Magnesium in PDB 6u01: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site, PDB code: 6u01 was solved by S.Saran, M.Majdi Yazdi, L.Lehnert, D.R.J.Palmer, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.44 / 1.87
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.990, 231.420, 200.650, 90.00, 90.00, 90.00
R / Rfree (%) 18.9 / 22.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active Site (pdb code 6u01). 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, N84D Mutant with Pyruvate Bound in the Active Site, PDB code: 6u01:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6;

Magnesium binding site 1 out of 6 in 6u01

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Magnesium binding site 1 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active 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, N84D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:23.3
occ:1.00
 O B:HOH436 1.9 31.4 1.0
O B:HOH402 2.0 35.6 1.0
O B:HOH445 2.0 25.7 1.0
O B:HOH433 3.9 28.8 1.0
O B:HOH449 4.0 25.4 1.0
O B:THR73 4.1 25.4 1.0
OD1 B:ASP102 4.1 26.2 1.0
O B:VAL75 4.2 23.5 1.0
OD2 B:ASP102 4.4 24.8 1.0
O B:CYS70 4.5 21.9 1.0
CG B:ASP102 4.6 21.5 1.0
O B:HOH418 4.8 25.8 1.0
CD B:LYS76 5.0 33.2 1.0

Magnesium binding site 2 out of 6 in 6u01

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Magnesium binding site 2 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active 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, N84D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:26.0
occ:1.00
 O B:HOH471 2.0 34.0 1.0
O B:HOH455 2.0 29.7 1.0
OD2 B:ASP227 2.1 23.3 1.0
CG B:ASP227 3.0 25.7 1.0
OD1 B:ASP227 3.4 29.0 1.0
O B:HOH502 4.1 30.3 1.0
CB B:ASP227 4.3 22.9 1.0
O B:HOH535 4.7 24.0 1.0

Magnesium binding site 3 out of 6 in 6u01

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Magnesium binding site 3 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active 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, N84D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:33.6
occ:1.00
 O2 B:EDO305 2.0 39.0 1.0
OD1 B:ASN195 2.8 21.1 1.0
O B:SER189 3.1 19.6 1.0
O B:ILE207 3.2 20.1 1.0
OD1 B:ASP192 3.3 23.2 1.0
C2 B:EDO305 3.3 29.4 1.0
N B:GLU191 3.5 22.8 1.0
N B:ASP192 3.5 21.5 1.0
OG B:SER189 3.6 20.5 1.0
CA B:ASP192 3.6 22.1 1.0
CG B:ASN195 3.6 18.3 1.0
C B:GLU191 3.6 20.3 1.0
CG B:ASP192 3.7 23.0 1.0
C B:SER189 3.7 22.7 1.0
C B:ILE207 3.7 20.9 1.0
ND2 B:ASN195 3.8 20.4 1.0
CA B:SER208 3.8 23.2 1.0
CB B:VAL206 3.9 18.3 1.0
C B:GLY190 3.9 24.7 1.0
CA B:GLY190 4.0 20.1 1.0
O B:GLU191 4.0 18.6 1.0
N B:ILE207 4.1 16.4 1.0
CA B:GLU191 4.1 19.8 1.0
N B:SER208 4.1 18.0 1.0
N B:GLY190 4.2 16.3 1.0
CB B:SER189 4.2 16.7 1.0
OD2 B:ASP192 4.2 23.7 1.0
CB B:SER208 4.2 18.6 1.0
CB B:ASP192 4.3 22.8 1.0
C1 B:EDO305 4.3 29.5 1.0
O1 B:EDO305 4.5 25.9 1.0
CA B:VAL206 4.5 20.6 1.0
CG1 B:VAL206 4.6 21.3 1.0
CA B:SER189 4.6 18.8 1.0
O B:GLY190 4.6 23.5 1.0
CA B:ILE207 4.6 14.6 1.0
CG2 B:VAL206 4.7 17.9 1.0
OG B:SER208 4.7 17.6 1.0
C B:VAL206 4.7 19.8 1.0
C B:ASP192 4.9 22.3 1.0
C B:SER208 4.9 25.2 1.0

Magnesium binding site 4 out of 6 in 6u01

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Magnesium binding site 4 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active 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, N84D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:48.5
occ:1.00
 OD1 C:ASP158 2.7 32.0 1.0
CG C:ASP158 3.6 32.8 1.0
OD2 C:ASP158 3.7 32.1 1.0
CB C:ARG157 4.1 25.9 1.0
CA C:LYS154 4.3 24.9 1.0
O C:LYS154 4.3 24.5 1.0
CG C:LYS154 4.4 33.6 1.0
CD C:ARG157 4.5 27.3 1.0
CB C:LYS154 4.6 30.9 1.0
C C:LYS154 4.8 22.8 1.0
CG C:ARG157 5.0 26.0 1.0
CB C:ASP158 5.0 29.1 1.0

Magnesium binding site 5 out of 6 in 6u01

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Magnesium binding site 5 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active 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, N84D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:54.5
occ:1.00
 CG2 E:THR55 4.1 30.0 1.0
CG F:HIS87 4.1 28.2 1.0
CD2 F:HIS87 4.1 28.9 1.0
ND1 F:HIS87 4.3 33.5 1.0
NH1 E:ARG272 4.3 36.9 1.0
NE2 F:HIS87 4.3 30.0 1.0
CZ E:ARG272 4.4 33.6 1.0
CE1 F:HIS87 4.4 31.2 1.0
NH2 E:ARG272 4.5 35.8 1.0
CB F:HIS87 4.5 27.2 1.0
NE E:ARG272 4.9 36.3 1.0

Magnesium binding site 6 out of 6 in 6u01

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Magnesium binding site 6 out of 6 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84D Mutant with Pyruvate Bound in the Active 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, N84D Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg302

b:34.8
occ:1.00
 O F:HOH459 1.9 31.8 1.0
O F:HOH430 2.2 34.0 1.0
OD2 F:ASP158 3.9 27.6 1.0
OD1 F:ASP158 4.2 25.7 1.0
CG F:ASP158 4.3 25.1 1.0
OH F:TYR120 4.8 29.5 1.0
O F:HOH460 4.8 31.7 1.0
O F:HOH539 4.8 28.6 1.0

Reference:

M.Majdi Yazdi, S.Saran, T.Mrozowich, C.Lehnert, T.R.Patel, D.A.R.Sanders, D.R.J.Palmer. Asparagine-84, A Regulatory Allosteric Site Residue, Helps Maintain the Quaternary Structure of Campylobacter Jejuni Dihydrodipicolinate Synthase. J.Struct.Biol. 07409 2019.
ISSN: ESSN 1095-8657
PubMed: 31678256
DOI: 10.1016/J.JSB.2019.107409
Page generated: Tue Dec 15 00:58:54 2020

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