0
O D:VAL75 4.5 28.9 1.0
O D:CYS70 4.6 35.2 1.0
CG D:ASP102 4.6 31.8 1.0
O D:THR73 4.6 36.3 1.0
O D:HOH428 4.8 27.9 1.0

Magnesium binding site 5 out of 7 in 7kr8

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Magnesium binding site 5 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:44.3
occ:1.00
 O D:HOH465 2.2 39.1 1.0
OD2 D:ASP227 2.2 33.7 1.0
CG D:ASP227 3.1 31.4 1.0
OD1 D:ASP227 3.4 31.1 1.0
O D:HOH444 4.2 28.2 1.0
CB D:ASP227 4.4 27.8 1.0
O D:HOH504 4.5 38.8 1.0
O D:HOH533 4.6 32.5 1.0

Magnesium binding site 6 out of 7 in 7kr8

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Magnesium binding site 6 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:50.8
occ:1.00
 O E:GLY297 2.9 42.9 1.0
ND2 E:ASN37 3.1 37.3 1.0
CE E:LYS296 3.9 50.6 1.0
C E:GLY297 4.0 42.3 1.0
CB E:LYS296 4.0 38.4 1.0
O E:PHE298 4.0 44.0 1.0
CG E:ASN37 4.0 38.2 1.0
OD1 E:ASN37 4.1 41.0 1.0
C E:PHE298 4.3 45.1 1.0
NZ E:LYS296 4.3 51.8 1.0
CG E:ARG33 4.3 30.3 1.0
CA E:PHE298 4.5 44.5 1.0
O E:HOH477 4.6 44.2 1.0
N E:GLY297 4.6 39.4 1.0
N E:PHE298 4.7 43.2 1.0
OE2 E:GLU36 4.7 46.4 1.0
CG E:LYS296 4.8 39.7 1.0
C E:LYS296 4.8 39.7 1.0
O E:ARG33 4.8 30.9 1.0
CD E:LYS296 4.9 44.8 1.0
NE E:ARG33 4.9 32.3 1.0
CA E:GLY297 4.9 40.4 1.0
CD E:ARG33 5.0 33.0 1.0
CA E:LYS296 5.0 37.5 1.0

Magnesium binding site 7 out of 7 in 7kr8

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Magnesium binding site 7 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:54.0
occ:1.00
 NH1 E:ARG184 3.4 42.4 1.0
CE2 E:PHE156 3.7 29.3 1.0
CZ E:ARG184 3.8 41.0 1.0
CE E:LYS3 3.9 40.0 1.0
CZ E:PHE156 4.0 31.7 1.0
NE E:ARG184 4.2 36.3 1.0
NH2 E:ARG184 4.3 38.5 1.0
CD E:ARG184 4.5 33.8 1.0
CD2 E:PHE156 4.5 28.8 1.0
O E:HOH535 4.6 41.3 1.0
CD E:LYS3 4.7 39.2 1.0
CG E:LYS3 4.8 41.9 1.0
CB E:ARG184 5.0 31.8 1.0
NZ E:LYS3 5.0 38.4 1.0
O E:PHE156 5.0 29.7 1.0
CE1 E:PHE156 5.0 29.6 1.0

Reference:

S.Saran, Y.Skovpen, M.M.Yazdi, D.R.J.Palmer, D.A.R.Sanders. Allosteric Site Residue 'H56' Caps the Inhibitor at the Tight Dimer Interface For Transmitting the Allosteric Inhibition Signals in Cj.Dhdps To Be Published.
Page generated: Thu Nov 25 10:02:04 2021

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