Fluorine in PDB 5vrm: Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.

Enzymatic activity of Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.

All present enzymatic activity of Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.:
1.3.1.9;

Protein crystallography data

The structure of Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333., PDB code: 5vrm was solved by J.Abendroth, T.E.Edwards, D.Lorimer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.09 / 2.50
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 125.350, 92.680, 101.930, 90.00, 105.59, 90.00
R / Rfree (%) 19.2 / 22.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. (pdb code 5vrm). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333., PDB code: 5vrm:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5vrm

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Fluorine binding site 1 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


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 the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F300

b:67.8
occ:0.80
 F24 B:9JJ300 0.0 67.8 0.8
C23 B:9JJ300 1.3 71.5 0.8
F26 B:9JJ300 2.2 74.5 0.8
F25 B:9JJ300 2.2 67.6 0.8
C20 B:9JJ300 2.3 70.8 0.8
C21 B:9JJ300 2.8 68.9 0.8
C19 B:9JJ300 3.5 71.3 0.8
CE2 B:PHE149 4.1 41.9 1.0
SD B:MET155 4.1 55.2 1.0
C22 B:9JJ300 4.1 67.9 0.8
CZ B:PHE149 4.1 43.7 1.0
O B:PRO156 4.6 46.6 1.0
C18 B:9JJ300 4.6 69.4 0.8
CG B:MET155 4.7 50.4 1.0
C17 B:9JJ300 4.9 68.2 0.8
CB B:TYR158 4.9 45.2 1.0

Fluorine binding site 2 out of 9 in 5vrm

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Fluorine binding site 2 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


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 the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F300

b:67.6
occ:0.80
 F25 B:9JJ300 0.0 67.6 0.8
C23 B:9JJ300 1.3 71.5 0.8
F24 B:9JJ300 2.2 67.8 0.8
F26 B:9JJ300 2.2 74.5 0.8
C20 B:9JJ300 2.3 70.8 0.8
C21 B:9JJ300 3.0 68.9 0.8
C19 B:9JJ300 3.3 71.3 0.8
C22 B:9JJ300 4.3 67.9 0.8
C18 B:9JJ300 4.4 69.4 0.8
C17 B:9JJ300 4.9 68.2 0.8
CB B:LEU218 4.9 85.0 1.0

Fluorine binding site 3 out of 9 in 5vrm

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Fluorine binding site 3 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


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 the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F300

b:74.5
occ:0.80
 F26 B:9JJ300 0.0 74.5 0.8
C23 B:9JJ300 1.3 71.5 0.8
F24 B:9JJ300 2.2 67.8 0.8
F25 B:9JJ300 2.2 67.6 0.8
C20 B:9JJ300 2.3 70.8 0.8
C19 B:9JJ300 2.7 71.3 0.8
C21 B:9JJ300 3.6 68.9 0.8
O B:PRO156 3.8 46.6 1.0
CB B:ALA157 3.9 48.9 1.0
N B:TYR158 4.0 45.5 1.0
C18 B:9JJ300 4.1 69.4 0.8
CB B:TYR158 4.2 45.2 1.0
CA B:TYR158 4.4 44.5 1.0
CD1 B:TYR158 4.6 48.9 1.0
C B:ALA157 4.6 48.3 1.0
C22 B:9JJ300 4.7 67.9 0.8
CA B:ALA157 4.8 48.9 1.0
CG B:TYR158 4.8 45.9 1.0
C B:PRO156 4.9 48.9 1.0
C17 B:9JJ300 4.9 68.2 0.8

Fluorine binding site 4 out of 9 in 5vrm

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Fluorine binding site 4 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


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 the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F300

b:75.8
occ:1.00
 F24 C:9JJ300 0.0 75.8 1.0
C23 C:9JJ300 1.3 75.8 1.0
F25 C:9JJ300 2.2 74.0 1.0
F26 C:9JJ300 2.2 71.5 1.0
C20 C:9JJ300 2.3 71.9 1.0
C21 C:9JJ300 2.7 71.3 1.0
C19 C:9JJ300 3.6 72.9 1.0
C22 C:9JJ300 4.1 70.8 1.0
CZ C:PHE149 4.6 49.8 1.0
CE2 C:PHE149 4.7 48.2 1.0
C18 C:9JJ300 4.8 70.9 1.0
O C:PRO156 4.8 51.4 1.0
SD C:MET155 4.9 60.6 1.0
C17 C:9JJ300 5.0 69.9 1.0

Fluorine binding site 5 out of 9 in 5vrm

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Fluorine binding site 5 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


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 the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F300

b:74.0
occ:1.00
 F25 C:9JJ300 0.0 74.0 1.0
C23 C:9JJ300 1.3 75.8 1.0
F26 C:9JJ300 2.1 71.5 1.0
F24 C:9JJ300 2.2 75.8 1.0
C20 C:9JJ300 2.3 71.9 1.0
C19 C:9JJ300 3.0 72.9 1.0
C21 C:9JJ300 3.3 71.3 1.0
C18 C:9JJ300 4.3 70.9 1.0
C22 C:9JJ300 4.5 70.8 1.0
CB C:ALA157 4.5 53.2 1.0
C17 C:9JJ300 4.9 69.9 1.0
O C:PRO156 4.9 51.4 1.0

Fluorine binding site 6 out of 9 in 5vrm

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Fluorine binding site 6 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


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 the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F300

b:71.5
occ:1.00
 F26 C:9JJ300 0.0 71.5 1.0
C23 C:9JJ300 1.3 75.8 1.0
F25 C:9JJ300 2.1 74.0 1.0
F24 C:9JJ300 2.2 75.8 1.0
C20 C:9JJ300 2.3 71.9 1.0
C19 C:9JJ300 2.8 72.9 1.0
O C:PRO156 3.4 51.4 1.0
C21 C:9JJ300 3.5 71.3 1.0
N C:TYR158 3.7 53.6 1.0
CB C:TYR158 3.7 51.8 1.0
CB C:ALA157 4.0 53.2 1.0
CA C:TYR158 4.1 52.5 1.0
C18 C:9JJ300 4.1 70.9 1.0
CD1 C:TYR158 4.3 55.3 1.0
CG C:TYR158 4.4 54.0 1.0
C C:ALA157 4.4 53.1 1.0
SD C:MET155 4.6 60.6 1.0
C C:PRO156 4.6 53.7 1.0
C22 C:9JJ300 4.6 70.8 1.0
CG C:MET155 4.7 56.2 1.0
CA C:ALA157 4.7 53.2 1.0
C17 C:9JJ300 4.9 69.9 1.0
CE2 C:PHE149 5.0 48.2 1.0

Fluorine binding site 7 out of 9 in 5vrm

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Fluorine binding site 7 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F300

b:77.3
occ:0.70
 F24 D:9JJ300 0.0 77.3 0.7
C23 D:9JJ300 1.3 78.5 0.7
F25 D:9JJ300 2.1 81.1 0.7
F26 D:9JJ300 2.2 75.9 0.7
C20 D:9JJ300 2.3 75.7 0.7
C19 D:9JJ300 2.8 74.5 0.7
O D:HOH413 2.9 72.8 1.0
C21 D:9JJ300 3.5 73.6 0.7
O D:GLN100 3.6 89.0 1.0
O D:ALA157 3.9 78.5 1.0
ND2 D:ASN159 4.0 79.1 1.0
C18 D:9JJ300 4.1 72.2 0.7
CB D:ASN159 4.4 69.7 1.0
CG D:ASN159 4.6 74.6 1.0
C D:GLN100 4.6 91.0 1.0
C22 D:9JJ300 4.6 70.6 0.7
O D:PRO99 4.8 89.7 1.0
C17 D:9JJ300 4.9 70.1 0.7

Fluorine binding site 8 out of 9 in 5vrm

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Fluorine binding site 8 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F300

b:81.1
occ:0.70
 F25 D:9JJ300 0.0 81.1 0.7
C23 D:9JJ300 1.3 78.5 0.7
F24 D:9JJ300 2.1 77.3 0.7
F26 D:9JJ300 2.2 75.9 0.7
C20 D:9JJ300 2.3 75.7 0.7
C21 D:9JJ300 2.7 73.6 0.7
O D:PRO99 2.7 89.7 1.0
O D:GLN100 2.7 89.0 1.0
C D:GLN100 3.2 91.0 1.0
CA D:GLN100 3.6 92.6 1.0
C19 D:9JJ300 3.6 74.5 0.7
C D:PRO99 3.7 87.8 1.0
C22 D:9JJ300 4.0 70.6 0.7
N D:GLN100 4.1 91.4 1.0
CG D:MET98 4.5 67.7 1.0
C18 D:9JJ300 4.7 72.2 0.7
O D:MET98 4.8 77.1 1.0
C17 D:9JJ300 4.9 70.1 0.7
O D:HOH413 4.9 72.8 1.0
CB D:GLN100 4.9 95.0 1.0

Fluorine binding site 9 out of 9 in 5vrm

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Fluorine binding site 9 out of 9 in the Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333.


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Inha From Mycobacterium Tuberculosis in Complex with AN12855, Ebsi 4333. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F300

b:75.9
occ:0.70
 F26 D:9JJ300 0.0 75.9 0.7
C23 D:9JJ300 1.3 78.5 0.7
F25 D:9JJ300 2.2 81.1 0.7
F24 D:9JJ300 2.2 77.3 0.7
C20 D:9JJ300 2.3 75.7 0.7
C19 D:9JJ300 3.1 74.5 0.7
C21 D:9JJ300 3.2 73.6 0.7
CB D:ASN159 3.6 69.7 1.0
N D:TRP160 3.9 54.6 1.0
ND2 D:ASN159 4.2 79.1 1.0
O D:PRO99 4.3 89.7 1.0
C18 D:9JJ300 4.3 72.2 0.7
CG D:MET98 4.3 67.7 1.0
C22 D:9JJ300 4.4 70.6 0.7
CG D:ASN159 4.4 74.6 1.0
CB D:TRP160 4.5 51.1 1.0
O D:TYR158 4.5 59.0 1.0
O D:GLN100 4.5 89.0 1.0
CD1 D:TRP160 4.5 51.6 1.0
O D:ALA157 4.6 78.5 1.0
CA D:ASN159 4.7 63.0 1.0
CA D:TRP160 4.7 51.5 1.0
C D:ASN159 4.8 59.2 1.0
O D:HOH413 4.8 72.8 1.0
C17 D:9JJ300 4.9 70.1 0.7
N D:MET161 4.9 49.8 1.0
CG D:TRP160 5.0 50.8 1.0

Reference:

Y.Xia, Y.Zhou, D.S.Carter, M.B.Mcneil, W.Choi, J.Halladay, P.W.Berry, W.Mao, V.Hernandez, T.O'malley, A.Korkegian, B.Sunde, L.Flint, L.K.Woolhiser, M.S.Scherman, V.Gruppo, C.Hastings, G.T.Robertson, T.R.Ioerger, J.Sacchettini, P.J.Tonge, A.J.Lenaerts, T.Parish, M.Alley. Discovery of A Cofactor-Independent Inhibitor Ofmycobacterium Tuberculosisinha. Life Sci Alliance V. 1 00025 2018.
ISSN: ESSN 2575-1077
PubMed: 30456352
DOI: 10.26508/LSA.201800025
Page generated: Sun Dec 13 12:41:02 2020

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