Magnesium in PDB 7kwp: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group, PDB code: 7kwp 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) 45.84 / 2.26
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.4, 231.13, 199.73, 90, 90, 90
R / Rfree (%) 24.4 / 27.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group (pdb code 7kwp). 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 with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group, PDB code: 7kwp:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 7kwp

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Magnesium binding site 1 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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 with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:30.0
occ:1.00
 OD2 A:ASP227 2.0 38.1 1.0
O A:HOH441 2.5 30.1 1.0
OD1 A:ASP227 2.6 38.0 1.0
CG A:ASP227 2.6 35.2 1.0
CB A:ASP227 4.1 35.9 1.0

Magnesium binding site 2 out of 6 in 7kwp

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Magnesium binding site 2 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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 with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg303

b:30.0
occ:1.00
 OH A:TYR137 3.6 33.6 1.0
ND2 A:ASN252 3.8 26.3 1.0
C1 A:KPI166 3.8 27.2 1.0
CX1 A:KPI166 4.2 34.8 1.0
O1 A:KPI166 4.2 46.6 1.0
CX2 A:KPI166 4.3 41.2 1.0
O A:GLY190 4.5 34.3 1.0
CB A:THR47 4.5 34.2 1.0
CG2 A:THR47 4.7 26.3 1.0
CE2 A:PHE248 4.7 39.5 1.0
CG A:ASN252 4.7 27.9 1.0
OG1 A:THR47 4.8 26.2 1.0
OG1 A:THR48 4.8 28.9 1.0
CG2 A:VAL209 4.8 36.3 1.0
CZ A:TYR137 4.9 37.8 1.0
NZ A:KPI166 4.9 35.4 1.0
O2 A:KPI166 4.9 40.4 1.0
CG2 A:VAL139 5.0 28.1 1.0
CZ A:PHE248 5.0 40.0 1.0
CB A:ALA168 5.0 30.3 1.0

Magnesium binding site 3 out of 6 in 7kwp

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Magnesium binding site 3 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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 with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:30.0
occ:1.00
 CD2 B:PHE248 3.0 32.0 1.0
CE2 B:PHE248 3.3 34.0 1.0
NH2 B:ARG142 3.3 49.2 1.0
N B:ASN252 3.5 38.2 1.0
NE B:ARG142 3.7 53.4 1.0
CB B:ASN252 3.8 24.7 1.0
CZ B:ARG142 4.0 52.0 1.0
CA B:SER251 4.2 30.9 1.0
CA B:ASN252 4.3 42.0 1.0
CG B:PHE248 4.3 32.7 1.0
C B:SER251 4.4 31.8 1.0
CZ B:PHE248 4.6 32.0 1.0
CB B:PHE248 4.8 31.3 1.0
CD C:LYS113 4.8 50.3 1.0
CB B:SER251 4.8 33.0 1.0
O B:ASN252 4.9 33.9 1.0
OG B:SER251 5.0 37.0 1.0
O B:GLU250 5.0 36.4 1.0

Magnesium binding site 4 out of 6 in 7kwp

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Magnesium binding site 4 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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 with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:30.0
occ:1.00
 OD2 B:ASP227 2.0 30.0 1.0
CG B:ASP227 2.9 28.8 1.0
OD1 B:ASP227 3.2 30.4 1.0
O B:HOH477 4.1 43.7 1.0
CB B:ASP227 4.3 33.0 1.0

Magnesium binding site 5 out of 6 in 7kwp

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Magnesium binding site 5 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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 with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg306

b:30.0
occ:1.00
 CG2 C:THR55 4.0 41.4 1.0
ND1 B:HIS87 4.3 39.4 1.0
CE1 B:HIS87 4.4 38.5 1.0
CG B:HIS87 4.4 39.3 1.0
NE2 B:HIS87 4.5 38.2 1.0
CD2 B:HIS87 4.6 39.6 1.0
NH1 C:ARG272 4.6 32.0 1.0
CZ C:ARG272 4.8 33.7 1.0
NH2 C:ARG272 4.8 38.1 1.0
O C:HOH464 4.9 41.0 1.0
OE2 C:GLU58 5.0 38.9 1.0
CB B:HIS87 5.0 35.9 1.0

Magnesium binding site 6 out of 6 in 7kwp

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Magnesium binding site 6 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group


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 with Pyruvate Bound in the Active Site and L-Lysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:30.0
occ:1.00
 N C:GLY82 3.1 25.9 1.0
N C:VAL107 3.3 26.6 1.0
O C:LEU105 3.3 28.1 1.0
CA C:GLY82 3.6 25.0 1.0
N C:ALA81 3.6 33.1 1.0
O B:HOH414 3.7 28.0 1.0
CB C:VAL107 3.7 30.8 1.0
C C:LEU105 3.8 28.6 1.0
CA C:SER106 4.0 32.4 1.0
CA C:GLY80 4.0 39.8 1.0
CG1 C:VAL107 4.0 30.4 1.0
N C:SER106 4.0 34.1 1.0
C C:SER106 4.0 28.4 1.0
CA C:VAL107 4.1 29.9 1.0
O C:HOH418 4.1 38.0 1.0
C C:GLY80 4.1 37.1 1.0
CD2 C:LEU105 4.2 24.1 1.0
CG C:LEU105 4.2 25.8 1.0
C C:ALA81 4.2 26.7 1.0
CD2 C:TYR137 4.4 24.0 1.0
CB C:LEU105 4.5 24.2 1.0
CA C:ALA81 4.5 28.2 1.0
C C:GLY82 4.6 27.6 1.0
CA C:LEU105 4.8 26.3 1.0
O C:VAL45 4.8 44.5 1.0
O C:HOH457 4.8 39.5 1.0
CE2 C:TYR137 4.9 26.1 1.0
O C:GLY82 4.9 28.7 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: Fri Dec 17 10:33:06 2021

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