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Magnesium 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:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 9 binding sites of Magnesium where determined in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis, PDB code: 3fsx:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Magnesium binding site 1 out of 9 in 3fsx

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Magnesium binding site 1 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg332

b:43.1
occ:1.00
 OE2 B:GLU183 2.3 36.9 1.0
OE2 A:GLU183 2.4 41.0 1.0
OE2 C:GLU183 2.5 40.9 1.0
OE1 B:GLU183 2.7 38.1 1.0
OE1 A:GLU183 2.7 38.1 1.0
OE1 C:GLU183 2.8 41.5 1.0
CD B:GLU183 2.9 36.9 1.0
CD A:GLU183 2.9 32.0 1.0
CD C:GLU183 3.0 38.3 1.0
NH1 B:ARG167 3.9 28.2 1.0
NH1 C:ARG167 4.0 26.4 1.0
NH2 A:ARG201 4.0 31.2 0.4
NH1 A:ARG167 4.0 33.9 1.0
NH2 B:ARG167 4.1 27.1 1.0
NH2 C:ARG167 4.1 33.1 1.0
NH2 A:ARG167 4.1 33.4 1.0
O B:HOH483 4.1 32.0 1.0
CG B:GLU183 4.3 35.9 1.0
CG A:GLU183 4.4 31.4 1.0
CZ C:ARG167 4.4 32.8 1.0
CZ B:ARG167 4.4 35.7 1.0
CZ A:ARG167 4.4 36.1 1.0
CG C:GLU183 4.4 38.8 1.0
O C:HOH503 4.5 26.3 1.0
CZ A:ARG201 4.9 26.1 0.4

Magnesium binding site 2 out of 9 in 3fsx

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Magnesium binding site 2 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
A:Mg333

b:46.7
occ:1.00
 O D:HOH541 2.2 30.2 1.0
O A:HOH519 2.5 30.4 1.0
O A:HOH512 2.6 34.9 1.0
OD1 A:ASP210 4.2 28.4 1.0
O D:HOH527 4.3 32.3 1.0
OD2 A:ASP210 4.4 36.5 1.0
OD1 D:ASP210 4.4 28.4 1.0
O A:PRO176 4.4 28.7 1.0
OD2 D:ASP210 4.5 32.9 1.0
N A:ALA195 4.6 29.0 1.0
CG A:ASP210 4.7 29.3 1.0
CB A:ALA195 4.7 31.3 1.0
CG D:ASP210 4.9 26.1 1.0
O A:HOH542 5.0 34.8 1.0

Magnesium binding site 3 out of 9 in 3fsx

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Magnesium binding site 3 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
B:Mg332

b:53.6
occ:1.00
 O B:HOH547 2.3 28.3 1.0
O B:HOH534 2.3 35.5 1.0
OD2 B:ASP253 4.0 30.8 1.0
OG B:SER285 4.4 26.3 1.0
OD2 B:ASP252 4.4 34.3 1.0
CB B:ASP252 4.5 24.4 1.0
CB B:SER285 4.6 24.6 1.0
OD1 B:ASN286 4.6 33.0 1.0
ND2 B:ASN286 4.7 27.1 1.0
NH2 B:ARG237 4.7 48.4 1.0
CG B:ASP252 4.9 28.2 1.0

Magnesium binding site 4 out of 9 in 3fsx

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Magnesium binding site 4 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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
C:Mg332

b:27.1
occ:1.00
 O A:HOH401 2.1 34.9 1.0
OD2 C:ASP166 2.1 33.2 1.0
O C:HOH401 2.1 27.2 1.0
OD2 B:ASP166 2.2 31.8 1.0
OD2 A:ASP166 2.2 31.5 1.0
O B:HOH401 2.2 29.0 1.0
CG C:ASP166 3.1 34.0 1.0
CG B:ASP166 3.2 29.9 1.0
CG A:ASP166 3.2 28.9 1.0
NA A:NA334 3.4 40.3 1.0
OD1 C:ASP166 3.4 30.7 1.0
OD1 B:ASP166 3.5 36.2 1.0
OD1 A:ASP166 3.6 31.3 1.0
O B:HOH471 3.8 24.4 1.0
O C:HOH471 3.8 27.0 1.0
CB C:ASP166 4.5 28.3 1.0
CB B:ASP166 4.5 24.6 1.0
CB A:ASP166 4.6 24.0 1.0
OD1 C:ASP164 4.7 33.2 1.0
OD1 B:ASP164 4.8 30.3 1.0
OD1 A:ASP164 4.8 32.0 1.0

Magnesium binding site 5 out of 9 in 3fsx

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Magnesium binding site 5 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg332

b:21.8
occ:0.33
 OD2 D:ASP166 2.0 31.5 1.0
O D:HOH401 2.0 28.2 1.0
CG D:ASP166 3.0 32.0 1.0
NA D:NA334 3.1 48.3 0.3
OD1 D:ASP166 3.3 33.1 1.0
O D:HOH471 3.8 22.4 1.0
CB D:ASP166 4.4 27.6 1.0
OD1 D:ASP164 4.6 30.3 1.0

Magnesium binding site 6 out of 9 in 3fsx

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Magnesium binding site 6 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg333

b:62.8
occ:0.33
 OE2 D:GLU183 2.0 44.5 1.0
CD D:GLU183 2.9 48.3 1.0
OE1 D:GLU183 3.0 40.5 1.0
O D:HOH483 3.7 34.8 1.0
CG D:GLU183 4.3 34.4 1.0
NH1 D:ARG201 4.7 34.4 1.0
O D:HOH502 5.0 37.3 1.0
NH2 D:ARG167 5.0 37.1 1.0

Magnesium binding site 7 out of 9 in 3fsx

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Magnesium binding site 7 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg331

b:54.2
occ:0.33
 OD2 E:ASP166 2.4 41.7 1.0
CG E:ASP166 3.4 36.0 1.0
OD1 E:ASP166 3.6 30.8 1.0
O E:HOH411 3.8 38.8 1.0
NA E:NA334 3.9 49.9 0.3
CB E:ASP166 4.7 30.2 1.0
OD1 E:ASP164 4.9 25.8 1.0

Magnesium binding site 8 out of 9 in 3fsx

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Magnesium binding site 8 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg332

b:55.7
occ:0.33
 OE2 E:GLU183 2.0 39.3 1.0
CD E:GLU183 3.1 36.6 1.0
OE1 E:GLU183 3.5 38.4 1.0
O E:HOH412 3.9 47.6 1.0
CG E:GLU183 4.3 29.4 1.0
NH1 E:ARG201 4.6 33.9 1.0

Magnesium binding site 9 out of 9 in 3fsx

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Magnesium binding site 9 out of 9 in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 9 of Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C; Dapd) From Mycobacterium Tuberculosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mg333

b:44.6
occ:0.33
 O D:HOH511 2.5 32.2 1.0
O E:SER295 3.0 26.9 1.0
C E:SER295 3.8 25.5 1.0
CA E:SER295 4.1 25.6 1.0
O E:HOH419 4.4 32.1 1.0
CB E:SER295 4.5 26.0 1.0
O D:HOH512 4.6 33.2 1.0
O D:SER295 5.0 24.5 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: Sun Aug 10 21:03:59 2025

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