Magnesium in PDB 7kel: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site, PDB code: 7kel 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) 38.58 / 2.10
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 82.88, 201.44, 113.66, 90, 108.45, 90
R / Rfree (%) 20.6 / 25.3

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site (pdb code 7kel). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 6 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K Mutant with Pyruvate Bound in the Active Site, PDB code: 7kel:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7kel

Go back to Magnesium Binding Sites List in 7kel
Magnesium binding site 1 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K 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, H59K Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg304

b:44.7
occ:1.00
 O A:HOH425 2.4 33.9 1.0
OD2 A:ASP227 2.7 37.5 1.0
CG A:ASP227 3.2 35.9 1.0
OD1 A:ASP227 3.3 34.6 1.0
CB A:ASP227 4.4 32.8 1.0
O A:HOH475 5.0 36.4 1.0

Magnesium binding site 2 out of 6 in 7kel

Go back to Magnesium Binding Sites List in 7kel
Magnesium binding site 2 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K 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, H59K Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:33.8
occ:1.00
 O C:HOH409 2.0 25.6 1.0
O D:HOH444 2.4 23.7 1.0
O C:HOH431 2.4 24.9 1.0
OD2 C:ASP227 2.6 28.1 1.0
CG C:ASP227 3.0 26.7 1.0
OD1 D:ASP102 3.1 32.5 1.0
OD1 C:ASP227 3.2 28.7 1.0
OD2 D:ASP102 3.8 28.6 1.0
O D:HOH469 3.8 31.6 1.0
CG D:ASP102 3.9 29.0 1.0
O D:HOH428 4.0 18.0 1.0
CB C:ASP227 4.1 27.7 1.0
O C:HOH406 4.4 28.6 1.0
CD D:LYS76 4.5 25.6 1.0
CE D:LYS76 4.7 34.1 1.0
O D:VAL75 4.8 26.9 1.0

Magnesium binding site 3 out of 6 in 7kel

Go back to Magnesium Binding Sites List in 7kel
Magnesium binding site 3 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K 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, H59K Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:42.9
occ:1.00
 OD2 C:ASP177 2.6 26.6 1.0
O C:HOH505 3.1 30.4 1.0
CG C:ASP177 3.6 26.0 1.0
OD1 C:ASP177 3.8 26.6 1.0
CB C:THR149 4.0 27.2 1.0
O4 C:PGE302 4.0 34.5 1.0
OD1 C:ASP150 4.2 41.5 1.0
C6 C:PGE302 4.3 37.6 1.0
CG2 C:THR149 4.4 23.7 1.0
OD2 C:ASP150 4.4 37.2 1.0
CG C:ASP150 4.5 34.5 1.0
OG1 C:THR149 4.6 25.8 1.0
O C:HOH461 4.6 20.2 1.0
CB C:ASP177 4.9 24.7 1.0

Magnesium binding site 4 out of 6 in 7kel

Go back to Magnesium Binding Sites List in 7kel
Magnesium binding site 4 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K 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, H59K Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:31.1
occ:1.00
 O C:HOH419 2.0 32.2 1.0
O C:HOH463 2.0 30.6 1.0
OD2 D:ASP227 2.3 29.5 1.0
O C:HOH414 2.4 28.2 1.0
O C:HOH460 2.4 29.9 1.0
C1 C:EDO315 3.0 35.0 1.0
CG D:ASP227 3.1 28.0 1.0
O1 C:EDO315 3.6 32.1 1.0
O D:HOH423 3.6 30.7 1.0
OD1 D:ASP227 3.7 31.8 1.0
C2 C:EDO315 4.1 33.3 1.0
CB D:ASP227 4.1 23.9 1.0
OD1 C:ASP102 4.2 27.7 1.0
O2 C:EDO315 4.4 38.1 1.0
NZ C:LYS76 4.4 42.7 1.0
OD2 C:ASP102 4.4 26.2 1.0
O C:THR73 4.5 25.9 1.0
CD C:LYS71 4.5 36.8 1.0
O C:CYS70 4.6 24.8 1.0
NZ C:LYS71 4.7 40.1 1.0
CG C:ASP102 4.7 30.4 1.0
O C:VAL75 4.8 27.8 1.0
CD C:LYS76 4.9 36.8 1.0
CA C:LYS71 4.9 29.0 1.0

Magnesium binding site 5 out of 6 in 7kel

Go back to Magnesium Binding Sites List in 7kel
Magnesium binding site 5 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K 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, H59K Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg304

b:39.5
occ:1.00
 O E:HOH509 2.0 35.5 1.0
OD2 E:ASP227 2.3 38.9 1.0
CG E:ASP227 3.1 38.3 1.0
OD1 E:ASP227 3.5 37.4 1.0
O E:HOH414 3.8 25.7 1.0
CB E:ASP227 4.3 25.3 1.0

Magnesium binding site 6 out of 6 in 7kel

Go back to Magnesium Binding Sites List in 7kel
Magnesium binding site 6 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H59K 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, H59K Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg305

b:47.9
occ:1.00
 O E:HOH409 2.3 25.8 1.0
NZ E:LYS71 2.5 45.7 1.0
CE E:LYS71 3.6 49.6 1.0
O E:CYS70 3.7 22.5 1.0
O E:HOH472 3.8 26.4 1.0
O E:THR73 3.8 28.1 1.0
O E:VAL75 4.0 27.2 1.0
O1 E:EDO307 4.4 47.4 1.0
O E:HOH457 4.4 31.6 1.0
C E:CYS70 4.5 29.8 1.0
CD E:LYS71 4.5 47.0 1.0
OD1 E:ASP102 4.5 32.0 1.0
OD2 E:ASP102 4.6 28.0 1.0
CA E:LYS71 4.7 25.4 1.0
C E:THR73 4.9 26.9 1.0
N E:LYS71 4.9 25.3 1.0
CB E:CYS70 5.0 21.6 1.0
CG E:ASP102 5.0 27.1 1.0

Reference:

M.M.Yazdi, S.Saran, D.A.R.Sanders, D.R.J.Palmer. Reversing the Roles of A Crucial Hydrogen-Bonding Pair: A Lysine-Insensitive Mutant of Campylobacter Jejuni Dihydrodipicolinate Synthase, H59K, Binds Histidine in Its Allosteric Site To Be Published.
Page generated: Wed Oct 2 22:15:25 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy