Atomistry » Sodium » PDB 3fak-3fvi » 3fsx
Atomistry »
  Sodium »
    PDB 3fak-3fvi »
      3fsx »

Sodium in PDB 3fsx: Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis

Enzymatic activity of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis

All present enzymatic activity of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis:
2.3.1.117;

Protein crystallography data

The structure of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis, PDB code: 3fsx was solved by L.Schuldt, S.Weyand, G.Kefala, M.S.Weiss, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.15
Space group I 21 3 1
Cell size a, b, c (Å), α, β, γ (°) 216.990, 216.990, 216.990, 90.00, 90.00, 90.00
R / Rfree (%) 16.8 / 21.9

Other elements in 3fsx:

The structure of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis also contains other interesting chemical elements:

Magnesium (Mg) 9 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis (pdb code 3fsx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis, PDB code: 3fsx:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3fsx

Go back to Sodium Binding Sites List in 3fsx
Sodium binding site 1 out of 4 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na334

b:40.3
occ:1.00
OD2 A:ASP166 2.7 31.5 1.0
OD2 C:ASP166 2.7 33.2 1.0
OD2 B:ASP166 2.8 31.8 1.0
OD2 C:ASP164 3.0 39.3 1.0
OD2 A:ASP164 3.1 38.8 1.0
OD2 B:ASP164 3.3 34.6 1.0
MG C:MG332 3.4 27.1 1.0
CG C:ASP166 3.6 34.0 1.0
CG A:ASP166 3.7 28.9 1.0
OD1 C:ASP164 3.7 33.2 1.0
CG C:ASP164 3.8 32.2 1.0
CG B:ASP166 3.8 29.9 1.0
CB C:ASP166 3.9 28.3 1.0
CG A:ASP164 3.9 36.1 1.0
OD1 A:ASP164 3.9 32.0 1.0
CB A:ASP166 3.9 24.0 1.0
OD1 B:ASP164 4.0 30.3 1.0
CG B:ASP164 4.0 36.0 1.0
CB B:ASP166 4.1 24.6 1.0
O C:HOH432 4.8 15.4 1.0
OD1 C:ASP166 4.8 30.7 1.0
O A:HOH432 4.8 21.8 1.0
O B:HOH432 4.8 21.3 1.0
OD1 A:ASP166 4.8 31.3 1.0
O A:HOH401 4.9 34.9 1.0
OD1 B:ASP166 5.0 36.2 1.0

Sodium binding site 2 out of 4 in 3fsx

Go back to Sodium Binding Sites List in 3fsx
Sodium binding site 2 out of 4 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na333

b:32.7
occ:0.50
CB B:ALA195 4.2 28.2 1.0
OD1 B:ASP210 4.2 25.5 1.0
N B:ALA195 4.5 28.9 1.0
OD2 B:ASP210 4.6 32.9 1.0
CG B:ASP210 4.8 28.2 1.0
O B:PRO176 4.9 27.2 1.0
CA B:ALA195 5.0 30.6 1.0

Sodium binding site 3 out of 4 in 3fsx

Go back to Sodium Binding Sites List in 3fsx
Sodium binding site 3 out of 4 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na334

b:48.3
occ:0.33
OD2 D:ASP166 2.6 31.5 1.0
MG D:MG332 3.1 21.8 0.3
OD2 D:ASP164 3.2 39.2 1.0
CG D:ASP166 3.7 32.0 1.0
OD1 D:ASP164 3.8 30.3 1.0
CG D:ASP164 3.9 32.0 1.0
CB D:ASP166 4.0 27.6 1.0
OD1 D:ASP166 4.8 33.1 1.0
O D:HOH401 4.8 28.2 1.0
O D:HOH432 4.9 19.8 1.0

Sodium binding site 4 out of 4 in 3fsx

Go back to Sodium Binding Sites List in 3fsx
Sodium binding site 4 out of 4 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na334

b:49.9
occ:0.33
OD2 E:ASP166 2.9 41.7 1.0
OD2 E:ASP164 3.0 29.8 1.0
CG E:ASP164 3.9 35.5 1.0
CG E:ASP166 3.9 36.0 1.0
MG E:MG331 3.9 54.2 0.3
OD1 E:ASP164 4.0 25.8 1.0
CB E:ASP166 4.0 30.2 1.0
O E:HOH409 5.0 37.7 1.0

Reference:

L.Schuldt, S.Weyand, G.Kefala, M.S.Weiss. The Three-Dimensional Structure of A Mycobacterial Dapd Provides Insights Into Dapd Diversity and Reveals Unexpected Particulars About the Enzymatic Mechanism. J.Mol.Biol. V. 389 863 2009.
ISSN: ISSN 0022-2836
PubMed: 19394346
DOI: 10.1016/J.JMB.2009.04.046
Page generated: Tue Dec 15 06:11:03 2020

Last articles

Zn in 7VD8
Zn in 7V1R
Zn in 7V1Q
Zn in 7VPF
Zn in 7T85
Zn in 7T5F
Zn in 7NF9
Zn in 7M4M
Zn in 7M4O
Zn in 7M4N
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy