Atomistry » Magnesium » PDB 7lx0-7m4v » 7m06
Atomistry »
  Magnesium »
    PDB 7lx0-7m4v »
      7m06 »

Magnesium in PDB 7m06: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom, PDB code: 7m06 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) 43.15 / 2.70
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 72.03, 84.29, 200.94, 90, 90, 90
R / Rfree (%) 19.4 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom (pdb code 7m06). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom, PDB code: 7m06:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 1 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:40.7
occ:1.00
 N A:ASN252 3.4 42.7 1.0
O A:HOH418 3.6 36.1 1.0
CA A:SER251 3.6 47.5 1.0
CD2 A:PHE248 3.7 40.8 1.0
NH2 A:ARG142 3.7 57.2 1.0
C A:SER251 4.0 45.2 1.0
CB A:SER251 4.2 48.0 1.0
CB A:ASN252 4.2 39.6 1.0
CA A:ASN252 4.4 41.2 1.0
O A:GLU250 4.4 49.0 1.0
CE2 A:PHE248 4.5 41.0 1.0
CZ A:ARG142 4.6 54.8 1.0
CG A:PHE248 4.7 40.7 1.0
CB A:PHE248 4.7 41.0 1.0
OG A:SER251 4.7 49.0 1.0
MG A:MG302 4.7 50.3 1.0
N A:SER251 4.7 49.4 1.0
CD B:LYS113 4.7 58.2 1.0
CE B:LYS113 4.8 59.8 1.0
NE A:ARG142 4.9 52.0 1.0
C A:GLU250 4.9 49.5 1.0
O A:ASN252 5.0 41.8 1.0

Magnesium binding site 2 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 2 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:50.3
occ:1.00
 NE A:ARG142 3.5 52.0 1.0
ND2 A:ASN252 3.6 39.8 1.0
NH2 A:ARG142 3.6 57.2 1.0
CZ A:ARG142 4.0 54.8 1.0
CB A:ASN252 4.1 39.6 1.0
OH A:TYR137 4.1 46.7 1.0
CG2 A:THR47 4.3 50.6 1.0
CG A:ASN252 4.3 38.8 1.0
CE2 A:PHE248 4.3 41.0 1.0
CD A:ARG142 4.5 47.9 1.0
MG A:MG301 4.7 40.7 1.0

Magnesium binding site 3 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 3 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:45.5
occ:1.00
 O B:HOH402 3.9 48.7 1.0
O B:VAL75 4.0 40.2 1.0
OD2 B:ASP102 4.1 45.5 1.0
OD1 B:ASP102 4.1 48.2 1.0
O B:CYS70 4.3 43.9 1.0
CG B:ASP102 4.5 45.7 1.0
O B:THR73 4.6 45.9 1.0
C B:CYS70 5.0 43.8 1.0

Magnesium binding site 4 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 4 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:30.7
occ:1.00
 O C:HOH426 3.6 33.4 1.0
N C:VAL107 3.8 37.4 1.0
CB C:VAL107 3.9 37.3 1.0
N C:GLY82 3.9 44.1 1.0
CG1 C:VAL107 4.1 36.4 1.0
O C:LEU105 4.1 35.9 1.0
CA C:GLY82 4.3 44.8 1.0
CD2 C:LEU105 4.4 36.8 1.0
N C:ALA81 4.4 41.2 1.0
CA C:VAL107 4.5 37.8 1.0
CA C:GLY80 4.5 39.2 1.0
C C:LEU105 4.5 35.8 1.0
CG C:LEU105 4.6 36.7 1.0
CD2 C:TYR137 4.7 44.6 1.0
CA C:SER106 4.7 37.3 1.0
C C:SER106 4.7 37.1 1.0
N C:SER106 4.7 36.2 1.0
C C:GLY80 4.8 40.6 1.0
CA C:GLY46 4.8 44.2 1.0
CB C:LEU105 4.9 36.3 1.0
CG2 C:VAL107 5.0 37.7 1.0

Magnesium binding site 5 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 5 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:37.4
occ:1.00
 O C:VAL75 4.1 41.8 1.0
O C:CYS70 4.1 49.3 1.0
O C:THR73 4.1 46.7 1.0
O C:HOH404 4.2 36.8 1.0
OD2 C:ASP102 4.5 41.9 1.0
OD1 C:ASP102 4.6 43.6 1.0
C C:CYS70 4.8 48.9 1.0
CA C:LYS71 4.9 52.5 1.0
CG C:ASP102 5.0 42.2 1.0

Magnesium binding site 6 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 6 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg304

b:40.0
occ:1.00
 NZ D:LYS113 3.4 56.1 1.0
NH2 C:ARG142 3.4 81.2 1.0
N C:ASN252 3.5 39.2 1.0
CD2 C:PHE248 3.7 42.9 1.0
CA C:SER251 3.9 41.5 1.0
CE D:LYS113 4.0 53.3 1.0
CB C:ASN252 4.1 38.3 1.0
CE2 C:PHE248 4.2 42.0 1.0
O C:HOH410 4.2 30.0 1.0
C C:SER251 4.2 39.7 1.0
CZ C:ARG142 4.2 76.9 1.0
CB C:SER251 4.3 42.3 1.0
CA C:ASN252 4.4 37.7 1.0
NE C:ARG142 4.7 73.1 1.0
CG C:PHE248 4.7 43.5 1.0
O C:GLU250 4.8 42.8 1.0
OG C:SER251 4.8 44.0 1.0
O C:ASN252 4.9 37.9 1.0
CB C:PHE248 4.9 43.4 1.0

Magnesium binding site 7 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 7 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg305

b:51.3
occ:1.00
 O C:HOH424 2.3 44.8 1.0
N C:GLU160 3.3 57.4 1.0
N C:ASN161 3.6 52.4 1.0
O C:ALA127 3.7 52.7 1.0
CA C:CYS159 3.8 53.3 1.0
CB C:CYS159 3.8 51.4 1.0
C C:CYS159 3.9 54.7 1.0
C C:ALA127 4.1 52.0 1.0
OD1 C:ASN161 4.1 52.2 1.0
CB C:ALA127 4.2 48.1 1.0
CB C:ASN161 4.2 49.3 1.0
CA C:GLU160 4.2 60.8 1.0
CG C:ASN161 4.3 51.3 1.0
C C:GLU160 4.4 56.2 1.0
CB C:GLU160 4.5 69.4 1.0
CA C:ASN161 4.5 49.2 1.0
N C:GLN128 4.6 55.1 1.0
CG C:GLN128 4.6 63.2 1.0
SG C:CYS159 4.7 51.0 1.0
CA C:ALA127 4.7 48.1 1.0
CA C:GLN128 4.8 59.4 1.0
O C:CYS159 5.0 53.6 1.0

Magnesium binding site 8 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 8 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:41.0
occ:1.00
 N D:ASN252 3.5 42.0 1.0
NH2 D:ARG142 3.6 52.8 1.0
CD2 D:PHE248 3.7 48.2 1.0
CA D:SER251 3.9 44.4 1.0
CB D:ASN252 4.2 42.2 1.0
C D:SER251 4.2 42.5 1.0
CE2 D:PHE248 4.3 48.6 1.0
MG D:MG302 4.4 53.0 1.0
CA D:ASN252 4.4 41.3 1.0
CE C:LYS113 4.4 55.2 1.0
CZ D:ARG142 4.5 50.8 1.0
CB D:SER251 4.5 44.4 1.0
O D:GLU250 4.6 47.2 1.0
CD C:LYS113 4.7 53.6 1.0
CG D:PHE248 4.7 45.5 1.0
CB D:PHE248 4.9 44.6 1.0
NE D:ARG142 4.9 48.9 1.0
OG D:SER251 4.9 45.6 1.0
N D:SER251 4.9 45.6 1.0
O D:ASN252 5.0 41.6 1.0

Magnesium binding site 9 out of 9 in 7m06

Go back to Magnesium Binding Sites List in 7m06
Magnesium binding site 9 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom


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, Y110F Mutant with R,R-Bislysine Bound at the Allosteric Site at 2.7 Angstrom within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:53.0
occ:1.00
 NE D:ARG142 3.5 48.9 1.0
NH2 D:ARG142 3.6 52.8 1.0
ND2 D:ASN252 3.8 44.9 1.0
CZ D:ARG142 4.1 50.8 1.0
CE2 D:PHE248 4.1 48.6 1.0
CB D:ASN252 4.3 42.2 1.0
OH D:TYR137 4.3 46.7 1.0
MG D:MG301 4.4 41.0 1.0
CG D:ASN252 4.5 42.9 1.0
CG2 D:THR47 4.6 59.1 1.0
CD D:ARG142 4.6 45.3 1.0
CD2 D:PHE248 4.9 48.2 1.0
CZ D:PHE248 4.9 46.8 1.0

Reference:

S.Saran, D.A.R.Sanders. B-Factor Analysis Suggest That L-Lysine and R, R-Bislysine Allosterically Inhibit Cj.Dhdps Enzyme By Decreasing Protein Dynamics To Be Published.
Page generated: Wed Oct 2 23:36:33 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy