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Magnesium in PDB 3fpa: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate, PDB code: 3fpa was solved by S.Dey, J.C.Sacchettini, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.00 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.128, 104.453, 151.133, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 26

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate (pdb code 3fpa). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate, PDB code: 3fpa:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in 3fpa

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Magnesium binding site 1 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg901

b:32.9
occ:1.00
 OG1 A:THR16 2.0 27.8 1.0
O4 A:PO45254 2.1 32.0 1.0
O2 A:PO45256 2.1 30.6 1.0
OD1 A:ASP49 2.3 31.1 1.0
OE1 A:GLU108 2.3 34.8 1.0
CG A:ASP49 2.9 31.0 1.0
CB A:THR16 3.1 24.7 1.0
OD2 A:ASP49 3.2 31.1 1.0
P A:PO45254 3.3 22.7 1.0
O1 A:PO45254 3.3 27.6 1.0
CD A:GLU108 3.4 16.8 1.0
P A:PO45256 3.6 27.9 1.0
OE2 A:GLU108 3.9 24.3 1.0
N A:THR16 3.9 23.5 1.0
CB A:ASP49 4.0 21.9 1.0
CG2 A:THR16 4.1 24.4 1.0
CA A:THR16 4.1 26.4 1.0
NZ A:LYS37 4.1 17.0 1.0
O A:HOH270 4.2 22.2 1.0
O1 A:PO45256 4.2 38.5 1.0
O2 A:PO45254 4.2 26.2 1.0
O A:HOH234 4.2 13.8 1.0
O4 A:PO45256 4.3 26.1 1.0
O3 A:PO45254 4.3 22.2 1.0
O3 A:PO45256 4.5 25.9 1.0
O A:HOH228 4.6 20.8 1.0
CB A:LYS15 4.7 22.2 1.0
CG A:GLU108 4.7 23.1 1.0
NZ A:LYS15 4.7 23.3 1.0
CE A:LYS15 4.9 21.6 1.0
C A:LYS15 5.0 28.0 1.0

Magnesium binding site 2 out of 4 in 3fpa

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Magnesium binding site 2 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg901

b:46.2
occ:1.00
 OG1 B:THR16 2.0 30.5 1.0
O2 B:PO45255 2.3 35.6 1.0
O1 B:PO45257 2.3 37.9 1.0
OD1 B:ASP49 2.4 30.2 1.0
OE1 B:GLU108 2.9 38.5 1.0
CG B:ASP49 2.9 36.0 1.0
CB B:THR16 3.0 22.5 1.0
OD2 B:ASP49 3.0 33.7 1.0
P B:PO45255 3.5 27.8 1.0
O4 B:PO45255 3.6 31.8 1.0
P B:PO45257 3.7 32.4 1.0
O B:HOH269 3.9 33.1 1.0
CB B:ASP49 4.0 30.0 1.0
CD B:GLU108 4.0 25.2 1.0
N B:THR16 4.0 28.3 1.0
CA B:THR16 4.0 26.1 1.0
CG2 B:THR16 4.0 29.7 1.0
NZ B:LYS37 4.1 33.7 1.0
O2 B:PO45257 4.1 43.7 1.0
O B:HOH237 4.2 19.4 1.0
O1 B:PO45255 4.3 29.2 1.0
O3 B:PO45257 4.3 35.5 1.0
OE2 B:GLU108 4.4 37.7 1.0
O3 B:PO45255 4.5 25.2 1.0
O4 B:PO45257 4.7 32.4 1.0
O B:HOH267 4.8 21.2 1.0
O B:HOH263 4.9 38.5 1.0

Magnesium binding site 3 out of 4 in 3fpa

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Magnesium binding site 3 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg901

b:29.9
occ:1.00
 OD2 C:ASP49 2.0 30.6 1.0
O2 C:PO45261 2.0 21.4 1.0
OE1 C:GLU108 2.0 29.7 1.0
OG1 C:THR16 2.1 26.9 1.0
O C:HOH241 2.2 31.9 1.0
O2 C:PO45262 2.4 33.1 1.0
O1 C:PO45262 3.0 37.5 1.0
CG C:ASP49 3.0 32.1 1.0
CD C:GLU108 3.1 25.3 1.0
P C:PO45262 3.3 26.5 1.0
CB C:THR16 3.3 31.7 1.0
P C:PO45261 3.5 28.0 1.0
OE2 C:GLU108 3.6 29.9 1.0
OD1 C:ASP49 3.7 39.8 1.0
NZ C:LYS37 3.7 26.9 1.0
N C:THR16 3.9 32.8 1.0
CA C:THR16 4.1 31.3 1.0
O3 C:PO45261 4.1 28.1 1.0
CB C:ASP49 4.1 29.0 1.0
O1 C:PO45261 4.1 29.9 1.0
O4 C:PO45262 4.3 34.1 1.0
O3 C:PO45262 4.3 32.8 1.0
O4 C:PO45261 4.4 30.7 1.0
CG2 C:THR16 4.4 31.8 1.0
CG C:GLU108 4.4 26.1 1.0
CB C:LYS15 4.5 24.1 1.0
O C:HOH278 4.5 23.8 1.0
CE C:LYS15 4.5 18.6 1.0
NZ C:LYS15 4.6 24.0 1.0
CE C:LYS37 4.8 22.7 1.0
C C:LYS15 4.8 27.4 1.0

Magnesium binding site 4 out of 4 in 3fpa

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Magnesium binding site 4 out of 4 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase Complexed with Dethiobiotin and Phosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg901

b:44.7
occ:1.00
 O4 D:PO45259 1.8 41.4 1.0
OG1 D:THR16 2.0 45.8 1.0
OE1 D:GLU108 2.3 44.7 1.0
O4 D:PO45260 2.3 37.9 1.0
OD2 D:ASP49 2.6 48.1 1.0
P D:PO45259 3.1 33.8 1.0
CG D:ASP49 3.2 47.7 1.0
CB D:THR16 3.3 38.4 1.0
CD D:GLU108 3.3 43.8 1.0
OD1 D:ASP49 3.5 49.5 1.0
O3 D:PO45259 3.6 56.2 1.0
P D:PO45260 3.6 34.2 1.0
OE2 D:GLU108 3.7 43.9 1.0
N D:THR16 3.7 32.2 1.0
O2 D:PO45259 3.8 49.5 1.0
O1 D:PO45260 3.9 43.4 1.0
CA D:THR16 4.0 40.0 1.0
NZ D:LYS37 4.1 29.8 1.0
O1 D:PO45259 4.1 39.9 1.0
CB D:ASP49 4.3 44.3 1.0
CG2 D:THR16 4.3 44.4 1.0
O D:HOH231 4.4 24.0 1.0
O3 D:PO45260 4.4 37.7 1.0
CB D:LYS15 4.6 32.6 1.0
O2 D:PO45260 4.6 39.3 1.0
CG D:GLU108 4.6 35.9 1.0
NZ D:LYS15 4.6 29.6 1.0
O D:HOH253 4.7 33.1 1.0
C D:LYS15 4.7 33.5 1.0
CE D:LYS15 4.9 22.7 1.0

Reference:

S.Dey, J.M.Lane, R.E.Lee, E.J.Rubin, J.C.Sacchettini. Structural Characterization of the Mycobacterium Tuberculosis Biotin Biosynthesis Enzymes 7,8-Diaminopelargonic Acid Synthase and Dethiobiotin Synthetase. Biochemistry V. 49 6746 2010.
ISSN: ISSN 0006-2960
PubMed: 20565114
DOI: 10.1021/BI902097J
Page generated: Mon Dec 14 08:08:54 2020

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