Atomistry » Sodium » PDB 3r9b-3rn1 » 3re3
Atomistry »
  Sodium »
    PDB 3r9b-3rn1 »
      3re3 »

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

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy