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Magnesium in PDB 6cve: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid, PDB code: 6cve was solved by A.P.Thompson, J.B.Bruning, K.L.Wegener, S.W.Polyak, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 51.92 / 2.20
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 54.810, 103.841, 152.620, 90.00, 90.00, 90.00
R / Rfree (%) 19.4 / 27.1

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid (pdb code 6cve). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid, PDB code: 6cve:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 6cve

Go back to Magnesium Binding Sites List in 6cve
Magnesium binding site 1 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid


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 in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:23.7
occ:0.59
 OG1 A:THR16 1.9 27.3 1.0
O1G A:CTP301 2.0 34.7 0.9
O1B A:CTP301 2.0 25.1 0.9
O A:HOH429 2.2 34.6 1.0
OE1 A:GLU108 2.2 43.8 1.0
OD2 A:ASP49 2.5 33.8 1.0
CG A:ASP49 3.0 32.5 1.0
CB A:THR16 3.2 28.7 1.0
PG A:CTP301 3.2 59.2 0.9
OD1 A:ASP49 3.2 30.5 1.0
PB A:CTP301 3.3 24.0 0.9
CD A:GLU108 3.3 32.8 1.0
N A:THR16 3.6 32.4 1.0
O3B A:CTP301 3.6 28.4 0.9
CA A:THR16 3.9 25.2 1.0
OE2 A:GLU108 3.9 29.2 1.0
O3G A:CTP301 4.0 41.8 0.9
O2A A:CTP301 4.0 28.9 0.9
CB A:ASP49 4.2 23.8 1.0
O A:HOH527 4.3 29.3 1.0
O2B A:CTP301 4.3 26.2 0.9
CG2 A:THR16 4.3 27.7 1.0
O3A A:CTP301 4.4 25.4 0.9
O2G A:CTP301 4.4 40.0 0.9
OXT B:DSD301 4.4 32.7 0.9
O1A A:CTP301 4.4 19.3 0.9
CB A:LYS15 4.4 24.6 1.0
NZ A:LYS37 4.4 23.3 1.0
PA A:CTP301 4.5 28.9 0.9
CG A:GLU108 4.5 31.6 1.0
O A:HOH427 4.6 38.9 1.0
C A:LYS15 4.6 31.6 1.0
NZ A:LYS15 4.7 31.1 1.0
CE A:LYS15 4.8 27.5 1.0
CA A:LYS15 4.9 18.8 1.0
N A:LYS15 5.0 25.9 1.0

Magnesium binding site 2 out of 3 in 6cve

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Magnesium binding site 2 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid


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 in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:36.5
occ:0.49
 O3G C:CTP301 2.0 44.7 0.9
OG1 C:THR16 2.1 33.7 1.0
OD2 C:ASP49 2.2 35.7 1.0
OE1 C:GLU108 2.2 37.5 1.0
O2B C:CTP301 2.5 34.6 0.9
O C:HOH423 2.7 40.3 1.0
CG C:ASP49 2.9 33.3 1.0
PG C:CTP301 3.2 59.6 0.9
CD C:GLU108 3.3 35.0 1.0
OD1 C:ASP49 3.4 36.0 1.0
CB C:THR16 3.5 34.9 1.0
O2A C:CTP301 3.5 45.5 0.9
O2G C:CTP301 3.7 55.9 0.9
PB C:CTP301 3.7 31.7 0.9
O C:HOH401 3.7 47.3 1.0
O3B C:CTP301 3.8 38.6 0.9
OE2 C:GLU108 3.9 34.9 1.0
NZ C:LYS37 3.9 23.8 1.0
CB C:ASP49 3.9 31.2 1.0
N C:THR16 4.0 38.4 1.0
OXT C:DSD303 4.2 44.5 0.8
CA C:THR16 4.2 30.8 1.0
O C:DSD303 4.3 42.9 0.8
CG2 C:THR16 4.4 34.9 1.0
CG C:GLU108 4.4 38.9 1.0
O1G C:CTP301 4.5 38.2 0.9
C C:DSD303 4.7 47.2 0.8
PA C:CTP301 4.7 36.3 0.9
O3A C:CTP301 4.7 30.9 0.9
O1B C:CTP301 4.7 38.6 0.9
CB C:LYS15 4.7 27.8 1.0
CE C:LYS37 4.8 29.3 1.0
CE C:LYS15 4.9 31.1 1.0
C C:LYS15 4.9 32.4 1.0

Magnesium binding site 3 out of 3 in 6cve

Go back to Magnesium Binding Sites List in 6cve
Magnesium binding site 3 out of 3 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid


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 in Complex with Cytidine Triphosphate and 7,8- Diaminopelargonic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:36.3
occ:0.55
 O1B D:CTP301 2.0 39.0 0.7
O1G D:CTP301 2.0 38.1 0.7
OG1 D:THR16 2.3 35.8 1.0
O D:HOH401 2.4 49.0 1.0
OD2 D:ASP49 2.4 40.8 1.0
OE1 D:GLU108 2.5 32.2 1.0
PB D:CTP301 3.0 38.8 0.7
PG D:CTP301 3.1 41.4 0.7
O3B D:CTP301 3.2 37.2 0.7
CB D:THR16 3.4 30.9 1.0
CG D:ASP49 3.4 39.6 1.0
N D:THR16 3.6 32.6 1.0
CD D:GLU108 3.7 30.1 1.0
O2A D:CTP301 3.7 51.0 0.7
O3A D:CTP301 3.7 42.2 0.7
NZ D:LYS15 3.8 42.1 1.0
O1A D:CTP301 3.8 39.8 0.7
O D:HOH405 3.8 49.6 1.0
OD1 D:ASP49 3.9 40.4 1.0
PA D:CTP301 3.9 43.9 0.7
O3G D:CTP301 3.9 37.4 0.7
CA D:THR16 4.0 34.4 1.0
O2G D:CTP301 4.2 46.9 0.7
OE2 D:GLU108 4.2 36.1 1.0
O2B D:CTP301 4.3 32.8 0.7
NZ D:LYS37 4.3 25.5 1.0
CB D:LYS15 4.4 31.7 1.0
C D:LYS15 4.6 31.2 1.0
N D:LYS15 4.6 33.9 1.0
CG2 D:THR16 4.6 23.7 1.0
CB D:ASP49 4.6 29.6 1.0
CA D:LYS15 4.8 30.6 1.0
O D:HOH515 4.8 40.9 1.0
CE D:LYS37 4.8 31.1 1.0
O C:HOH503 4.8 35.4 1.0
CG D:GLU108 4.9 29.2 1.0
O D:HOH436 5.0 50.8 1.0

Reference:

A.P.Thompson, W.Salaemae, J.L.Pederick, A.D.Abell, G.W.Booker, J.B.Bruning, S.W.Polyak. Mycobacterium Tuberculosis Dethiobiotin Synthetase Facilitates Nucleoside Triphosphate Promiscuity Through Alternate Binding Modes Acs Catalysis V.(11) 10774 2018.
ISSN: ESSN 2155-5435
DOI: 10.1021/ACSCATAL.8B03475
Page generated: Mon Sep 30 22:45:54 2024

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