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Fluorine in PDB 6nl4: Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine:
6.3.3.3;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine, PDB code: 6nl4 was solved by A.P.Thompson, S.W.Polyak, K.L.Wegener, J.B.Bruning, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.35 / 1.99
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.514, 106.076, 151.951, 90.00, 90.00, 90.00
R / Rfree (%) 19.7 / 25.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine (pdb code 6nl4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine, PDB code: 6nl4:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6nl4

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Fluorine binding site 1 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:46.9
occ:0.72
 F1 A:GEO302 0.0 46.9 0.7
C2' A:GEO302 1.4 40.0 0.7
C1' A:GEO302 2.2 40.2 0.7
F2 A:GEO302 2.3 37.8 0.7
C3' A:GEO302 2.3 40.6 0.7
O3' A:GEO302 2.5 49.3 0.7
C4' A:GEO302 3.0 36.0 0.7
O4' A:GEO302 3.1 37.9 0.7
N1 A:GEO302 3.5 35.9 0.7
O2 A:GEO302 3.8 30.4 0.7
CB A:ALA201 3.9 33.3 1.0
C2 A:GEO302 4.1 39.2 0.7
O A:HOH443 4.2 33.2 1.0
C5' A:GEO302 4.5 44.8 0.7
C6 A:GEO302 4.5 38.2 0.7
OE1 A:GLU52 4.9 66.3 1.0

Fluorine binding site 2 out of 6 in 6nl4

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Fluorine binding site 2 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:37.8
occ:0.72
 F2 A:GEO302 0.0 37.8 0.7
C2' A:GEO302 1.4 40.0 0.7
F1 A:GEO302 2.3 46.9 0.7
C1' A:GEO302 2.3 40.2 0.7
C3' A:GEO302 2.3 40.6 0.7
N1 A:GEO302 2.6 35.9 0.7
O3' A:GEO302 3.0 49.3 0.7
CB A:ALA201 3.1 33.3 1.0
C2 A:GEO302 3.1 39.2 0.7
O2 A:GEO302 3.2 30.4 0.7
O A:HOH443 3.4 33.2 1.0
C6 A:GEO302 3.4 38.2 0.7
O4' A:GEO302 3.5 37.9 0.7
C4' A:GEO302 3.6 36.0 0.7
OE1 A:GLU52 4.0 66.3 1.0
O A:HOH505 4.1 22.4 1.0
N3 A:GEO302 4.1 34.9 0.7
C5 A:GEO302 4.4 35.4 0.7
CA A:ALA201 4.4 39.9 1.0
O5' A:GEO302 4.5 51.6 0.7
CB A:VAL17 4.6 31.2 1.0
C5' A:GEO302 4.6 44.8 0.7
N A:ALA201 4.6 39.0 1.0
C4 A:GEO302 4.7 36.4 0.7
CG1 A:VAL17 4.9 41.2 1.0
CD A:GLU52 5.0 61.8 1.0

Fluorine binding site 3 out of 6 in 6nl4

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Fluorine binding site 3 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:32.0
occ:0.65
 F1 B:GEO302 0.0 32.0 0.7
C2' B:GEO302 1.4 39.2 0.7
C1' B:GEO302 2.2 39.4 0.7
F2 B:GEO302 2.2 46.0 0.7
C3' B:GEO302 2.3 41.8 0.7
O3' B:GEO302 2.5 39.7 0.7
C4' B:GEO302 3.0 40.4 0.7
O4' B:GEO302 3.2 39.0 0.7
N1 B:GEO302 3.4 39.1 0.7
O2 B:GEO302 3.7 38.0 0.7
O B:HOH581 3.7 54.7 1.0
CB B:ALA201 3.7 38.5 0.9
C2 B:GEO302 4.0 36.2 0.7
O B:HOH516 4.3 55.6 1.0
C6 B:GEO302 4.4 38.0 0.7
C5' B:GEO302 4.5 38.9 0.7
O5' B:GEO302 4.9 35.4 0.7

Fluorine binding site 4 out of 6 in 6nl4

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Fluorine binding site 4 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F302

b:46.0
occ:0.65
 F2 B:GEO302 0.0 46.0 0.7
C2' B:GEO302 1.4 39.2 0.7
F1 B:GEO302 2.2 32.0 0.7
C1' B:GEO302 2.3 39.4 0.7
C3' B:GEO302 2.3 41.8 0.7
N1 B:GEO302 2.6 39.1 0.7
CB B:ALA201 3.0 38.5 0.9
O3' B:GEO302 3.0 39.7 0.7
C6 B:GEO302 3.1 38.0 0.7
C2 B:GEO302 3.2 36.2 0.7
O2 B:GEO302 3.5 38.0 0.7
O4' B:GEO302 3.5 39.0 0.7
C4' B:GEO302 3.6 40.4 0.7
O B:HOH480 3.6 30.4 1.0
O B:HOH516 3.7 55.6 1.0
OE2 B:GLU52 4.0 51.2 1.0
C5 B:GEO302 4.1 36.9 0.7
N3 B:GEO302 4.1 32.9 0.7
CG1 B:VAL17 4.3 33.5 1.0
CA B:ALA201 4.4 36.9 0.9
O B:HOH581 4.4 54.7 1.0
CB B:VAL17 4.4 27.3 1.0
O5' B:GEO302 4.4 35.4 0.7
C4 B:GEO302 4.5 31.4 0.7
C5' B:GEO302 4.7 38.9 0.7
N B:ALA201 4.7 31.4 0.9

Fluorine binding site 5 out of 6 in 6nl4

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Fluorine binding site 5 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F302

b:83.4
occ:1.00
 F1 D:GEO302 0.0 83.4 1.0
C2' D:GEO302 1.4 83.6 1.0
F2 D:GEO302 2.2 76.3 1.0
C1' D:GEO302 2.2 81.3 1.0
C3' D:GEO302 2.3 83.6 1.0
O3' D:GEO302 2.5 85.8 1.0
CB D:ALA201 3.1 52.1 1.0
O2 D:GEO302 3.2 70.0 1.0
N1 D:GEO302 3.3 74.9 1.0
O4' D:GEO302 3.5 81.5 1.0
C4' D:GEO302 3.6 86.5 1.0
C2 D:GEO302 3.6 70.5 1.0
O D:HOH443 4.0 46.8 1.0
C6 D:GEO302 4.3 69.9 1.0
OE2 D:GLU52 4.5 65.6 1.0
CA D:ALA201 4.6 60.6 1.0
C5' D:GEO302 4.6 83.0 1.0
N3 D:GEO302 4.9 57.9 1.0
CG1 D:VAL17 4.9 47.8 1.0
N D:ALA201 5.0 54.7 1.0

Fluorine binding site 6 out of 6 in 6nl4

Go back to Fluorine Binding Sites List in 6nl4
Fluorine binding site 6 out of 6 in the Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F302

b:76.3
occ:1.00
 F2 D:GEO302 0.0 76.3 1.0
C2' D:GEO302 1.4 83.6 1.0
F1 D:GEO302 2.2 83.4 1.0
C1' D:GEO302 2.3 81.3 1.0
C3' D:GEO302 2.3 83.6 1.0
N1 D:GEO302 2.6 74.9 1.0
CG1 D:VAL17 3.0 47.8 1.0
O D:HOH443 3.0 46.8 1.0
C6 D:GEO302 3.1 69.9 1.0
C4' D:GEO302 3.2 86.5 1.0
O4' D:GEO302 3.3 81.5 1.0
C2 D:GEO302 3.3 70.5 1.0
O D:HOH484 3.4 41.0 1.0
C5' D:GEO302 3.4 83.0 1.0
O3' D:GEO302 3.4 85.8 1.0
O2 D:GEO302 3.6 70.0 1.0
CB D:ALA201 3.7 52.1 1.0
OE2 D:GLU52 4.0 65.6 1.0
C5 D:GEO302 4.1 65.6 1.0
N3 D:GEO302 4.2 57.9 1.0
CB D:VAL17 4.4 49.4 1.0
C4 D:GEO302 4.6 61.1 1.0
O5' D:GEO302 4.7 80.1 1.0
CA D:ALA201 4.9 60.6 1.0

Reference:

A.P.Thompson, S.W.Polyak, K.L.Wegener, J.B.Bruning. Crystal Structure of Mycobacterium Tuberculosis Dethiobiotin Synthetase in Complex with Gemcitabine To Be Published.
Page generated: Thu Aug 1 23:08:15 2024

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