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Magnesium in PDB 7kxh: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 R,R-Bislysine 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 R,R-Bislysine 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 R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group, PDB code: 7kxh 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) 43.58 / 1.94
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.09, 231.56, 198.62, 90, 90, 90
R / Rfree (%) 16.4 / 19.2

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 R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group (pdb code 7kxh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group, PDB code: 7kxh:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 7kxh

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Magnesium binding site 1 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:31.2
occ:1.00
 O A:HOH446 1.9 38.7 1.0
O A:HOH499 2.1 33.9 1.0
OD2 A:ASP227 2.1 40.0 1.0
CG A:ASP227 3.0 34.0 1.0
OD1 A:ASP227 3.3 36.2 1.0
O A:HOH417 3.9 30.5 1.0
O A:HOH492 4.2 34.0 1.0
CB A:ASP227 4.4 30.5 1.0
O A:HOH531 4.5 36.3 1.0

Magnesium binding site 2 out of 10 in 7kxh

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Magnesium binding site 2 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 R,R-Bislysine 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
 O A:LEU54 2.6 37.3 1.0
O D:HOH526 2.8 38.6 1.0
OE2 D:GLU88 3.1 33.0 1.0
C A:LEU54 3.2 34.2 1.0
CE1 D:HIS87 3.4 41.9 1.0
O A:ALA52 3.5 31.4 1.0
N A:THR55 3.6 35.6 1.0
NE2 D:HIS87 3.6 42.1 1.0
CA A:THR55 3.7 36.2 1.0
O A:THR53 3.8 34.7 1.0
C A:THR53 3.8 31.4 1.0
CD D:GLU88 3.8 34.2 1.0
C07 A:3VN301 3.9 49.3 1.0
N A:LEU54 4.1 30.9 1.0
C06 A:3VN301 4.2 60.0 1.0
N01 A:3VN301 4.2 71.5 1.0
CA A:THR53 4.2 33.5 1.0
CG D:GLU88 4.3 34.1 1.0
CA A:LEU54 4.3 29.7 1.0
C08 A:3VN301 4.3 41.3 1.0
CB D:ALA85 4.4 31.0 1.0
C A:ALA52 4.4 31.7 1.0
CG2 A:THR55 4.6 39.5 1.0
C A:THR55 4.6 34.5 1.0
ND1 D:HIS87 4.6 41.7 1.0
C09 A:3VN301 4.7 38.4 1.0
CB A:THR55 4.7 37.1 1.0
OE1 D:GLU88 4.7 33.0 1.0
O A:HOH477 4.7 39.8 1.0
O D:HOH476 4.7 35.9 1.0
N A:THR53 4.8 29.5 1.0
C02 A:3VN301 4.9 70.1 1.0
CD2 D:HIS87 5.0 42.6 1.0

Magnesium binding site 3 out of 10 in 7kxh

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Magnesium binding site 3 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:33.6
occ:1.00
 O B:HOH477 2.1 36.5 1.0
O B:HOH485 2.1 34.8 1.0
OD2 B:ASP227 2.1 20.0 1.0
CG B:ASP227 3.0 20.0 1.0
OD1 B:ASP227 3.3 20.0 1.0
O B:HOH461 4.1 29.9 1.0
CB B:ASP227 4.4 20.0 1.0
O B:HOH500 4.5 30.4 1.0

Magnesium binding site 4 out of 10 in 7kxh

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Magnesium binding site 4 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:27.1
occ:1.00
 O C:HOH430 3.2 44.3 1.0
N C:GLY82 3.2 32.4 1.0
N C:VAL107 3.3 29.2 1.0
O C:LEU105 3.5 27.6 1.0
O B:HOH411 3.6 36.2 1.0
CA C:GLY82 3.7 31.4 1.0
N C:ALA81 3.7 29.5 1.0
CB C:VAL107 3.7 31.5 1.0
C C:LEU105 3.8 26.6 1.0
CA C:SER106 3.9 27.1 1.0
CG1 C:VAL107 4.0 30.5 1.0
N C:SER106 4.0 27.1 1.0
C C:SER106 4.0 30.9 1.0
CA C:VAL107 4.1 29.0 1.0
CA C:GLY80 4.1 34.2 1.0
CD2 C:LEU105 4.1 27.2 1.0
CG C:LEU105 4.2 28.8 1.0
C C:GLY80 4.3 32.6 1.0
C C:ALA81 4.3 30.4 1.0
CD2 C:TYR137 4.3 31.0 1.0
CB C:LEU105 4.5 27.9 1.0
CA C:ALA81 4.6 26.7 1.0
C C:GLY82 4.7 30.6 1.0
CA C:LEU105 4.8 28.1 1.0
CE2 C:TYR137 4.9 30.7 1.0
O C:VAL45 4.9 35.0 1.0
O C:GLY82 4.9 29.6 1.0

Magnesium binding site 5 out of 10 in 7kxh

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Magnesium binding site 5 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:70.0
occ:1.00
 O C:GLU24 3.4 36.6 1.0
C C:GLU24 3.8 35.7 1.0
CB C:GLU24 4.1 39.8 1.0
CB C:ALA28 4.1 34.3 1.0
CG2 C:ILE65 4.2 37.7 1.0
N C:GLN25 4.3 36.0 1.0
CD1 C:ILE65 4.3 38.4 1.0
CG1 C:ILE65 4.3 37.6 1.0
CA C:GLN25 4.4 38.3 1.0
CA C:GLU24 4.5 36.4 1.0
OE1 C:GLU24 4.9 44.0 1.0
CB C:ILE65 4.9 37.4 1.0

Magnesium binding site 6 out of 10 in 7kxh

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Magnesium binding site 6 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:56.1
occ:1.00
 ND2 D:ASN252 3.3 27.7 1.0
NH2 D:ARG142 3.9 42.7 1.0
CB D:ASN252 4.0 29.3 1.0
CG2 D:THR47 4.1 33.1 1.0
CG D:ASN252 4.2 27.8 1.0
CZ D:ARG142 4.2 38.9 1.0
CB D:THR47 4.2 31.6 1.0
CE2 D:PHE248 4.3 38.1 1.0
OH D:TYR137 4.4 34.2 1.0
NE D:ARG142 4.6 39.1 1.0
OG1 D:THR47 4.7 33.3 1.0
NH1 D:ARG142 4.7 29.6 1.0
O2 D:KPI166 4.9 32.5 1.0
C1 D:KPI166 4.9 37.3 1.0
CZ D:PHE248 4.9 38.8 1.0
O D:HOH512 4.9 33.1 1.0
OG1 D:THR48 4.9 27.9 1.0
O D:ASN252 5.0 29.4 1.0

Magnesium binding site 7 out of 10 in 7kxh

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Magnesium binding site 7 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 7 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:31.4
occ:1.00
 O D:HOH435 3.1 43.9 1.0
N D:VAL107 3.1 28.9 1.0
N D:GLY82 3.3 31.7 1.0
O D:LEU105 3.5 35.3 1.0
CA D:GLY82 3.6 35.0 1.0
O A:HOH404 3.6 45.7 1.0
CB D:VAL107 3.7 29.3 1.0
CA D:SER106 3.7 31.4 1.0
N D:ALA81 3.8 29.8 1.0
C D:LEU105 3.8 35.2 1.0
CG1 D:VAL107 3.8 29.1 1.0
C D:SER106 3.9 29.9 1.0
N D:SER106 3.9 34.7 1.0
CA D:VAL107 4.0 29.3 1.0
CA D:GLY80 4.2 31.3 1.0
CG D:LEU105 4.2 32.5 1.0
CD2 D:TYR137 4.3 27.2 1.0
CD2 D:LEU105 4.3 32.2 1.0
C D:GLY80 4.4 34.6 1.0
C D:ALA81 4.4 33.0 1.0
CB D:LEU105 4.5 31.9 1.0
C D:GLY82 4.7 32.1 1.0
CA D:ALA81 4.7 32.1 1.0
CA D:LEU105 4.8 32.3 1.0
CE2 D:TYR137 4.9 30.2 1.0
O D:GLY82 4.9 32.5 1.0
O D:VAL45 5.0 34.6 1.0

Magnesium binding site 8 out of 10 in 7kxh

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Magnesium binding site 8 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 8 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:60.8
occ:1.00
 CG D:LYS32 3.8 50.8 1.0
CD1 D:ILE35 4.2 34.5 1.0
CG2 D:ILE35 4.2 36.9 1.0
CB D:ILE35 4.5 37.2 1.0
CB D:LYS32 4.6 42.4 1.0
CG2 D:THR73 4.6 47.1 1.0
O D:LYS32 4.7 35.8 1.0
CA D:LYS32 4.7 38.2 1.0
CD D:LYS32 4.7 57.1 1.0
CE D:LYS32 5.0 60.6 1.0

Magnesium binding site 9 out of 10 in 7kxh

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Magnesium binding site 9 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 9 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:31.1
occ:1.00
 N F:VAL107 3.3 27.9 1.0
N F:GLY82 3.3 30.4 1.0
O F:HOH481 3.4 41.8 1.0
O F:LEU105 3.4 32.8 1.0
O E:HOH403 3.5 50.9 1.0
C F:LEU105 3.8 31.4 1.0
CA F:GLY82 3.8 32.3 1.0
N F:ALA81 3.8 29.1 1.0
CB F:VAL107 3.8 28.7 1.0
CA F:SER106 3.9 29.2 1.0
N F:SER106 4.0 29.8 1.0
CG1 F:VAL107 4.0 28.7 1.0
C F:SER106 4.0 29.5 1.0
CG F:LEU105 4.1 26.2 1.0
CA F:GLY80 4.1 32.0 1.0
CA F:VAL107 4.1 27.9 1.0
CD2 F:LEU105 4.2 25.7 1.0
CD2 F:TYR137 4.2 26.8 1.0
C F:GLY80 4.3 32.3 1.0
CB F:LEU105 4.4 26.4 1.0
C F:ALA81 4.4 30.9 1.0
CA F:ALA81 4.7 29.8 1.0
CE2 F:TYR137 4.7 29.4 1.0
CA F:LEU105 4.7 28.7 1.0
O F:VAL45 4.8 33.5 1.0
C F:GLY82 4.8 31.1 1.0
CA F:GLY46 4.9 31.5 1.0

Magnesium binding site 10 out of 10 in 7kxh

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Magnesium binding site 10 out of 10 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine 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 10 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site in C2221 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:66.7
occ:1.00
 O F:TYR261 3.9 47.1 1.0
O F:LEU262 4.3 50.4 1.0
O F:HOH418 4.3 47.4 1.0
CE2 F:TYR261 4.4 46.8 1.0
CZ F:TYR261 4.5 49.6 1.0
CA F:LEU262 4.6 51.3 1.0
OH F:TYR261 4.7 52.9 1.0
C F:LEU262 4.7 50.0 1.0
C F:TYR261 4.8 48.7 1.0
CD2 F:TYR261 4.9 47.4 1.0
CD2 F:LEU262 5.0 49.5 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 22:59:41 2024

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