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Fluorine in PDB 6hfv: Mycobacterium Tuberculosis DPRE1 in Complex with CMP2

Enzymatic activity of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2

All present enzymatic activity of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2:
1.1.98.3;

Protein crystallography data

The structure of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2, PDB code: 6hfv was solved by C.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.40 / 2.05
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.080, 84.430, 80.450, 90.00, 103.00, 90.00
R / Rfree (%) 17.6 / 20.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP2 (pdb code 6hfv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP2, PDB code: 6hfv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6hfv

Go back to Fluorine Binding Sites List in 6hfv
Fluorine binding site 1 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:57.4
occ:1.00
 F3 A:G1T503 0.0 57.4 1.0
C14 A:G1T503 1.3 55.7 1.0
F2 A:G1T503 2.1 61.9 1.0
F1 A:G1T503 2.1 55.8 1.0
C2 A:G1T503 2.3 49.5 1.0
C3 A:G1T503 2.9 49.3 1.0
C A:GLY133 3.1 41.4 1.0
O A:GLY133 3.2 41.9 1.0
C1 A:G1T503 3.4 51.1 1.0
N A:LYS134 3.5 43.2 1.0
CA A:GLY133 3.5 41.2 1.0
CD2 A:HIS132 3.7 45.8 1.0
CD A:LYS367 3.9 53.5 1.0
CA A:LYS134 4.0 46.7 1.0
O A:HOH715 4.0 67.3 1.0
N A:GLY133 4.1 41.0 1.0
C4 A:G1T503 4.3 50.0 1.0
O4 A:FAD501 4.4 47.8 1.0
NE2 A:HIS132 4.4 41.9 1.0
O A:HIS132 4.4 37.3 1.0
CG A:LYS134 4.5 58.7 1.0
C A:HIS132 4.5 38.9 1.0
C6 A:G1T503 4.6 52.5 1.0
CG A:HIS132 4.8 40.4 1.0
CE1 A:PHE369 4.8 44.0 1.0
CB A:LYS134 4.9 50.1 1.0
CG A:LYS367 4.9 55.6 1.0
C5 A:G1T503 4.9 55.4 1.0
CB A:LYS367 5.0 54.1 1.0
CE A:LYS367 5.0 49.4 1.0

Fluorine binding site 2 out of 6 in 6hfv

Go back to Fluorine Binding Sites List in 6hfv
Fluorine binding site 2 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:55.8
occ:1.00
 F1 A:G1T503 0.0 55.8 1.0
C14 A:G1T503 1.3 55.7 1.0
F2 A:G1T503 2.1 61.9 1.0
F3 A:G1T503 2.1 57.4 1.0
C2 A:G1T503 2.3 49.5 1.0
C1 A:G1T503 2.7 51.1 1.0
ND2 A:ASN385 3.4 51.8 1.0
C3 A:G1T503 3.6 49.3 1.0
CD A:LYS367 3.7 53.5 1.0
CD2 A:HIS132 3.7 45.8 1.0
CB A:LYS367 3.7 54.1 1.0
CE1 A:PHE369 3.8 44.0 1.0
CG A:LYS367 3.9 55.6 1.0
NE2 A:HIS132 4.0 41.9 1.0
C6 A:G1T503 4.1 52.5 1.0
CG A:ASN385 4.3 45.3 1.0
CZ A:PHE369 4.3 43.5 1.0
O A:GLY133 4.6 41.9 1.0
C4 A:G1T503 4.7 50.0 1.0
NE2 A:GLN336 4.8 48.0 1.0
CD1 A:PHE369 4.8 42.6 1.0
CG1 A:VAL365 4.8 55.2 1.0
C5 A:G1T503 4.9 55.4 1.0
C A:GLY133 4.9 41.4 1.0
OD1 A:ASN385 4.9 48.4 1.0
CG A:HIS132 5.0 40.4 1.0
CB A:ASN385 5.0 43.8 1.0
N3 A:G1T503 5.0 60.9 1.0

Fluorine binding site 3 out of 6 in 6hfv

Go back to Fluorine Binding Sites List in 6hfv
Fluorine binding site 3 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:61.9
occ:1.00
 F2 A:G1T503 0.0 61.9 1.0
C14 A:G1T503 1.3 55.7 1.0
F3 A:G1T503 2.1 57.4 1.0
F1 A:G1T503 2.1 55.8 1.0
C2 A:G1T503 2.3 49.5 1.0
C3 A:G1T503 2.9 49.3 1.0
C1 A:G1T503 3.4 51.1 1.0
CD A:LYS367 3.5 53.5 1.0
CB A:LYS367 3.6 54.1 1.0
CB A:SER228 3.8 51.4 1.0
CG1 A:VAL365 3.9 55.2 1.0
CG A:LYS367 4.1 55.6 1.0
C4 A:G1T503 4.2 50.0 1.0
CG A:LYS134 4.2 58.7 1.0
CA A:LYS134 4.2 46.7 1.0
N A:LYS134 4.4 43.2 1.0
O A:GLY133 4.5 41.9 1.0
C A:GLY133 4.5 41.4 1.0
C6 A:G1T503 4.6 52.5 1.0
O A:SER227 4.7 48.0 1.0
OG A:SER228 4.7 54.5 1.0
O A:PHE366 4.7 51.2 1.0
CA A:SER228 4.8 49.3 1.0
CB A:LYS134 4.8 50.1 1.0
CE A:LYS367 4.8 49.4 1.0
C5 A:G1T503 4.9 55.4 1.0
CA A:LYS367 5.0 51.7 1.0

Fluorine binding site 4 out of 6 in 6hfv

Go back to Fluorine Binding Sites List in 6hfv
Fluorine binding site 4 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:69.7
occ:1.00
 F3 B:G1T502 0.0 69.7 1.0
C14 B:G1T502 1.3 68.5 1.0
F2 B:G1T502 2.1 65.7 1.0
F1 B:G1T502 2.1 67.6 1.0
C2 B:G1T502 2.3 63.0 1.0
C3 B:G1T502 2.9 67.6 1.0
C B:GLY133 3.0 48.1 1.0
O B:GLY133 3.1 50.0 1.0
N B:LYS134 3.3 47.1 1.0
C1 B:G1T502 3.5 66.4 1.0
O B:HOH703 3.6 76.1 1.0
CA B:GLY133 3.6 51.7 1.0
CA B:LYS134 3.7 52.4 1.0
CD B:LYS367 3.8 57.2 1.0
ND1 B:HIS132 3.8 55.7 1.0
C4 B:G1T502 4.2 74.3 1.0
N B:GLY133 4.3 47.3 1.0
CE1 B:HIS132 4.3 51.4 1.0
O4 B:FAD501 4.4 58.8 1.0
O B:HIS132 4.5 50.8 1.0
CB B:LYS134 4.5 59.4 1.0
C B:HIS132 4.6 49.0 1.0
C6 B:G1T502 4.7 81.7 1.0
CE B:LYS367 4.8 57.2 1.0
C B:LYS134 4.9 54.8 1.0
CG B:LYS367 4.9 61.1 1.0
O1 B:G1T502 4.9 72.6 1.0
C5 B:G1T502 5.0 77.3 1.0
CB B:LYS367 5.0 58.2 1.0

Fluorine binding site 5 out of 6 in 6hfv

Go back to Fluorine Binding Sites List in 6hfv
Fluorine binding site 5 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:67.6
occ:1.00
 F1 B:G1T502 0.0 67.6 1.0
C14 B:G1T502 1.3 68.5 1.0
F2 B:G1T502 2.1 65.7 1.0
F3 B:G1T502 2.1 69.7 1.0
C2 B:G1T502 2.3 63.0 1.0
C1 B:G1T502 2.7 66.4 1.0
ND1 B:HIS132 3.5 55.7 1.0
ND2 B:ASN385 3.5 63.6 1.0
CE1 B:HIS132 3.5 51.4 1.0
CD B:LYS367 3.5 57.2 1.0
C3 B:G1T502 3.6 67.6 1.0
CE1 B:PHE369 3.8 52.4 1.0
CB B:LYS367 3.9 58.2 1.0
CG B:LYS367 4.0 61.1 1.0
C6 B:G1T502 4.1 81.7 1.0
CZ B:PHE369 4.3 47.7 1.0
O B:GLY133 4.4 50.0 1.0
CG B:ASN385 4.5 55.9 1.0
C B:GLY133 4.7 48.1 1.0
C4 B:G1T502 4.8 74.3 1.0
CD1 B:PHE369 4.8 50.7 1.0
NE2 B:HIS132 4.8 50.0 1.0
CG B:HIS132 4.8 48.0 1.0
NE2 B:GLN336 4.9 50.6 1.0
CE B:LYS367 4.9 57.2 1.0
C5 B:G1T502 5.0 77.3 1.0

Fluorine binding site 6 out of 6 in 6hfv

Go back to Fluorine Binding Sites List in 6hfv
Fluorine binding site 6 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP2


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Mycobacterium Tuberculosis DPRE1 in Complex with CMP2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:65.7
occ:1.00
 F2 B:G1T502 0.0 65.7 1.0
C14 B:G1T502 1.3 68.5 1.0
F1 B:G1T502 2.1 67.6 1.0
F3 B:G1T502 2.1 69.7 1.0
C2 B:G1T502 2.3 63.0 1.0
C3 B:G1T502 3.0 67.6 1.0
CD B:LYS367 3.3 57.2 1.0
C1 B:G1T502 3.3 66.4 1.0
CB B:LYS367 3.4 58.2 1.0
CB B:SER228 3.8 57.5 1.0
CG1 B:VAL365 3.9 67.3 1.0
CG B:LYS367 3.9 61.1 1.0
C4 B:G1T502 4.3 74.3 1.0
CA B:LYS134 4.4 52.4 1.0
C6 B:G1T502 4.6 81.7 1.0
O B:GLY133 4.6 50.0 1.0
O B:SER227 4.6 54.7 1.0
CE B:LYS367 4.7 57.2 1.0
O B:PHE366 4.7 60.4 1.0
N B:LYS134 4.7 47.1 1.0
C B:GLY133 4.7 48.1 1.0
OG B:SER228 4.8 60.9 1.0
CA B:SER228 4.8 56.4 1.0
CA B:LYS367 4.8 57.9 1.0
ND2 B:ASN385 4.9 63.6 1.0
C5 B:G1T502 4.9 77.3 1.0
C B:PHE366 4.9 58.8 1.0
N B:LYS367 5.0 54.6 1.0

Reference:

A.Richter, I.Rudolph, U.Mollmann, K.Voigt, C.W.Chung, O.M.P.Singh, M.Rees, A.Mendoza-Losana, R.Bates, L.Ballell, S.Batt, N.Veerapen, K.Futterer, G.Besra, P.Imming, A.Argyrou. Novel Insight Into the Reaction of Nitro, Nitroso and Hydroxylamino Benzothiazinones and of Benzoxacinones with Mycobacterium Tuberculosis DPRE1. Sci Rep V. 8 13473 2018.
ISSN: ESSN 2045-2322
PubMed: 30194385
DOI: 10.1038/S41598-018-31316-6
Page generated: Thu Aug 1 21:06:26 2024

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