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Magnesium 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:

Sodium (Na) 4 atoms

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 10 binding sites of Magnesium where determined in the Structure of Tetrahydrodipicolinate N-Succinyltransferase (RV1201C;Dapd) in Complex with Succinyl-Coa From Mycobacterium Tuberculosis, PDB code: 3fsy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Magnesium binding site 1 out of 10 in 3fsy

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Magnesium binding site 1 out of 10 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 Magnesium with other atoms in the Mg 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:Mg333

b:23.7
occ:1.00
 OD2 C:ASP166 2.0 33.0 1.0
O A:HOH401 2.0 26.8 1.0
OD2 B:ASP166 2.0 31.9 1.0
O B:HOH401 2.1 27.8 1.0
OD2 A:ASP166 2.1 29.6 1.0
O C:HOH401 2.1 24.7 1.0
CG C:ASP166 3.0 35.4 1.0
CG B:ASP166 3.1 33.8 1.0
CG A:ASP166 3.1 33.5 1.0
NA A:NA337 3.3 36.4 1.0
OD1 C:ASP166 3.4 35.5 1.0
OD1 B:ASP166 3.5 36.1 1.0
OD1 A:ASP166 3.5 35.8 1.0
O C:HOH402 3.9 31.5 1.0
O B:HOH402 3.9 32.4 1.0
O A:HOH402 4.0 29.1 1.0
CB C:ASP166 4.4 30.9 1.0
CB B:ASP166 4.4 30.6 1.0
CB A:ASP166 4.5 29.7 1.0
OD1 C:ASP164 4.6 34.8 1.0
OD1 B:ASP164 4.6 34.4 1.0
OD1 A:ASP164 4.7 34.4 1.0

Magnesium binding site 2 out of 10 in 3fsy

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Magnesium binding site 2 out of 10 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 Magnesium with other atoms in the Mg 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
A:Mg334

b:29.9
occ:1.00
 OE2 A:GLU183 1.9 38.0 1.0
OE2 B:GLU183 1.9 39.8 1.0
OE2 C:GLU183 2.0 39.6 1.0
O A:HOH547 2.0 25.3 1.0
O B:HOH512 2.2 40.9 1.0
CD A:GLU183 2.8 37.6 1.0
CD B:GLU183 2.8 46.5 1.0
CD C:GLU183 2.9 41.7 1.0
OE1 A:GLU183 3.0 47.8 1.0
OE1 B:GLU183 3.1 46.6 1.0
OE1 C:GLU183 3.1 40.9 1.0
O B:HOH466 3.8 34.9 1.0
O A:HOH466 3.9 30.7 1.0
O C:HOH466 3.9 34.4 1.0
CG A:GLU183 4.1 34.7 1.0
CG B:GLU183 4.2 40.4 1.0
CG C:GLU183 4.2 39.2 1.0
O A:HOH507 4.6 39.0 1.0
NH2 C:ARG167 4.7 36.2 1.0
NH2 B:ARG167 4.7 32.2 1.0
NH1 B:ARG201 4.7 34.4 1.0
NH2 A:ARG167 4.7 33.0 1.0
NH1 C:ARG201 4.8 32.3 1.0
NH1 A:ARG201 4.8 30.4 1.0
O B:HOH507 4.8 30.6 1.0

Magnesium binding site 3 out of 10 in 3fsy

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Magnesium binding site 3 out of 10 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 Magnesium with other atoms in the Mg 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
A:Mg335

b:50.2
occ:1.00
 O A:HOH582 2.0 39.2 1.0
O A:HOH583 2.1 34.6 1.0
O A:HOH580 2.1 28.9 1.0
O A:HOH581 2.5 45.0 1.0
OD2 A:ASP253 3.9 35.9 1.0
OD2 A:ASP252 4.1 38.2 1.0
CB A:ASP252 4.2 28.8 1.0
OG A:SER285 4.4 32.2 1.0
OD1 A:ASN286 4.5 32.9 1.0
NH2 A:ARG237 4.5 48.7 1.0
CB A:SER285 4.6 30.5 1.0
ND2 A:ASN286 4.7 30.5 1.0
CG A:ASP252 4.7 34.5 1.0

Magnesium binding site 4 out of 10 in 3fsy

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Magnesium binding site 4 out of 10 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 Magnesium with other atoms in the Mg 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
A:Mg336

b:45.4
occ:1.00
 O D:HOH579 1.9 35.1 1.0
O A:HOH575 2.0 42.9 1.0
O A:HOH577 2.2 30.1 1.0
O A:HOH578 2.2 41.3 1.0
O A:HOH576 2.4 40.5 1.0
OD1 A:ASP210 4.1 36.6 1.0
O D:HOH549 4.2 32.2 1.0
OD2 D:ASP210 4.2 34.5 1.0
OD1 D:ASP210 4.2 34.1 1.0
OD2 A:ASP210 4.3 41.2 1.0
O A:PRO176 4.4 31.6 1.0
N A:ALA195 4.5 32.5 1.0
CB A:ALA195 4.6 32.8 1.0
CG A:ASP210 4.6 36.3 1.0
CG D:ASP210 4.6 33.3 1.0
O A:HOH566 4.8 37.6 1.0
CA A:GLY194 5.0 31.8 1.0

Magnesium binding site 5 out of 10 in 3fsy

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Magnesium binding site 5 out of 10 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 Magnesium with other atoms in the Mg binding site number 5 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:Mg333

b:48.5
occ:1.00
 O B:HOH564 1.9 40.7 1.0
O B:HOH565 2.0 49.2 1.0
O B:HOH563 2.1 45.8 1.0
O B:HOH560 2.2 43.3 1.0
O B:HOH561 2.3 31.2 1.0
O B:HOH562 2.4 45.9 1.0
OD2 B:ASP252 4.3 36.4 1.0
OG B:SER285 4.4 30.4 1.0
CB B:SER285 4.4 28.1 1.0
CB B:ASP252 4.5 30.9 1.0
OD2 B:ASP253 4.5 32.7 1.0
ND2 B:ASN286 4.6 30.5 1.0
OD1 B:ASN286 4.6 32.0 1.0
CG B:ASP252 4.9 34.9 1.0
NH2 B:ARG237 5.0 53.1 1.0

Magnesium binding site 6 out of 10 in 3fsy

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Magnesium binding site 6 out of 10 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 Magnesium with other atoms in the Mg binding site number 6 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:Mg332

b:21.7
occ:0.33
 OD2 D:ASP166 2.0 29.7 1.0
O D:HOH401 2.1 29.9 1.0
CG D:ASP166 3.1 31.9 1.0
NA D:NA334 3.4 39.9 0.3
OD1 D:ASP166 3.5 35.5 1.0
O D:HOH402 4.0 27.8 1.0
CB D:ASP166 4.4 29.9 1.0
OD1 D:ASP164 4.6 35.0 1.0

Magnesium binding site 7 out of 10 in 3fsy

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Magnesium binding site 7 out of 10 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 Magnesium with other atoms in the Mg binding site number 7 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:Mg333

b:51.9
occ:0.33
 OE2 D:GLU183 2.0 46.2 1.0
O D:HOH552 2.3 25.4 0.3
O D:HOH572 2.5 24.9 0.3
CD D:GLU183 2.8 51.5 1.0
OE1 D:GLU183 3.0 45.7 1.0
O D:HOH466 3.8 38.4 1.0
CG D:GLU183 4.2 39.0 1.0
NH1 D:ARG201 4.7 35.7 1.0
O D:HOH507 4.8 34.7 1.0
NH2 D:ARG167 4.8 39.0 1.0

Magnesium binding site 8 out of 10 in 3fsy

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Magnesium binding site 8 out of 10 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 Magnesium with other atoms in the Mg binding site number 8 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:Mg332

b:52.7
occ:0.33
 O E:HOH401 2.1 48.6 1.0
OD2 E:ASP166 2.2 29.3 1.0
CG E:ASP166 3.3 36.2 1.0
OD1 E:ASP166 3.6 38.2 1.0
NA E:NA335 3.8 29.2 0.3
CB E:ASP166 4.6 33.6 1.0
OD1 E:ASP164 4.9 27.8 1.0

Magnesium binding site 9 out of 10 in 3fsy

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Magnesium binding site 9 out of 10 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 Magnesium with other atoms in the Mg binding site number 9 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:Mg333

b:45.9
occ:0.33
 OE2 E:GLU183 2.0 37.4 1.0
CD E:GLU183 3.0 40.0 1.0
OE1 E:GLU183 3.4 46.0 1.0
O E:HOH405 3.7 53.6 1.0
CG E:GLU183 4.4 33.8 1.0
O E:HOH413 4.8 48.0 1.0
NH2 E:ARG167 4.8 28.8 1.0
NH1 E:ARG201 4.8 33.4 1.0

Magnesium binding site 10 out of 10 in 3fsy

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Magnesium binding site 10 out of 10 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 Magnesium with other atoms in the Mg binding site number 10 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:Mg334

b:38.9
occ:0.33
 O E:HOH417 2.0 35.3 1.0
O D:HOH536 2.2 31.4 1.0
O E:SER295 3.9 29.8 1.0
O D:SER295 4.1 28.2 1.0
O E:HOH416 4.3 36.9 1.0
O D:HOH547 4.4 27.8 1.0
CA E:SER295 4.7 29.9 1.0
C E:SER295 4.7 29.9 1.0
CA D:SER295 4.8 27.9 1.0
C D:SER295 4.9 27.5 1.0
CB E:SER295 5.0 30.6 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 Dec 14 08:09:15 2020

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