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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: Mon Oct 7 09:49:21 2024

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