Atomistry » Magnesium » PDB 7k5i-7khc » 7kg9
Atomistry »
  Magnesium »
    PDB 7k5i-7khc »
      7kg9 »

Magnesium in PDB 7kg9: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W 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, H56W 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kg9 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) 49.04 / 2.06
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.83, 225.17, 200.7, 90, 90, 90
R / Rfree (%) 27.5 / 33.1

Magnesium 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 and L-Lysine Bound at the Allosteric Site (pdb code 7kg9). 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, H56W Mutant with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site, PDB code: 7kg9:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 1 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W 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:HOH427 1.9 20.8 1.0
O B:HOH420 2.3 27.5 1.0
OD2 B:ASP102 3.8 21.8 1.0
O B:VAL75 4.1 27.0 1.0
O B:HOH405 4.2 19.8 1.0
OD1 B:ASP102 4.3 21.0 1.0
O B:THR73 4.3 20.2 1.0
CG B:ASP102 4.5 21.9 1.0
O B:CYS70 4.5 24.6 1.0

Magnesium binding site 2 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 2 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W 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:26.9
occ:1.00
OD2 B:ASP227 2.6 25.5 1.0
CG B:ASP227 3.5 26.1 1.0
OD1 B:ASP227 4.0 26.8 1.0
O B:HOH439 4.2 20.0 1.0
CB B:ASP227 4.7 21.6 1.0

Magnesium binding site 3 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 3 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W 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:32.1
occ:1.00
O C:HOH508 2.0 24.3 1.0
O C:HOH418 2.4 23.0 1.0
OD2 C:ASP177 3.2 17.3 1.0
OD1 C:ASP177 3.9 22.6 1.0
CG C:ASP177 3.9 18.0 1.0
O C:HOH468 4.0 25.9 1.0
OD1 C:ASP150 4.2 31.4 1.0
O E:HOH443 4.5 21.7 1.0
O C:HOH404 4.7 23.0 1.0
O E:HOH526 4.8 18.3 1.0
CB C:THR149 4.9 18.3 1.0
CG C:ASP150 4.9 25.2 1.0
OD2 C:ASP150 4.9 31.2 1.0

Magnesium binding site 4 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 4 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W 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:Mg304

b:24.4
occ:1.00
O D:LEU105 2.9 20.9 1.0
N D:VAL107 2.9 21.5 1.0
N D:GLY82 3.2 23.3 1.0
O D:HOH469 3.2 19.4 1.0
CA D:GLY82 3.3 22.4 1.0
CB D:VAL107 3.5 26.2 1.0
C D:LEU105 3.5 21.3 1.0
CG1 D:VAL107 3.6 20.5 1.0
CA D:SER106 3.6 23.4 1.0
C D:SER106 3.7 19.2 1.0
CA D:VAL107 3.7 20.7 1.0
N D:SER106 3.8 19.6 1.0
N D:ALA81 4.0 14.3 1.0
C D:ALA81 4.3 18.0 1.0
CG D:LEU105 4.3 19.5 1.0
CD2 D:TYR137 4.4 25.6 1.0
C D:GLY82 4.5 23.2 1.0
CA D:GLY80 4.5 17.5 1.0
CB D:LEU105 4.6 17.6 1.0
C D:GLY80 4.6 18.0 1.0
CA D:LEU105 4.7 21.5 1.0
CD2 D:LEU105 4.7 20.2 1.0
O D:SER106 4.8 20.4 1.0
CA D:ALA81 4.8 16.6 1.0
CG2 D:VAL107 4.8 19.4 1.0
O D:GLY82 4.9 19.6 1.0

Magnesium binding site 5 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 5 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W 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:Mg305

b:39.5
occ:1.00
O D:HOH428 2.4 21.9 1.0
O D:HOH539 2.9 26.6 1.0
O D:HOH519 3.0 28.1 1.0
OD1 D:ASP150 4.0 27.4 1.0
OD2 D:ASP177 4.4 19.0 1.0
OD2 D:ASP150 4.6 36.8 1.0
OD1 D:ASP177 4.6 25.0 1.0
CG D:ASP150 4.7 29.8 1.0
CG D:ASP177 5.0 21.7 1.0

Magnesium binding site 6 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 6 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W 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:Mg306

b:31.4
occ:1.00
O F:HOH485 2.1 19.4 1.0
O F:HOH501 2.5 23.7 1.0
OD1 F:ASP150 2.7 34.0 1.0
O F:HOH492 2.9 22.4 1.0
CG F:ASP150 3.7 32.2 1.0
OD1 F:ASP177 3.9 29.1 1.0
OD2 F:ASP150 4.1 29.3 1.0
O F:HOH470 4.1 26.0 1.0
OD2 F:ASP177 4.2 20.8 1.0
NE2 F:HIS181 4.3 22.9 1.0
CE1 F:HIS181 4.3 19.6 1.0
ND1 F:HIS181 4.4 19.6 1.0
CD2 F:HIS181 4.4 28.0 1.0
CG F:HIS181 4.4 24.2 1.0
CG F:ASP177 4.5 21.1 1.0
CG2 F:THR149 4.6 19.7 1.0

Magnesium binding site 7 out of 7 in 7kg9

Go back to Magnesium Binding Sites List in 7kg9
Magnesium binding site 7 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56W 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, H56W 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:Mg307

b:29.8
occ:1.00
O F:HOH464 2.3 27.4 1.0
ND1 F:HIS223 2.9 31.7 1.0
OG F:SER219 3.2 29.4 1.0
CE1 F:HIS223 3.7 28.9 1.0
O F:SER219 3.8 21.4 1.0
CA F:ALA220 3.9 19.1 1.0
N F:ALA220 3.9 18.1 1.0
C F:SER219 3.9 18.4 1.0
CG F:HIS223 4.0 26.9 1.0
CB F:SER219 4.2 20.2 1.0
CB F:HIS223 4.2 23.6 1.0
CB F:ALA220 4.5 19.6 1.0
CA F:SER219 4.7 21.4 1.0
O F:GLY38 4.8 27.2 1.0
NE2 F:HIS223 4.9 28.1 1.0
CA F:GLY38 5.0 28.0 1.0

Reference:

M.Majdi Yazd, K.Reddy Annadi, S.Saran, A.Bhagwat, 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 22:16:06 2024

Last articles

Mg in 7WI4
Mg in 7WHT
Mg in 7WHS
Mg in 7WIW
Mg in 7WJH
Mg in 7WIX
Mg in 7WIK
Mg in 7WDC
Mg in 7WHW
Mg in 7WGR
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy