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Fluorine in PDB 6hfw: Mycobacterium Tuberculosis DPRE1 in Complex with CMP1

Enzymatic activity of Mycobacterium Tuberculosis DPRE1 in Complex with CMP1

All present enzymatic activity of Mycobacterium Tuberculosis DPRE1 in Complex with CMP1:
1.1.98.3;

Protein crystallography data

The structure of Mycobacterium Tuberculosis DPRE1 in Complex with CMP1, PDB code: 6hfw was solved by C.Chung, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.69 / 2.47
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 78.340, 84.730, 80.900, 90.00, 103.20, 90.00
R / Rfree (%) 16.8 / 22

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP1 (pdb code 6hfw). 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 CMP1, PDB code: 6hfw:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6hfw

Go back to Fluorine Binding Sites List in 6hfw
Fluorine binding site 1 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP1


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 CMP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:73.5
occ:1.00
 F3 A:G1T503 0.0 73.5 1.0
C14 A:G1T503 1.4 73.3 1.0
F2 A:G1T503 2.2 77.1 1.0
F1 A:G1T503 2.2 78.8 1.0
C2 A:G1T503 2.3 71.6 1.0
C3 A:G1T503 3.1 66.6 1.0
C A:GLY133 3.1 35.5 1.0
O A:GLY133 3.2 35.1 1.0
C1 A:G1T503 3.2 65.6 1.0
CA A:GLY133 3.5 34.4 1.0
N A:LYS134 3.6 36.6 1.0
CD2 A:HIS132 3.6 33.1 1.0
CD A:LYS367 3.9 45.5 1.0
CA A:LYS134 4.1 41.4 1.0
N A:GLY133 4.1 34.5 1.0
NE2 A:HIS132 4.3 31.4 1.0
C4 A:G1T503 4.4 72.7 1.0
C6 A:G1T503 4.5 78.8 1.0
O4 A:FAD501 4.5 42.5 1.0
C A:HIS132 4.5 33.9 1.0
O A:HIS132 4.5 33.8 1.0
CG A:HIS132 4.7 32.8 1.0
CE1 A:PHE369 4.8 36.4 1.0
CG A:LYS134 4.8 50.5 1.0
CE A:LYS367 4.9 47.1 1.0
CG A:LYS367 4.9 45.3 1.0
C5 A:G1T503 4.9 75.7 1.0
CB A:LYS367 4.9 43.3 1.0

Fluorine binding site 2 out of 6 in 6hfw

Go back to Fluorine Binding Sites List in 6hfw
Fluorine binding site 2 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP1


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 CMP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:78.8
occ:1.00
 F1 A:G1T503 0.0 78.8 1.0
C14 A:G1T503 1.4 73.3 1.0
F2 A:G1T503 2.2 77.1 1.0
F3 A:G1T503 2.2 73.5 1.0
C2 A:G1T503 2.4 71.6 1.0
C1 A:G1T503 2.8 65.6 1.0
CB A:LYS367 3.3 43.3 1.0
CD A:LYS367 3.4 45.5 1.0
ND2 A:ASN385 3.5 44.2 1.0
C3 A:G1T503 3.6 66.6 1.0
CG A:LYS367 3.7 45.3 1.0
C6 A:G1T503 4.2 78.8 1.0
CE1 A:PHE369 4.2 36.4 1.0
CD2 A:HIS132 4.3 33.1 1.0
CG A:ASN385 4.5 41.9 1.0
CG1 A:VAL365 4.5 46.0 1.0
NE2 A:HIS132 4.6 31.4 1.0
CA A:LYS367 4.6 41.6 1.0
O A:GLY133 4.8 35.1 1.0
N A:LYS367 4.8 39.3 1.0
C4 A:G1T503 4.8 72.7 1.0
CZ A:PHE369 4.8 35.4 1.0
CE A:LYS367 4.8 47.1 1.0
C5 A:G1T503 5.0 75.7 1.0

Fluorine binding site 3 out of 6 in 6hfw

Go back to Fluorine Binding Sites List in 6hfw
Fluorine binding site 3 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP1


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 CMP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F503

b:77.1
occ:1.00
 F2 A:G1T503 0.0 77.1 1.0
C14 A:G1T503 1.4 73.3 1.0
F3 A:G1T503 2.2 73.5 1.0
F1 A:G1T503 2.2 78.8 1.0
C2 A:G1T503 2.4 71.6 1.0
C3 A:G1T503 2.8 66.6 1.0
CB A:SER228 3.5 46.6 1.0
C1 A:G1T503 3.6 65.6 1.0
CD A:LYS367 3.6 45.5 1.0
CG A:LYS134 3.8 50.5 1.0
CA A:LYS134 3.9 41.4 1.0
CB A:LYS367 4.0 43.3 1.0
CG1 A:VAL365 4.1 46.0 1.0
N A:LYS134 4.1 36.6 1.0
C4 A:G1T503 4.2 72.7 1.0
OG A:SER228 4.3 52.6 1.0
C A:GLY133 4.3 35.5 1.0
O A:SER227 4.4 43.1 1.0
O A:GLY133 4.4 35.1 1.0
CG A:LYS367 4.4 45.3 1.0
CB A:LYS134 4.4 47.2 1.0
CA A:SER228 4.6 43.9 1.0
NZ A:LYS134 4.6 64.1 1.0
C6 A:G1T503 4.8 78.8 1.0
O1 A:G1T503 4.8 84.8 1.0
CE A:LYS367 4.8 47.1 1.0
C5 A:G1T503 5.0 75.7 1.0

Fluorine binding site 4 out of 6 in 6hfw

Go back to Fluorine Binding Sites List in 6hfw
Fluorine binding site 4 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP1


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 CMP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:78.2
occ:1.00
 F3 B:G1T502 0.0 78.2 1.0
C14 B:G1T502 1.4 78.2 1.0
F2 B:G1T502 2.2 75.2 1.0
F1 B:G1T502 2.2 85.7 1.0
C2 B:G1T502 2.4 80.8 1.0
C3 B:G1T502 3.0 82.0 1.0
C B:GLY133 3.1 40.6 1.0
O B:GLY133 3.2 44.1 1.0
CA B:GLY133 3.4 41.0 1.0
C1 B:G1T502 3.5 73.3 1.0
N B:LYS134 3.5 43.2 1.0
CD2 B:HIS132 3.5 43.8 1.0
N B:GLY133 4.1 40.6 1.0
CD B:LYS367 4.1 49.8 1.0
CA B:LYS134 4.1 45.5 1.0
O4 B:FAD501 4.1 45.2 1.0
NE2 B:HIS132 4.3 41.9 1.0
C4 B:G1T502 4.3 87.9 1.0
O B:HIS132 4.3 37.2 1.0
C B:HIS132 4.4 39.2 1.0
C6 B:G1T502 4.6 88.0 1.0
CG B:HIS132 4.7 40.6 1.0
CD B:LYS134 5.0 68.8 1.0
C5 B:G1T502 5.0 89.3 1.0
N3 B:FAD501 5.0 44.4 1.0
C4 B:FAD501 5.0 45.4 1.0

Fluorine binding site 5 out of 6 in 6hfw

Go back to Fluorine Binding Sites List in 6hfw
Fluorine binding site 5 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP1


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 CMP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:85.7
occ:1.00
 F1 B:G1T502 0.0 85.7 1.0
C14 B:G1T502 1.4 78.2 1.0
F2 B:G1T502 2.2 75.2 1.0
F3 B:G1T502 2.2 78.2 1.0
C2 B:G1T502 2.4 80.8 1.0
C1 B:G1T502 2.8 73.3 1.0
ND2 B:ASN385 3.3 48.7 1.0
CD2 B:HIS132 3.6 43.8 1.0
C3 B:G1T502 3.6 82.0 1.0
CD B:LYS367 3.8 49.8 1.0
NE2 B:HIS132 3.8 41.9 1.0
CB B:LYS367 3.8 46.9 1.0
CE1 B:PHE369 4.0 48.8 1.0
CG B:LYS367 4.1 47.6 1.0
C6 B:G1T502 4.2 88.0 1.0
CG B:ASN385 4.3 47.4 1.0
CZ B:PHE369 4.5 47.3 1.0
O B:GLY133 4.6 44.1 1.0
NE2 B:GLN336 4.7 47.4 1.0
C4 B:G1T502 4.8 87.9 1.0
CG B:HIS132 4.9 40.6 1.0
C B:GLY133 4.9 40.6 1.0
CD1 B:PHE369 5.0 47.0 1.0
CG1 B:VAL365 5.0 60.0 1.0

Fluorine binding site 6 out of 6 in 6hfw

Go back to Fluorine Binding Sites List in 6hfw
Fluorine binding site 6 out of 6 in the Mycobacterium Tuberculosis DPRE1 in Complex with CMP1


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 CMP1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:75.2
occ:1.00
 F2 B:G1T502 0.0 75.2 1.0
C14 B:G1T502 1.4 78.2 1.0
F1 B:G1T502 2.2 85.7 1.0
F3 B:G1T502 2.2 78.2 1.0
C2 B:G1T502 2.4 80.8 1.0
C3 B:G1T502 2.8 82.0 1.0
CD B:LYS367 3.4 49.8 1.0
C1 B:G1T502 3.5 73.3 1.0
CB B:LYS367 3.7 46.9 1.0
CG1 B:VAL365 3.9 60.0 1.0
CB B:SER228 3.9 49.8 1.0
CG B:LYS367 4.1 47.6 1.0
C4 B:G1T502 4.2 87.9 1.0
CA B:LYS134 4.4 45.5 1.0
O B:GLY133 4.4 44.1 1.0
N B:LYS134 4.5 43.2 1.0
C B:GLY133 4.5 40.6 1.0
CD B:LYS134 4.6 68.8 1.0
C6 B:G1T502 4.6 88.0 1.0
CG B:LYS134 4.7 59.3 1.0
CE B:LYS367 4.7 49.7 1.0
O B:SER227 4.8 47.0 1.0
OG B:SER228 4.8 54.0 1.0
C5 B:G1T502 4.9 89.3 1.0
O1 B:G1T502 4.9 95.9 1.0
ND2 B:ASN385 4.9 48.7 1.0
O B:PHE366 5.0 47.3 1.0
CA B:SER228 5.0 47.0 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 21:06:34 2024

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