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Sodium in PDB 3fsy: Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis

Enzymatic activity of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis

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

Protein crystallography data

The structure of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis, PDB code: 3fsy 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 / 1.97
Space group I 21 3 1
Cell size a, b, c (Å), α, β, γ (°) 216.960, 216.960, 216.960, 90.00, 90.00, 90.00
R / Rfree (%) 16.1 / 20

Other elements in 3fsy:

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

Magnesium (Mg) 10 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis (pdb code 3fsy). 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) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis, PDB code: 3fsy:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in 3fsy

Go back to Sodium Binding Sites List in 3fsy
Sodium binding site 1 out of 4 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa 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) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na337

b:36.4
occ:1.00
 OD2 A:ASP166 2.7 29.6 1.0
OD2 C:ASP166 2.7 33.0 1.0
OD2 B:ASP166 2.9 31.9 1.0
OD2 C:ASP164 2.9 37.2 1.0
OD2 A:ASP164 3.0 38.8 1.0
OD2 B:ASP164 3.2 39.4 1.0
MG A:MG333 3.3 23.7 1.0
CG C:ASP166 3.6 35.4 1.0
CG A:ASP166 3.6 33.5 1.0
OD1 C:ASP164 3.7 34.8 1.0
CG C:ASP164 3.7 31.7 1.0
CB C:ASP166 3.8 30.9 1.0
CB A:ASP166 3.8 29.7 1.0
CG B:ASP166 3.8 33.8 1.0
CG A:ASP164 3.9 39.4 1.0
OD1 A:ASP164 3.9 34.4 1.0
CG B:ASP164 4.0 39.5 1.0
O C:HOH561 4.0 32.0 1.0
CB B:ASP166 4.0 30.6 1.0
OD1 B:ASP164 4.0 34.4 1.0
O A:HOH442 4.6 25.4 1.0
O C:HOH442 4.6 24.4 1.0
O B:HOH442 4.7 27.1 1.0
OD1 C:ASP166 4.8 35.5 1.0
OD1 A:ASP166 4.8 35.8 1.0
O A:HOH401 4.8 26.8 1.0
O B:HOH401 4.9 27.8 1.0
OD1 B:ASP166 5.0 36.1 1.0

Sodium binding site 2 out of 4 in 3fsy

Go back to Sodium Binding Sites List in 3fsy
Sodium binding site 2 out of 4 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa 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) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na334

b:39.0
occ:0.50
 O B:HOH571 1.9 44.3 1.0
OD2 B:ASP210 3.6 33.7 1.0
O B:HOH487 3.8 33.5 1.0
OD1 B:ASP210 4.0 37.5 1.0
CG B:ASP210 4.2 31.9 1.0

Sodium binding site 3 out of 4 in 3fsy

Go back to Sodium Binding Sites List in 3fsy
Sodium binding site 3 out of 4 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa 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) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Na334

b:39.9
occ:0.33
 OD2 D:ASP166 2.8 29.7 1.0
OD2 D:ASP164 3.0 43.1 1.0
MG D:MG332 3.4 21.7 0.3
CG D:ASP166 3.8 31.9 1.0
CG D:ASP164 3.8 38.6 1.0
OD1 D:ASP164 3.8 35.0 1.0
CB D:ASP166 3.9 29.9 1.0
O D:HOH442 4.6 22.9 1.0
OD1 D:ASP166 4.9 35.5 1.0
O D:HOH401 5.0 29.9 1.0

Sodium binding site 4 out of 4 in 3fsy

Go back to Sodium Binding Sites List in 3fsy
Sodium binding site 4 out of 4 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa 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) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Na335

b:29.2
occ:0.33
 OD2 E:ASP166 3.0 29.3 1.0
OD2 E:ASP164 3.2 31.4 1.0
MG E:MG332 3.8 52.7 0.3
CG E:ASP166 3.9 36.2 1.0
CB E:ASP166 4.0 33.6 1.0
CG E:ASP164 4.0 33.5 1.0
OD1 E:ASP164 4.1 27.8 1.0
O E:HOH401 4.9 48.6 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 09:49:47 2024

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