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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

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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

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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

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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

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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

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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

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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

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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

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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

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