Magnesium in PDB 7kxg: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site

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

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site:
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-Histidine Bound at the Allosteric Site, PDB code: 7kxg 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) 46.36 / 2.28
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 85.31, 231.72, 202.35, 90, 90, 90
R / Rfree (%) 17 / 20.8

Magnesium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 17;

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-Histidine Bound at the Allosteric Site (pdb code 7kxg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 17 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site, PDB code: 7kxg:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 17 in 7kxg

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Magnesium binding site 1 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric 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 with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:37.3
occ:1.00
 OD1 A:ASN171 3.2 34.9 1.0
N A:ASP173 3.2 26.5 1.0
O B:GLY170 3.3 45.0 1.0
CB A:ASP173 3.4 29.9 1.0
O A:HOH481 3.4 24.8 1.0
CA B:GLY170 3.5 34.5 1.0
N A:ILE172 3.6 29.5 1.0
C B:GLY170 3.6 38.2 1.0
CG2 A:ILE172 3.9 30.9 1.0
CA A:ASP173 3.9 29.3 1.0
CA A:ASN171 4.0 30.7 1.0
C A:ASN171 4.0 30.0 1.0
CG A:ASN171 4.2 32.5 1.0
C A:ILE172 4.2 28.8 1.0
CA A:ILE172 4.3 30.7 1.0
CG2 B:ILE194 4.5 25.9 1.0
N B:ASN171 4.6 32.5 1.0
CB A:ILE172 4.7 31.8 1.0
CD1 B:ILE194 4.7 22.4 1.0
CB A:ASN171 4.7 31.1 1.0
CG A:ASP173 4.7 34.0 1.0
O A:GLY170 4.8 41.5 1.0
O A:ASN171 4.9 28.8 1.0
N B:GLY170 4.9 34.7 1.0

Magnesium binding site 2 out of 17 in 7kxg

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Magnesium binding site 2 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric 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 with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:28.6
occ:1.00
 N A:GLY82 3.0 33.5 1.0
N A:VAL107 3.1 28.1 1.0
O A:LEU105 3.1 32.0 1.0
CA A:GLY82 3.5 31.1 1.0
CA A:SER106 3.6 31.2 1.0
C A:LEU105 3.7 31.2 1.0
N A:ALA81 3.7 27.4 1.0
CB A:VAL107 3.7 26.4 1.0
CG1 A:VAL107 3.7 28.0 1.0
C A:SER106 3.8 29.1 1.0
N A:SER106 3.9 27.7 1.0
CA A:VAL107 4.0 24.8 1.0
C A:ALA81 4.2 31.2 1.0
CA A:GLY80 4.3 28.1 1.0
C A:GLY80 4.4 26.9 1.0
CG A:LEU105 4.5 25.7 1.0
C A:GLY82 4.5 28.2 1.0
CA A:ALA81 4.5 31.3 1.0
CD2 A:LEU105 4.6 22.8 1.0
CB A:LEU105 4.7 25.2 1.0
O A:GLY82 4.7 33.1 1.0
CA A:LEU105 4.8 27.7 1.0
CB A:SER106 4.9 28.2 1.0
O A:SER106 5.0 29.1 1.0

Magnesium binding site 3 out of 17 in 7kxg

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Magnesium binding site 3 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric 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 with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:40.7
occ:1.00
 O B:HOH472 2.2 36.7 1.0
OD2 B:ASP227 2.4 39.2 1.0
O B:HOH415 2.5 32.2 1.0
CG B:ASP227 2.9 38.7 1.0
OD1 B:ASP227 2.9 38.3 1.0
CB B:ASP227 4.2 37.6 1.0
O B:HOH420 4.5 51.7 1.0
O B:HOH453 4.6 29.6 1.0

Magnesium binding site 4 out of 17 in 7kxg

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Magnesium binding site 4 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric 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 with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:61.5
occ:1.00
 O B:HOH530 2.0 60.5 1.0
CD1 B:ILE5 4.2 26.8 1.0
CD1 B:ILE7 4.3 22.7 1.0
CE B:MET186 4.3 31.4 1.0
SD B:MET186 4.5 35.0 1.0
CE B:LYS204 4.8 43.8 1.0
CG B:LYS204 4.8 34.7 1.0
CD B:LYS204 4.8 40.5 1.0

Magnesium binding site 5 out of 17 in 7kxg

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Magnesium binding site 5 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric 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 with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:40.9
occ:1.00
 O B:HOH439 2.0 32.0 1.0
OD1 B:ASP102 3.6 41.5 1.0
OD2 B:ASP102 3.9 39.1 1.0
O B:HOH410 4.1 44.7 1.0
CG B:ASP102 4.2 39.5 1.0
O B:HOH486 4.2 54.1 1.0
O B:HOH461 4.4 32.2 1.0
O B:HOH421 4.4 33.1 1.0
O B:VAL75 4.5 37.2 1.0
O B:CYS70 4.7 33.9 1.0
O B:THR73 4.9 42.8 1.0

Magnesium binding site 6 out of 17 in 7kxg

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Magnesium binding site 6 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric 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 with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:34.4
occ:1.00
 O B:LEU105 3.1 37.0 1.0
N B:GLY82 3.1 34.8 1.0
N B:VAL107 3.1 30.4 1.0
CA B:GLY82 3.6 29.6 1.0
CG1 B:VAL107 3.6 31.9 1.0
C B:LEU105 3.7 35.8 1.0
CA B:SER106 3.7 31.7 1.0
N B:ALA81 3.7 29.2 1.0
CB B:VAL107 3.7 35.2 1.0
C B:SER106 3.9 29.6 1.0
N B:SER106 3.9 33.1 1.0
CA B:VAL107 4.0 31.0 1.0
CA B:GLY80 4.2 30.8 1.0
C B:ALA81 4.2 33.7 1.0
C B:GLY80 4.4 29.2 1.0
CG B:LEU105 4.4 27.2 1.0
CD2 B:LEU105 4.5 30.0 1.0
CA B:ALA81 4.6 33.1 1.0
O B:HOH426 4.6 39.1 1.0
C B:GLY82 4.6 27.6 1.0
CB B:LEU105 4.6 29.5 1.0
CA B:LEU105 4.8 33.0 1.0
O B:GLY82 4.8 29.3 1.0

Magnesium binding site 7 out of 17 in 7kxg

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Magnesium binding site 7 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site


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 L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:35.6
occ:1.00
 N C:ASN252 3.2 26.6 1.0
CD2 C:PHE248 3.3 35.3 1.0
CA C:SER251 3.6 26.3 1.0
NH2 C:ARG142 3.6 30.6 1.0
CB C:ASN252 3.9 22.6 1.0
CE2 C:PHE248 3.9 33.6 1.0
C C:SER251 3.9 26.5 1.0
CE A:LYS113 4.1 61.7 1.0
CA C:ASN252 4.1 22.8 1.0
CB C:SER251 4.2 31.0 1.0
O C:HOH464 4.3 51.3 1.0
CG C:PHE248 4.4 35.0 1.0
O C:GLU250 4.5 25.9 1.0
CZ C:ARG142 4.5 30.5 1.0
CB C:PHE248 4.6 29.5 1.0
N C:SER251 4.7 24.5 1.0
OG C:SER251 4.7 39.9 1.0
O C:ASN252 4.8 30.0 1.0
NE C:ARG142 4.9 29.7 1.0
C C:GLU250 5.0 26.9 1.0

Magnesium binding site 8 out of 17 in 7kxg

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Magnesium binding site 8 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site


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 L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:48.9
occ:1.00
 CE2 C:PHE156 3.6 29.5 1.0
NH1 C:ARG184 3.6 40.6 1.0
CZ C:PHE156 3.7 29.5 1.0
CE C:LYS3 3.7 35.9 1.0
CZ C:ARG184 3.8 39.8 1.0
O C:HOH520 3.9 44.5 1.0
NE C:ARG184 4.0 38.0 1.0
CD C:ARG184 4.2 32.7 1.0
OD1 C:ASP2 4.3 74.0 1.0
NH2 C:ARG184 4.3 39.4 1.0
CD C:LYS3 4.4 37.5 1.0
CD2 C:PHE156 4.6 29.3 1.0
CG C:LYS3 4.6 43.2 1.0
CB C:ARG184 4.7 29.2 1.0
CE1 C:PHE156 4.8 28.0 1.0
CG C:ASP2 4.8 73.2 1.0
CB C:ASP2 4.9 67.6 1.0
NZ C:LYS3 5.0 32.9 1.0

Magnesium binding site 9 out of 17 in 7kxg

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Magnesium binding site 9 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site


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 L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:47.0
occ:1.00
 N C:LYS231 3.1 33.5 1.0
N C:TYR230 3.2 31.8 1.0
O C:HOH440 3.3 60.3 1.0
CB C:LYS231 3.8 46.5 1.0
CA C:TYR230 3.8 34.8 1.0
C C:ASN229 3.9 32.6 1.0
C C:TYR230 3.9 34.1 1.0
O C:GLU228 3.9 32.2 1.0
OD1 C:ASN229 4.0 32.9 1.0
CB C:TYR230 4.0 40.1 1.0
CA C:LYS231 4.0 38.8 1.0
CA C:ASN229 4.1 34.0 1.0
O C:HOH452 4.2 44.1 1.0
OE1 D:GLU228 4.7 60.1 1.0
CG C:ASN229 4.8 36.5 1.0
O C:ASN229 4.8 33.2 1.0
C C:GLU228 4.8 36.2 1.0
CE2 D:TYR230 4.8 55.5 1.0
CG C:TYR230 4.9 46.2 1.0
N C:ASN229 5.0 33.2 1.0

Magnesium binding site 10 out of 17 in 7kxg

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Magnesium binding site 10 out of 17 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni with Pyruvate Bound in the Active Site and L-Histidine Bound at the Allosteric Site


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 L-Histidine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:35.0
occ:1.00
 N D:GLY82 3.2 34.4 1.0
O D:LEU105 3.2 40.2 1.0
N D:VAL107 3.2 29.0 1.0
N D:ALA81 3.7 27.3 1.0
CA D:GLY82 3.7 32.1 1.0
CG1 D:VAL107 3.7 30.6 1.0
C D:LEU105 3.8 38.4 1.0
CB D:VAL107 3.8 30.9 1.0
CA D:SER106 3.8 33.0 1.0
C D:SER106 4.0 29.4 1.0
N D:SER106 4.0 37.6 1.0
CA D:GLY80 4.1 33.7 1.0
CA D:VAL107 4.1 29.0 1.0
C D:GLY80 4.3 30.1 1.0
C D:ALA81 4.3 35.9 1.0
CG D:LEU105 4.4 34.0 1.0
CD2 D:LEU105 4.5 31.7 1.0
CA D:ALA81 4.6 32.7 1.0
CB D:LEU105 4.6 35.4 1.0
C D:GLY82 4.6 35.0 1.0
O D:GLY82 4.7 37.4 1.0
CA D:LEU105 4.8 36.0 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: Fri Dec 17 10:33:06 2021

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