Magnesium in PDB 7kg5: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site, PDB code: 7kg5 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) 46.30 / 1.95
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.13, 231.25, 202.1, 90, 90, 90
R / Rfree (%) 17.4 / 21

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 13;

Binding sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site (pdb code 7kg5). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 13 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site, PDB code: 7kg5:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 13 in 7kg5

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Magnesium binding site 1 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:30.9
occ:1.00
 O A:HOH517 2.0 35.6 1.0
OD2 A:ASP227 2.2 33.2 1.0
CG A:ASP227 3.1 32.7 1.0
OD1 A:ASP227 3.4 33.3 1.0
CB A:ASP227 4.4 26.7 1.0
O A:HOH545 4.6 32.1 1.0

Magnesium binding site 2 out of 13 in 7kg5

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Magnesium binding site 2 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:46.4
occ:1.00
 OE1 A:GLN25 2.9 52.0 1.0
N A:GLU24 3.0 34.0 1.0
O A:VAL22 3.3 33.0 1.0
CB A:GLU24 3.4 31.9 1.0
CG A:GLU24 3.5 31.7 1.0
CA A:GLU24 3.7 35.7 1.0
CD A:GLN25 3.8 56.6 1.0
C A:ASP23 3.9 34.4 1.0
NE2 A:GLN25 4.0 59.3 1.0
CA A:ASP23 4.0 28.5 1.0
CD A:GLU24 4.0 37.6 1.0
N A:GLN25 4.2 37.3 1.0
C A:VAL22 4.4 31.6 1.0
OD1 A:ASP23 4.4 34.2 1.0
C A:GLU24 4.5 35.3 1.0
OE2 A:GLU24 4.5 41.2 1.0
OE1 A:GLU24 4.6 38.8 1.0
N A:ASP23 4.7 28.1 1.0

Magnesium binding site 3 out of 13 in 7kg5

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Magnesium binding site 3 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:31.4
occ:1.00
 O B:HOH457 2.0 36.2 1.0
O B:HOH509 2.0 31.8 1.0
OD2 B:ASP227 2.2 27.3 1.0
CG B:ASP227 3.0 29.9 1.0
OD1 B:ASP227 3.3 33.2 1.0
CB B:ASP227 4.3 25.4 1.0
O B:HOH540 4.6 35.7 1.0

Magnesium binding site 4 out of 13 in 7kg5

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Magnesium binding site 4 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:48.3
occ:1.00
 O B:HOH411 2.6 37.5 1.0
O B:HOH452 2.8 31.2 1.0
O B:HOH441 3.0 29.4 1.0
O B:THR73 3.3 27.9 1.0
O B:LYS74 4.1 30.0 1.0
CD B:LYS76 4.2 35.0 1.0
O B:VAL75 4.2 25.3 1.0
C B:LYS74 4.3 29.8 1.0
CE B:LYS76 4.3 39.8 1.0
C B:THR73 4.5 24.7 1.0
CA B:LYS74 4.5 35.0 1.0
OD1 B:ASP102 4.8 27.6 1.0
C B:VAL75 4.9 26.0 1.0
N B:VAL75 4.9 25.9 1.0
O B:HOH427 4.9 27.5 1.0

Magnesium binding site 5 out of 13 in 7kg5

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Magnesium binding site 5 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:39.7
occ:1.00
 O B:HOH537 2.6 41.2 1.0
N B:ASN252 2.9 21.7 1.0
O B:HOH461 3.1 33.1 1.0
NH2 B:ARG142 3.4 33.9 1.0
O1 B:EDO306 3.4 56.4 1.0
CA B:SER251 3.4 21.5 1.0
CD2 B:PHE248 3.6 27.6 1.0
O C:HOH406 3.7 34.3 1.0
C B:SER251 3.7 21.9 1.0
CB B:ASN252 3.7 19.4 1.0
CA B:ASN252 3.9 20.4 1.0
CB B:SER251 4.1 26.0 1.0
CE2 B:PHE248 4.2 28.4 1.0
CZ B:ARG142 4.3 35.2 1.0
O2 B:EDO306 4.4 35.9 1.0
O B:GLU250 4.4 21.7 1.0
OG B:SER251 4.5 25.1 1.0
N B:SER251 4.5 21.2 1.0
O B:ASN252 4.6 23.4 1.0
C1 B:EDO306 4.6 36.9 1.0
CG B:PHE248 4.6 27.9 1.0
C2 B:EDO306 4.7 37.8 1.0
NE B:ARG142 4.7 26.9 1.0
CB B:PHE248 4.8 25.3 1.0
C B:ASN252 4.8 21.8 1.0
C B:GLU250 4.9 22.1 1.0
O B:SER251 4.9 20.9 1.0

Magnesium binding site 6 out of 13 in 7kg5

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Magnesium binding site 6 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:56.3
occ:1.00
 O B:HOH425 2.5 38.7 1.0
O C:HOH422 2.9 37.8 1.0
CZ2 C:TRP56 3.9 45.4 0.5
OE1 C:GLU88 3.9 46.6 1.0
O C:HOH433 4.0 32.9 1.0
OE1 B:GLU88 4.0 48.5 1.0
O B:HOH405 4.3 34.0 1.0
OE2 C:GLU88 4.4 39.7 1.0
CE2 C:TRP56 4.5 42.8 0.5
CD C:GLU88 4.6 40.8 1.0
OE2 B:GLU88 4.6 37.8 1.0
O B:HOH449 4.6 29.9 1.0
CH2 C:TRP56 4.6 42.2 0.5
NE1 C:TRP56 4.7 41.7 0.5
CZ2 B:TRP56 4.7 47.6 0.5
C1 C:PEG310 4.7 56.8 1.0
CD B:GLU88 4.7 42.4 1.0

Magnesium binding site 7 out of 13 in 7kg5

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Magnesium binding site 7 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:51.4
occ:1.00
 O1 C:PEG309 2.5 56.2 1.0
O C:SER51 2.7 28.9 1.0
C1 C:PEG309 3.0 38.6 1.0
NE2 C:HIS59 3.4 37.6 1.0
C C:SER51 3.6 34.0 1.0
CH2 C:TRP56 3.7 42.2 0.5
CZ3 C:TRP56 3.8 41.9 0.5
CA C:ALA52 3.8 32.1 1.0
O C:LEU54 3.9 35.5 1.0
O C:ALA52 3.9 29.0 1.0
C C:ALA52 4.0 30.5 1.0
CE1 C:HIS59 4.1 45.0 1.0
O B:HOH449 4.1 29.9 1.0
N C:ALA52 4.1 25.8 1.0
CD2 C:HIS59 4.4 38.1 1.0
C2 C:PEG309 4.5 50.2 1.0
CZ2 C:TRP56 4.5 45.4 0.5
CE3 C:TRP56 4.5 43.0 0.5
CA C:SER51 4.6 29.8 1.0
CB C:SER51 4.7 32.1 1.0
O4 C:PEG309 4.9 39.2 1.0
N C:THR53 4.9 26.3 1.0

Magnesium binding site 8 out of 13 in 7kg5

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Magnesium binding site 8 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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 8 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:58.3
occ:1.00
 O A:HOH404 2.4 41.2 1.0
O D:HOH433 2.7 35.3 1.0
O D:HOH426 3.8 34.7 1.0
OE2 D:GLU88 4.0 49.5 1.0
O A:HOH421 4.1 35.6 1.0
OE1 A:GLU88 4.1 46.1 1.0
CZ2 D:TRP56 4.2 56.7 0.9
O A:HOH446 4.4 31.3 1.0
OE1 D:GLU88 4.4 42.5 1.0
OE2 A:GLU88 4.4 34.6 1.0
CZ2 A:TRP56 4.6 41.8 0.5
CD D:GLU88 4.7 45.2 1.0
CD A:GLU88 4.7 39.6 1.0
CH2 D:TRP56 4.7 48.1 0.9

Magnesium binding site 9 out of 13 in 7kg5

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Magnesium binding site 9 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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 9 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:36.7
occ:1.00
 OD1 D:ASP40 2.1 32.4 1.0
O D:HOH524 2.1 35.7 1.0
O D:HOH441 2.1 39.3 1.0
O D:HOH513 2.3 34.8 1.0
CG D:ASP40 3.3 32.1 1.0
O D:HOH536 3.8 37.9 1.0
OD2 D:ASP40 4.2 28.3 1.0
CB D:ASP40 4.2 23.7 1.0
CA D:ASP40 4.3 22.9 1.0
O D:GLY38 4.3 24.3 1.0
O D:ACT308 4.4 43.4 1.0
NE2 D:HIS223 4.5 26.2 1.0
CH3 D:ACT308 4.5 31.1 1.0
O D:ILE39 4.5 31.0 1.0
CE1 D:HIS223 4.7 25.9 1.0
N D:ASP40 4.8 21.7 1.0
C D:ILE39 4.9 26.8 1.0
C D:ACT308 4.9 41.4 1.0
O D:HOH456 5.0 25.9 1.0

Magnesium binding site 10 out of 13 in 7kg5

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Magnesium binding site 10 out of 13 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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 10 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:42.8
occ:1.00
 O F:HOH556 2.8 43.0 1.0
N E:GLN116 2.9 26.6 1.0
O E:HOH455 3.1 34.8 1.0
CB E:THR115 3.4 29.8 1.0
CG E:GLN116 3.5 26.9 1.0
CA E:THR115 3.6 30.7 1.0
CB E:GLN116 3.7 26.7 1.0
C E:THR115 3.8 28.0 1.0
CA E:GLN116 3.9 31.6 1.0
CG2 E:THR115 4.2 30.7 1.0
O F:HOH424 4.4 38.8 1.0
OG1 E:THR115 4.5 28.2 1.0
CD E:GLN116 4.6 29.5 1.0
NE2 E:GLN116 4.7 27.4 1.0
O E:HOH553 4.7 42.3 1.0
O E:HOH543 4.8 47.9 1.0
N E:GLN117 4.8 31.5 1.0
O F:HOH550 4.9 35.2 1.0
C E:GLN116 4.9 29.7 1.0
O E:HOH535 5.0 36.1 1.0
O E:THR115 5.0 24.2 1.0
O F:HOH538 5.0 39.8 1.0

Reference:

M.Majdi Yazd, K.Reddy Annadi, S.Saran, A.Bhagwa, D.A.R.Sanders, D.R.J.Palmer. Fluorescence-Based Assay Development For Screening Novel Inhibitors of Dihydrodipicolinate Synthase From Campylobacter Jejuni To Be Published.
Page generated: Wed Oct 2 22:16:02 2024

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