Atomistry » Magnesium » PDB 7koc-7kum » 7kr8
Atomistry »
  Magnesium »
    PDB 7koc-7kum »
      7kr8 »

Magnesium in PDB 7kr8: Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site

Enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site

All present enzymatic activity of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site:
4.3.3.7;

Protein crystallography data

The structure of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site, PDB code: 7kr8 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) 43.74 / 2.12
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 84.93, 231.65, 200.17, 90, 90, 90
R / Rfree (%) 17.3 / 20.9

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site (pdb code 7kr8). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 7 binding sites of Magnesium where determined in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site, PDB code: 7kr8:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7;

Magnesium binding site 1 out of 7 in 7kr8

Go back to Magnesium Binding Sites List in 7kr8
Magnesium binding site 1 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg301

b:42.8
occ:1.00
 OD1 B:ASN171 3.1 25.6 1.0
N B:ASP173 3.2 26.2 1.0
CB B:ASP173 3.4 23.6 1.0
N B:ILE172 3.5 28.1 1.0
CA B:ASN171 3.9 29.5 1.0
C B:ASN171 3.9 28.7 1.0
CA B:ASP173 3.9 26.3 1.0
CG2 B:ILE172 4.0 27.1 1.0
CG B:ASN171 4.1 25.2 1.0
C B:ILE172 4.2 26.5 1.0
CA B:ILE172 4.3 26.9 1.0
CB B:ASN171 4.6 28.0 1.0
O B:GLY170 4.6 40.0 1.0
CB B:ILE172 4.8 25.4 1.0
CG B:ASP173 4.8 28.9 1.0
O B:ASN171 4.8 24.7 1.0
N B:ASN171 5.0 29.2 1.0

Magnesium binding site 2 out of 7 in 7kr8

Go back to Magnesium Binding Sites List in 7kr8
Magnesium binding site 2 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg301

b:54.5
occ:1.00
 CB C:ALA220 4.1 26.3 1.0
O C:HOH519 4.3 42.5 1.0
CE2 C:PHE224 4.5 25.9 1.0
CZ C:PHE224 4.6 20.5 1.0
O C:HOH534 4.9 48.6 1.0

Magnesium binding site 3 out of 7 in 7kr8

Go back to Magnesium Binding Sites List in 7kr8
Magnesium binding site 3 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:36.5
occ:1.00
 O D:PRO109 2.7 27.7 1.0
O D:THR143 2.8 26.7 1.0
N D:LYS113 2.8 24.2 1.0
CA D:LYS113 3.0 25.8 1.0
N D:TYR111 3.2 28.3 1.0
CB D:CYS145 3.4 36.2 1.0
C D:TYR110 3.5 30.0 1.0
CA D:TYR110 3.6 27.8 1.0
C D:PRO109 3.7 24.3 1.0
C D:THR143 3.7 27.3 1.0
CG D:LYS113 3.8 41.6 1.0
N D:ASN112 3.8 27.1 1.0
CB D:LYS113 3.8 26.8 1.0
CD D:PRO114 3.8 28.0 1.0
N D:CYS145 3.9 27.4 1.0
C D:TYR111 3.9 28.2 1.0
SG D:CYS145 3.9 44.4 1.0
C D:ASN112 4.0 24.9 1.0
C D:GLY144 4.0 30.4 1.0
CA D:TYR111 4.1 27.7 1.0
N D:TYR110 4.1 25.3 1.0
O D:TYR110 4.1 27.4 1.0
CA D:CYS145 4.2 28.8 1.0
C D:LYS113 4.2 26.3 1.0
OD1 D:ASN112 4.3 29.2 1.0
CB D:THR143 4.4 26.9 1.0
N D:PRO114 4.4 27.8 1.0
CA D:GLY144 4.4 27.4 1.0
O D:GLY144 4.4 30.9 1.0
O D:TYR111 4.5 26.2 1.0
N D:GLY144 4.5 26.8 1.0
CA D:ASN112 4.5 27.0 1.0
CA D:THR143 4.6 25.5 1.0
CD D:LYS113 4.7 51.4 1.0
OG1 D:THR143 4.8 27.4 1.0
CA D:PRO109 4.9 21.5 1.0

Magnesium binding site 4 out of 7 in 7kr8

Go back to Magnesium Binding Sites List in 7kr8
Magnesium binding site 4 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:38.3
occ:1.00
 O D:HOH443 2.3 35.1 1.0
O D:HOH461 2.3 27.0 1.0
O D:HOH459 3.8 36.4 1.0
OD1 D:ASP102 4.0 34.5 1.0
OD2 D:ASP102 4.3 29.0 1.0
O D:VAL75 4.5 28.9 1.0
O D:CYS70 4.6 35.2 1.0
CG D:ASP102 4.6 31.8 1.0
O D:THR73 4.6 36.3 1.0
O D:HOH428 4.8 27.9 1.0

Magnesium binding site 5 out of 7 in 7kr8

Go back to Magnesium Binding Sites List in 7kr8
Magnesium binding site 5 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg303

b:44.3
occ:1.00
 O D:HOH465 2.2 39.1 1.0
OD2 D:ASP227 2.2 33.7 1.0
CG D:ASP227 3.1 31.4 1.0
OD1 D:ASP227 3.4 31.1 1.0
O D:HOH444 4.2 28.2 1.0
CB D:ASP227 4.4 27.8 1.0
O D:HOH504 4.5 38.8 1.0
O D:HOH533 4.6 32.5 1.0

Magnesium binding site 6 out of 7 in 7kr8

Go back to Magnesium Binding Sites List in 7kr8
Magnesium binding site 6 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A 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, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg301

b:50.8
occ:1.00
 O E:GLY297 2.9 42.9 1.0
ND2 E:ASN37 3.1 37.3 1.0
CE E:LYS296 3.9 50.6 1.0
C E:GLY297 4.0 42.3 1.0
CB E:LYS296 4.0 38.4 1.0
O E:PHE298 4.0 44.0 1.0
CG E:ASN37 4.0 38.2 1.0
OD1 E:ASN37 4.1 41.0 1.0
C E:PHE298 4.3 45.1 1.0
NZ E:LYS296 4.3 51.8 1.0
CG E:ARG33 4.3 30.3 1.0
CA E:PHE298 4.5 44.5 1.0
O E:HOH477 4.6 44.2 1.0
N E:GLY297 4.6 39.4 1.0
N E:PHE298 4.7 43.2 1.0
OE2 E:GLU36 4.7 46.4 1.0
CG E:LYS296 4.8 39.7 1.0
C E:LYS296 4.8 39.7 1.0
O E:ARG33 4.8 30.9 1.0
CD E:LYS296 4.9 44.8 1.0
NE E:ARG33 4.9 32.3 1.0
CA E:GLY297 4.9 40.4 1.0
CD E:ARG33 5.0 33.0 1.0
CA E:LYS296 5.0 37.5 1.0

Magnesium binding site 7 out of 7 in 7kr8

Go back to Magnesium Binding Sites List in 7kr8
Magnesium binding site 7 out of 7 in the Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A 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 7 of Dihydrodipicolinate Synthase (Dhdps) From C.Jejuni, H56A Mutant with Pyruvate Bound in the Active Site within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg302

b:54.0
occ:1.00
 NH1 E:ARG184 3.4 42.4 1.0
CE2 E:PHE156 3.7 29.3 1.0
CZ E:ARG184 3.8 41.0 1.0
CE E:LYS3 3.9 40.0 1.0
CZ E:PHE156 4.0 31.7 1.0
NE E:ARG184 4.2 36.3 1.0
NH2 E:ARG184 4.3 38.5 1.0
CD E:ARG184 4.5 33.8 1.0
CD2 E:PHE156 4.5 28.8 1.0
O E:HOH535 4.6 41.3 1.0
CD E:LYS3 4.7 39.2 1.0
CG E:LYS3 4.8 41.9 1.0
CB E:ARG184 5.0 31.8 1.0
NZ E:LYS3 5.0 38.4 1.0
O E:PHE156 5.0 29.7 1.0
CE1 E:PHE156 5.0 29.6 1.0

Reference:

S.Saran, Y.Skovpen, M.M.Yazdi, D.R.J.Palmer, D.A.R.Sanders. Allosteric Site Residue 'H56' Caps the Inhibitor at the Tight Dimer Interface For Transmitting the Allosteric Inhibition Signals in Cj.Dhdps To Be Published.
Page generated: Wed Oct 2 22:33:20 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy