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Magnesium in PDB 7kkd: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site, PDB code: 7kkd was solved by S.Saran, M.Majdi Yazdi, D.A.R.Sanders, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.11 / 1.60
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.55, 225.54, 199.98, 90, 90, 90
R / Rfree (%) 15.3 / 18.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site (pdb code 7kkd). 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site, PDB code: 7kkd:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 7kkd

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Magnesium binding site 1 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:15.4
occ:1.00
 O A:HOH421 3.2 19.0 1.0
N A:VAL107 3.2 14.0 1.0
N A:GLY82 3.3 16.7 1.0
O F:HOH443 3.4 23.9 1.0
O A:LEU105 3.5 15.2 1.0
CB A:VAL107 3.7 11.2 1.0
N A:ALA81 3.8 12.2 1.0
CA A:GLY82 3.8 16.7 1.0
CG1 A:VAL107 3.8 16.0 1.0
CA A:SER106 3.9 9.7 1.0
C A:LEU105 3.9 11.3 1.0
C A:SER106 4.0 11.7 1.0
CA A:VAL107 4.1 13.5 1.0
N A:SER106 4.1 9.6 1.0
CA A:GLY80 4.1 10.9 1.0
C A:GLY80 4.3 15.8 1.0
CG A:LEU105 4.3 11.2 1.0
C A:ALA81 4.4 15.7 1.0
CD2 A:TYR137 4.4 16.5 1.0
CD2 A:LEU105 4.5 13.0 1.0
CB A:LEU105 4.7 12.6 1.0
CA A:ALA81 4.7 13.8 1.0
O A:HOH513 4.8 31.2 1.0
C A:GLY82 4.9 13.2 1.0
CE2 A:TYR137 5.0 15.9 1.0
CA A:LEU105 5.0 10.6 1.0
CA A:GLY46 5.0 15.9 1.0

Magnesium binding site 2 out of 9 in 7kkd

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Magnesium binding site 2 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg302

b:14.2
occ:1.00
 O B:HOH482 2.1 15.4 1.0
O B:HOH423 2.1 20.4 1.0
O B:HOH416 2.1 18.1 1.0
O B:HOH479 4.1 18.6 1.0
OD1 B:ASP102 4.2 18.2 1.0
O B:THR73 4.2 16.8 1.0
O B:VAL75 4.3 13.3 1.0
OD2 B:ASP102 4.3 15.4 1.0
O B:HOH627 4.4 39.2 1.0
O B:CYS70 4.5 12.6 1.0
CG B:ASP102 4.7 16.8 1.0
O B:HOH438 4.9 14.3 1.0

Magnesium binding site 3 out of 9 in 7kkd

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Magnesium binding site 3 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:32.8
occ:1.00
 O2 B:EDO311 2.5 53.6 1.0
NH2 B:ARG157 3.3 14.7 1.0
NH1 B:ARG157 3.4 16.1 1.0
CZ B:ARG157 3.8 15.8 1.0
C2 B:EDO311 3.8 39.3 1.0
CB B:HIS181 3.9 14.7 1.0
O B:HIS181 3.9 14.1 1.0
C1 B:EDO311 4.2 38.9 1.0
CD2 B:HIS181 4.4 18.2 1.0
CG B:HIS181 4.4 16.9 1.0
C B:HIS181 4.6 14.7 1.0
CA B:HIS181 4.6 12.9 1.0
CG2 B:ILE153 4.8 11.3 1.0
CD1 B:ILE153 4.9 12.8 1.0

Magnesium binding site 4 out of 9 in 7kkd

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Magnesium binding site 4 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:39.6
occ:1.00
 O B:HOH658 2.5 31.0 1.0
O B:HOH566 2.8 24.6 1.0
O B:HOH620 3.0 40.8 1.0
NZ B:LYS245 3.0 21.4 1.0
CB B:PHE248 3.6 14.8 1.0
CE B:LYS245 3.7 23.0 1.0
CG B:PHE248 4.0 16.7 1.0
O B:HOH668 4.0 28.9 1.0
CD B:LYS245 4.0 21.9 1.0
O B:HOH705 4.1 38.2 1.0
O B:HOH564 4.3 14.6 1.0
CD1 B:PHE248 4.4 20.0 1.0
O B:HOH576 4.5 26.6 1.0
O A:HOH445 4.6 17.2 1.0
O B:HOH507 4.6 31.8 1.0
CD2 B:PHE248 4.6 23.5 1.0
O B:LYS245 4.7 14.3 1.0
O B:HOH652 4.8 16.1 1.0
CA B:LYS245 4.8 12.5 1.0
OD2 A:ASP173 5.0 15.1 1.0

Magnesium binding site 5 out of 9 in 7kkd

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Magnesium binding site 5 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg305

b:22.8
occ:1.00
 O B:HOH588 1.8 15.5 1.0
OD2 B:ASP227 2.1 17.4 1.0
O B:HOH524 2.7 20.0 1.0
CG B:ASP227 3.2 20.9 1.0
OD1 B:ASP227 3.6 18.6 1.0
O B:HOH508 3.8 13.4 1.0
O B:HOH642 3.9 23.6 1.0
O B:HOH648 4.0 45.9 1.0
CB B:ASP227 4.4 13.1 1.0

Magnesium binding site 6 out of 9 in 7kkd

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Magnesium binding site 6 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:35.6
occ:1.00
 O C:HOH729 2.7 45.6 1.0
O C:LYS231 2.8 15.6 1.0
O C:HOH467 3.0 22.3 1.0
N C:LYS235 3.5 12.1 1.0
CG C:LYS234 3.7 13.1 1.0
C C:LYS231 3.7 15.3 1.0
CB C:LYS234 3.8 13.3 1.0
CD C:LYS234 3.9 14.5 1.0
CG C:LYS231 3.9 24.1 1.0
CA C:LYS231 3.9 17.4 1.0
CA C:LYS235 4.0 12.4 1.0
CB C:LYS235 4.0 13.7 1.0
C C:LYS234 4.1 12.1 1.0
CE C:LYS234 4.1 15.4 1.0
CB C:LYS231 4.5 22.6 1.0
CA C:LYS234 4.5 12.4 1.0
O C:LYS234 4.8 12.7 1.0
CG C:LYS235 4.9 29.1 1.0
O C:TYR230 4.9 16.1 1.0
N C:GLU232 4.9 15.8 1.0
O C:HOH724 4.9 35.0 1.0
N C:LYS234 4.9 12.8 1.0

Magnesium binding site 7 out of 9 in 7kkd

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Magnesium binding site 7 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:14.9
occ:1.00
 O D:HOH434 3.1 18.4 1.0
N D:VAL107 3.2 11.2 1.0
N D:GLY82 3.3 16.3 1.0
O D:LEU105 3.4 15.1 1.0
O C:HOH471 3.5 24.5 1.0
CB D:VAL107 3.7 11.3 1.0
N D:ALA81 3.7 12.4 1.0
CA D:GLY82 3.8 16.2 1.0
CG1 D:VAL107 3.8 12.2 1.0
C D:LEU105 3.9 11.5 1.0
CA D:SER106 3.9 8.1 1.0
C D:SER106 4.0 13.1 1.0
CA D:VAL107 4.0 10.0 1.0
N D:SER106 4.1 9.5 1.0
CA D:GLY80 4.2 13.7 1.0
CG D:LEU105 4.3 11.6 1.0
C D:GLY80 4.4 12.4 1.0
C D:ALA81 4.4 17.5 1.0
CD2 D:TYR137 4.4 18.8 1.0
CD2 D:LEU105 4.4 14.1 1.0
O D:HOH448 4.6 29.1 1.0
CA D:ALA81 4.7 12.0 1.0
CB D:LEU105 4.7 10.1 1.0
C D:GLY82 4.8 17.0 1.0
CA D:LEU105 4.9 8.8 1.0
CE2 D:TYR137 5.0 19.5 1.0

Magnesium binding site 8 out of 9 in 7kkd

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Magnesium binding site 8 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:37.3
occ:1.00
 O D:HOH504 2.8 29.9 1.0
O D:HOH551 3.0 21.7 1.0
O D:HOH715 3.6 39.2 1.0
CG D:ASN242 3.8 13.0 1.0
OD1 D:ASN242 3.8 15.2 1.0
CG2 D:VAL289 3.8 15.1 1.0
O D:HOH568 4.0 25.6 1.0
CB D:ASN242 4.1 11.4 1.0
O D:HOH666 4.1 37.2 1.0
ND2 D:ASN242 4.2 15.7 1.0
O D:HOH713 4.7 42.2 1.0
NZ D:LYS292 4.7 40.9 1.0
CA D:ASN242 4.7 10.8 1.0
O D:HOH696 4.8 38.1 1.0
O D:HOH590 5.0 26.3 1.0

Magnesium binding site 9 out of 9 in 7kkd

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Magnesium binding site 9 out of 9 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine 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, N84A Mutant with Pyruvate Bound in the Active Site and R,R-Bislysine Bound at the Allosteric Site within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mg301

b:23.7
occ:1.00
 OD1 F:ASP40 2.0 15.9 1.0
O F:HOH571 2.2 20.7 1.0
O F:HOH492 2.2 28.8 1.0
O F:HOH607 2.4 27.4 1.0
CG F:ASP40 3.2 12.6 1.0
OD2 F:ASP40 4.0 12.5 1.0
CB F:ASP40 4.2 12.7 1.0
O F:GLY38 4.2 15.6 1.0
NE2 F:HIS223 4.2 12.3 1.0
OXT F:ACT303 4.3 41.9 1.0
O F:ACT303 4.3 33.1 1.0
CA F:ASP40 4.3 13.9 1.0
CE1 F:HIS223 4.4 12.8 1.0
O F:HOH444 4.4 36.5 1.0
O F:ILE39 4.6 19.6 1.0
C F:ACT303 4.7 42.0 1.0
N F:ASP40 4.8 14.0 1.0
C F:ILE39 4.9 15.5 1.0

Reference:

S.Saran, M.Majdi Yazd, D.R.J.Palmer, D.A.R.Sanders. A Tight Dimer Interface N84 Residue, Plays A Critical Role in the Transmission of the Allosteric Inhibition Signals in Cj.Dhdps To Be Published.
Page generated: Wed Oct 2 22:22:24 2024

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