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Sodium in PDB 3d5t: Crystal Structure of Malate Dehydrogenase From Burkholderia Pseudomallei

Enzymatic activity of Crystal Structure of Malate Dehydrogenase From Burkholderia Pseudomallei

All present enzymatic activity of Crystal Structure of Malate Dehydrogenase From Burkholderia Pseudomallei:
1.1.1.37;

Protein crystallography data

The structure of Crystal Structure of Malate Dehydrogenase From Burkholderia Pseudomallei, PDB code: 3d5t was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.62 / 2.51
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 59.387, 79.608, 288.874, 90.00, 90.00, 90.00
R / Rfree (%) 17.8 / 24.1

Other elements in 3d5t:

The structure of Crystal Structure of Malate Dehydrogenase From Burkholderia Pseudomallei also contains other interesting chemical elements:

Magnesium (Mg) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Malate Dehydrogenase From Burkholderia Pseudomallei (pdb code 3d5t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Malate Dehydrogenase From Burkholderia Pseudomallei, PDB code: 3d5t:

Sodium binding site 1 out of 1 in 3d5t

Go back to Sodium Binding Sites List in 3d5t
Sodium binding site 1 out of 1 in the Crystal Structure of Malate Dehydrogenase From Burkholderia Pseudomallei


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 Malate Dehydrogenase From Burkholderia Pseudomallei within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na402

b:43.0
occ:1.00
 O B:HOH485 2.0 22.0 1.0
O B:HOH486 2.2 30.1 1.0
OD2 B:ASP43 3.9 20.9 1.0
N B:GLY15 4.2 17.4 1.0
OD1 B:ASP43 4.2 28.0 1.0
C B:ALA14 4.3 17.5 1.0
CA B:GLY15 4.3 16.8 1.0
O B:ALA14 4.4 17.2 1.0
CB B:ALA14 4.4 17.3 1.0
CG B:ASP43 4.5 24.2 1.0
CA B:ALA14 4.9 17.6 1.0
CB B:ALA47 4.9 28.1 1.0

Reference:

Seattle Structural Genomics Center For Infectious Disease(Ssgcid), Seattle Structural Genomics Center For Infectious Disease (Ssgcid). N/A N/A.
Page generated: Sun Aug 17 14:17:19 2025

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