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Sodium in PDB 3re3: Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis

Enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis

All present enzymatic activity of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis:
4.6.1.12;

Protein crystallography data

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis, PDB code: 3re3 was solved by Y.Kim, M.Makowska-Grzyska, K.Kwon, W.F.Anderson, A.Joachimiak, Center Forstructural Genomics Of Infectious Diseases (Csgid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.62 / 2.65
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 96.116, 96.116, 155.308, 90.00, 90.00, 120.00
R / Rfree (%) 17.3 / 22.7

Other elements in 3re3:

The structure of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis (pdb code 3re3). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis, PDB code: 3re3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in 3re3

Go back to Sodium Binding Sites List in 3re3
Sodium binding site 1 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na165

b:70.5
occ:1.00
 O A:GLY53 2.9 44.8 1.0
NH2 A:ARG4 3.5 54.9 1.0
O A:ALA54 3.6 59.4 1.0
N A:GLY56 3.8 47.4 1.0
C A:ALA54 4.0 45.1 1.0
CA A:GLY56 4.0 38.0 1.0
C A:GLY53 4.0 44.8 1.0
CA A:ALA54 4.3 40.3 1.0
N A:ALA54 4.6 36.8 1.0
N A:LEU55 4.7 42.1 1.0
O A:ILE5 4.7 59.0 1.0
C A:LEU55 4.7 52.0 1.0
CZ A:ARG4 4.7 68.5 1.0

Sodium binding site 2 out of 3 in 3re3

Go back to Sodium Binding Sites List in 3re3
Sodium binding site 2 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na160

b:68.2
occ:1.00
 ND2 B:ASN96 2.9 50.4 1.0
O D:GLY53 3.0 50.9 1.0
O B:ILE97 3.0 50.4 1.0
NH2 D:ARG4 3.5 41.2 1.0
CB B:ASN131 3.5 35.5 1.0
C B:ILE97 3.6 47.2 1.0
N B:ASN131 3.7 41.4 1.0
N B:ILE97 3.8 50.6 1.0
CB B:ASN96 3.8 48.7 1.0
CG B:ASN96 3.8 54.7 1.0
O D:ALA54 3.9 54.5 1.0
O B:GLN129 3.9 45.3 1.0
C D:ALA54 4.1 49.3 1.0
C D:GLY53 4.1 46.7 1.0
N D:GLY56 4.1 55.5 1.0
N B:ASP98 4.2 48.8 1.0
CA D:ALA54 4.2 49.9 1.0
CA B:ASN131 4.2 42.6 1.0
C B:GLN129 4.3 50.6 1.0
CZ D:ARG4 4.3 57.5 1.0
CA B:ILE97 4.3 49.3 1.0
CB B:ASP98 4.3 52.8 1.0
CA B:ASP98 4.4 52.5 1.0
C B:ILE130 4.4 48.9 1.0
CA B:ILE130 4.5 47.8 1.0
CA D:GLY56 4.5 50.4 1.0
C B:ASN96 4.5 52.5 1.0
N B:ILE130 4.6 45.7 1.0
NE D:ARG4 4.6 59.5 1.0
O B:SER128 4.6 54.2 1.0
N D:ALA54 4.6 48.0 1.0
CA B:ASN96 4.7 50.9 1.0
O D:ILE5 4.7 49.2 1.0
CG B:ASN131 4.8 44.6 1.0
N D:LEU55 4.8 47.8 1.0
CG B:ASP98 4.9 61.2 1.0

Sodium binding site 3 out of 3 in 3re3

Go back to Sodium Binding Sites List in 3re3
Sodium binding site 3 out of 3 in the Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Na161

b:71.9
occ:1.00
 O C:GLY53 3.0 64.7 1.0
ND2 D:ASN96 3.1 47.6 1.0
O D:ILE97 3.2 61.1 1.0
NH2 C:ARG4 3.3 62.2 1.0
CB D:ASN131 3.6 61.5 1.0
O C:ALA54 3.6 72.1 1.0
CB D:ASN96 3.6 56.1 1.0
O D:GLN129 3.8 72.0 1.0
CG D:ASN96 3.8 61.8 1.0
O D:SER128 3.9 78.5 1.0
C D:ILE97 3.9 56.9 1.0
N D:ASN131 4.0 62.5 1.0
N C:GLY56 4.0 66.9 1.0
N D:ILE97 4.0 50.8 1.0
C D:GLN129 4.0 67.2 1.0
C C:ALA54 4.0 70.1 1.0
C C:GLY53 4.2 61.7 1.0
CA C:GLY56 4.2 63.8 1.0
CZ C:ARG4 4.3 77.5 1.0
CA C:ALA54 4.4 61.3 1.0
N D:ILE130 4.4 54.3 1.0
CA D:ASN131 4.4 59.1 1.0
CA D:GLN129 4.5 68.9 1.0
C D:ILE130 4.6 61.8 1.0
CA D:ILE130 4.6 57.5 1.0
CA D:ASN96 4.6 53.2 1.0
CA D:ILE97 4.7 49.4 1.0
C D:ASN96 4.7 57.8 1.0
N D:ASP98 4.7 55.7 1.0
N C:LEU55 4.7 73.7 1.0
CG D:ASN131 4.7 64.4 1.0
N C:ALA54 4.8 60.9 1.0
C C:LEU55 4.8 74.1 1.0
O C:ILE5 4.8 66.6 1.0
CA D:ASP98 4.9 52.7 1.0
CB D:ASP98 4.9 59.5 1.0
C D:SER128 4.9 72.0 1.0
CD C:ARG4 4.9 83.1 1.0

Reference:

Y.Kim, M.Makowska-Grzyska, K.Kwon, W.F.Anderson, A.Joachimiak, Center For Structural Genomics Of Infectious Diseases(Csgid). Crystal Structure of 2-C-Methyl-D-Erythritol 2,4-Cyclodiphosphate Synthase From Francisella Tularensis To Be Published.
Page generated: Mon Oct 7 12:47:33 2024

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