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Fluorine in PDB 3gwc: Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad

Enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad

All present enzymatic activity of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad:
2.1.1.148;

Protein crystallography data

The structure of Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad, PDB code: 3gwc was solved by Seattle Structural Genomics Center For Infectious Disease (Ssgcid), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.70 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 81.044, 78.447, 168.959, 90.00, 96.80, 90.00
R / Rfree (%) 18.7 / 22.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad (pdb code 3gwc). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad, PDB code: 3gwc:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 3gwc

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Fluorine binding site 1 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad


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 Thymidylate Synthase X Bound to Fdump and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F260

b:19.8
occ:1.00
F5 A:UFP260 0.0 19.8 1.0
C5 A:UFP260 1.4 20.2 1.0
C6 A:UFP260 2.3 18.9 1.0
C4 A:UFP260 2.4 19.4 1.0
O4 A:UFP260 2.9 18.7 1.0
O A:HOH566 2.9 31.0 1.0
OG A:SER105 3.0 18.1 1.0
O1P A:UFP260 3.1 15.0 1.0
CD A:ARG107 3.2 19.6 1.0
N5 D:FAD259 3.3 23.6 1.0
N1 A:UFP260 3.6 18.0 1.0
C5X D:FAD259 3.7 22.4 1.0
N3 A:UFP260 3.7 16.2 1.0
NH1 A:ARG107 3.8 20.5 1.0
CG A:ARG107 3.8 18.3 1.0
C6 D:FAD259 3.9 23.8 1.0
C4X D:FAD259 3.9 22.5 1.0
CB A:SER105 4.0 16.1 1.0
O4 D:FAD259 4.0 23.0 1.0
CB A:ARG107 4.0 18.1 1.0
C2 A:UFP260 4.1 17.6 1.0
P A:UFP260 4.2 15.2 1.0
C4 D:FAD259 4.2 22.1 1.0
NE A:ARG107 4.3 18.0 1.0
O5' A:UFP260 4.4 12.2 1.0
O2P A:UFP260 4.5 12.0 1.0
NZ A:LYS165 4.5 27.1 1.0
CZ A:ARG107 4.5 19.9 1.0
OE2 D:GLU92 4.5 13.9 1.0
C9A D:FAD259 4.6 23.5 1.0
C1' A:UFP260 4.7 13.9 1.0
C10 D:FAD259 4.7 20.2 1.0
C7 D:FAD259 4.9 23.6 1.0
O4' A:UFP260 5.0 13.1 1.0
CA A:SER105 5.0 14.9 1.0

Fluorine binding site 2 out of 8 in 3gwc

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Fluorine binding site 2 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad


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 Thymidylate Synthase X Bound to Fdump and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F260

b:18.0
occ:1.00
F5 B:UFP260 0.0 18.0 1.0
C5 B:UFP260 1.4 16.4 1.0
C6 B:UFP260 2.4 16.0 1.0
C4 B:UFP260 2.4 17.6 1.0
O4 B:UFP260 2.9 18.0 1.0
OG B:SER105 3.2 13.2 1.0
N5 C:FAD259 3.2 21.0 1.0
O1P B:UFP260 3.2 14.7 1.0
CE2 B:TYR108 3.4 34.3 1.0
CD B:ARG107 3.4 16.6 1.0
C5X C:FAD259 3.6 23.1 1.0
N1 B:UFP260 3.6 17.1 1.0
N3 B:UFP260 3.7 16.9 1.0
C6 C:FAD259 3.7 23.6 1.0
NH1 B:ARG107 3.8 20.1 1.0
C4X C:FAD259 3.8 20.2 1.0
CD2 B:TYR108 3.9 31.1 1.0
CG B:ARG107 4.0 16.9 1.0
CB B:ARG107 4.0 15.5 1.0
CB B:SER105 4.0 12.9 1.0
O4 C:FAD259 4.1 19.9 1.0
C2 B:UFP260 4.2 16.6 1.0
C4 C:FAD259 4.3 19.0 1.0
P B:UFP260 4.3 13.9 1.0
CZ B:TYR108 4.4 35.3 1.0
NE B:ARG107 4.4 17.6 1.0
O5' B:UFP260 4.5 14.7 1.0
C9A C:FAD259 4.5 21.6 1.0
O2P B:UFP260 4.5 14.1 1.0
CZ B:ARG107 4.5 19.8 1.0
OE2 C:GLU92 4.5 14.8 1.0
OH B:TYR108 4.6 36.4 1.0
C7 C:FAD259 4.7 24.6 1.0
C10 C:FAD259 4.7 18.2 1.0
C1' B:UFP260 4.7 16.9 1.0
C5' B:UFP260 5.0 13.7 1.0
N10 C:FAD259 5.0 19.0 1.0
O4' B:UFP260 5.0 14.3 1.0

Fluorine binding site 3 out of 8 in 3gwc

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Fluorine binding site 3 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad


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 Thymidylate Synthase X Bound to Fdump and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F260

b:15.1
occ:1.00
F5 C:UFP260 0.0 15.1 1.0
C5 C:UFP260 1.3 15.6 1.0
C6 C:UFP260 2.4 14.8 1.0
C4 C:UFP260 2.4 15.6 1.0
O4 C:UFP260 2.7 13.0 1.0
N5 B:FAD259 3.2 18.7 1.0
O1P C:UFP260 3.2 13.3 1.0
CD C:ARG107 3.3 14.9 1.0
OG C:SER105 3.3 13.6 1.0
CE2 C:TYR108 3.5 27.6 1.0
C5X B:FAD259 3.5 18.9 1.0
N1 C:UFP260 3.6 12.7 1.0
N3 C:UFP260 3.6 14.3 1.0
C6 B:FAD259 3.7 19.0 1.0
C4X B:FAD259 3.8 16.3 1.0
CB C:ARG107 3.8 14.7 1.0
CG C:ARG107 3.8 13.3 1.0
NH1 C:ARG107 3.9 11.9 1.0
CD2 C:TYR108 4.0 27.1 1.0
CB C:SER105 4.0 12.3 1.0
C2 C:UFP260 4.1 13.9 1.0
O4 B:FAD259 4.1 20.6 1.0
C4 B:FAD259 4.2 18.8 1.0
CZ C:TYR108 4.3 29.6 1.0
NE C:ARG107 4.3 12.7 1.0
P C:UFP260 4.3 12.0 1.0
C9A B:FAD259 4.4 17.6 1.0
O5' C:UFP260 4.4 11.3 1.0
OE2 B:GLU92 4.5 14.9 1.0
OH C:TYR108 4.5 32.0 1.0
CZ C:ARG107 4.5 14.2 1.0
O2P C:UFP260 4.6 12.7 1.0
C10 B:FAD259 4.6 17.0 1.0
C1' C:UFP260 4.7 13.7 1.0
C7 B:FAD259 4.7 21.5 1.0
N10 B:FAD259 4.9 16.9 1.0
O4' C:UFP260 5.0 13.0 1.0

Fluorine binding site 4 out of 8 in 3gwc

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Fluorine binding site 4 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad


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 Thymidylate Synthase X Bound to Fdump and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F260

b:16.8
occ:1.00
F5 D:UFP260 0.0 16.8 1.0
C5 D:UFP260 1.4 13.3 1.0
C6 D:UFP260 2.3 14.1 1.0
C4 D:UFP260 2.4 13.7 1.0
O4 D:UFP260 2.8 14.9 1.0
O1P D:UFP260 3.2 15.0 1.0
CD D:ARG107 3.3 17.5 1.0
OG D:SER105 3.3 16.5 1.0
N5 A:FAD259 3.3 18.9 1.0
CE2 D:TYR108 3.4 31.0 1.0
N1 D:UFP260 3.6 13.8 1.0
N3 D:UFP260 3.7 13.5 1.0
C5X A:FAD259 3.7 19.9 1.0
CB D:ARG107 3.8 17.8 1.0
NH1 D:ARG107 3.8 17.9 1.0
CG D:ARG107 3.8 16.9 1.0
C6 A:FAD259 3.8 21.6 1.0
CD2 D:TYR108 3.9 30.0 1.0
C4X A:FAD259 4.0 16.9 1.0
C2 D:UFP260 4.2 14.5 1.0
O4 A:FAD259 4.2 16.9 1.0
CB D:SER105 4.2 13.8 1.0
P D:UFP260 4.2 14.6 1.0
CZ D:TYR108 4.2 31.9 1.0
NE D:ARG107 4.3 18.4 1.0
C4 A:FAD259 4.3 18.1 1.0
OE2 A:GLU92 4.4 14.8 1.0
O2P D:UFP260 4.4 14.9 1.0
O5' D:UFP260 4.5 13.0 1.0
CZ D:ARG107 4.5 17.3 1.0
OH D:TYR108 4.5 35.8 1.0
C9A A:FAD259 4.6 19.9 1.0
C1' D:UFP260 4.7 14.2 1.0
C7 A:FAD259 4.8 21.1 1.0
C10 A:FAD259 4.8 17.8 1.0
O4' D:UFP260 4.9 12.6 1.0
CA D:ARG107 5.0 18.3 1.0
CG D:TYR108 5.0 28.0 1.0

Fluorine binding site 5 out of 8 in 3gwc

Go back to Fluorine Binding Sites List in 3gwc
Fluorine binding site 5 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad


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 Thymidylate Synthase X Bound to Fdump and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
E:F260

b:18.0
occ:1.00
F5 E:UFP260 0.0 18.0 1.0
C5 E:UFP260 1.4 19.3 1.0
C6 E:UFP260 2.4 19.4 1.0
C4 E:UFP260 2.4 20.6 1.0
O4 E:UFP260 2.7 20.6 1.0
N5 H:FAD259 3.2 22.2 1.0
OG E:SER105 3.3 14.1 1.0
CE2 E:TYR108 3.4 30.0 1.0
CD E:ARG107 3.4 13.7 1.0
O1P E:UFP260 3.5 11.8 1.0
C5X H:FAD259 3.5 20.4 1.0
NH1 E:ARG107 3.6 16.4 1.0
C6 H:FAD259 3.6 20.5 1.0
N1 E:UFP260 3.6 17.9 1.0
N3 E:UFP260 3.6 19.2 1.0
C4X H:FAD259 3.9 20.9 1.0
CD2 E:TYR108 3.9 28.4 1.0
CB E:ARG107 3.9 14.1 1.0
CZ E:TYR108 4.0 32.1 1.0
CG E:ARG107 4.0 13.9 1.0
C2 E:UFP260 4.2 20.1 1.0
OH E:TYR108 4.2 33.5 1.0
CB E:SER105 4.2 13.5 1.0
O4 H:FAD259 4.2 20.1 1.0
NE E:ARG107 4.3 13.1 1.0
C4 H:FAD259 4.3 19.2 1.0
CZ E:ARG107 4.4 16.5 1.0
C9A H:FAD259 4.4 20.7 1.0
P E:UFP260 4.5 13.4 1.0
OE2 H:GLU92 4.6 13.1 1.0
O5' E:UFP260 4.6 13.2 1.0
O2P E:UFP260 4.6 11.7 1.0
C7 H:FAD259 4.6 20.1 1.0
C10 H:FAD259 4.7 18.5 1.0
C1' E:UFP260 4.8 18.0 1.0
CG E:TYR108 4.9 23.9 1.0
CE1 E:TYR108 4.9 30.4 1.0
N10 H:FAD259 5.0 20.4 1.0

Fluorine binding site 6 out of 8 in 3gwc

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Fluorine binding site 6 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad


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 Thymidylate Synthase X Bound to Fdump and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F260

b:26.9
occ:1.00
F5 F:UFP260 0.0 26.9 1.0
C5 F:UFP260 1.4 21.8 1.0
C6 F:UFP260 2.4 21.8 1.0
C4 F:UFP260 2.4 22.7 1.0
O4 F:UFP260 2.7 20.8 1.0
N5 G:FAD259 3.2 23.9 1.0
O1P F:UFP260 3.3 17.4 1.0
CD F:ARG107 3.4 29.2 1.0
CE2 F:TYR108 3.4 41.5 1.0
OG F:SER105 3.4 24.6 1.0
C5X G:FAD259 3.6 25.0 1.0
N1 F:UFP260 3.6 22.0 1.0
N3 F:UFP260 3.6 20.9 1.0
C6 G:FAD259 3.7 27.0 1.0
NH1 F:ARG107 3.7 27.7 1.0
CD2 F:TYR108 3.9 40.0 1.0
CG F:ARG107 3.9 29.0 1.0
CB F:ARG107 3.9 29.7 1.0
C4X G:FAD259 3.9 23.2 1.0
C2 F:UFP260 4.1 20.4 1.0
CZ F:TYR108 4.2 41.9 1.0
CB F:SER105 4.2 24.0 1.0
O4 G:FAD259 4.2 25.8 1.0
NE F:ARG107 4.3 27.9 1.0
P F:UFP260 4.3 20.5 1.0
C4 G:FAD259 4.4 24.0 1.0
CZ F:ARG107 4.4 28.3 1.0
OH F:TYR108 4.5 43.5 1.0
C9A G:FAD259 4.5 25.6 1.0
O2P F:UFP260 4.5 19.4 1.0
O5' F:UFP260 4.5 19.5 1.0
C7 G:FAD259 4.6 28.4 1.0
OE2 G:GLU92 4.6 23.1 1.0
C1' F:UFP260 4.8 20.1 1.0
C10 G:FAD259 4.8 22.1 1.0
CG F:TYR108 4.9 37.5 1.0

Fluorine binding site 7 out of 8 in 3gwc

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Fluorine binding site 7 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad


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 Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
G:F260

b:27.5
occ:1.00
F5 G:UFP260 0.0 27.5 1.0
C5 G:UFP260 1.4 25.0 1.0
C6 G:UFP260 2.3 24.2 1.0
C4 G:UFP260 2.4 23.9 1.0
O4 G:UFP260 2.8 21.4 1.0
O1P G:UFP260 3.1 17.8 1.0
OG G:SER105 3.2 25.6 1.0
CE2 G:TYR108 3.3 41.0 1.0
CD G:ARG107 3.3 28.6 1.0
N5 F:FAD259 3.4 28.9 1.0
N1 G:UFP260 3.6 22.8 1.0
N3 G:UFP260 3.6 22.6 1.0
C5X F:FAD259 3.7 29.6 1.0
NH1 G:ARG107 3.8 27.2 1.0
CB G:ARG107 3.8 29.2 1.0
C6 F:FAD259 3.8 28.6 1.0
CD2 G:TYR108 3.8 39.9 1.0
CG G:ARG107 3.9 28.5 1.0
C4X F:FAD259 4.1 28.6 1.0
CZ G:TYR108 4.1 41.1 1.0
P G:UFP260 4.1 21.6 1.0
C2 G:UFP260 4.1 22.6 1.0
CB G:SER105 4.2 24.1 1.0
O2P G:UFP260 4.3 22.6 1.0
NE G:ARG107 4.3 28.6 1.0
O4 F:FAD259 4.3 29.9 1.0
OE2 F:GLU92 4.4 20.4 1.0
OH G:TYR108 4.4 43.2 1.0
O5' G:UFP260 4.5 20.9 1.0
CZ G:ARG107 4.5 29.1 1.0
C4 F:FAD259 4.5 29.6 1.0
C9A F:FAD259 4.6 28.1 1.0
C1' G:UFP260 4.7 21.6 1.0
C7 F:FAD259 4.8 29.9 1.0
C10 F:FAD259 4.9 26.9 1.0
CG G:TYR108 4.9 36.8 1.0
C5' G:UFP260 5.0 22.5 1.0
CA G:ARG107 5.0 29.2 1.0

Fluorine binding site 8 out of 8 in 3gwc

Go back to Fluorine Binding Sites List in 3gwc
Fluorine binding site 8 out of 8 in the Crystal Structure of Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad


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 Mycobacterium Tuberculosis Thymidylate Synthase X Bound to Fdump and Fad within 5.0Å range:
probe atom residue distance (Å) B Occ
H:F260

b:17.6
occ:1.00
F5 H:UFP260 0.0 17.6 1.0
C5 H:UFP260 1.4 19.4 1.0
C6 H:UFP260 2.4 18.3 1.0
C4 H:UFP260 2.4 20.8 1.0
O4 H:UFP260 2.7 24.1 1.0
O1P H:UFP260 3.1 13.6 1.0
N5 E:FAD259 3.2 21.4 1.0
CE2 H:TYR108 3.4 34.4 1.0
CD H:ARG107 3.4 16.6 1.0
OG H:SER105 3.4 13.2 1.0
C5X E:FAD259 3.6 21.8 1.0
N1 H:UFP260 3.6 18.5 1.0
N3 H:UFP260 3.7 17.4 1.0
NH1 H:ARG107 3.7 18.5 1.0
C6 E:FAD259 3.8 20.2 1.0
C4X E:FAD259 3.9 20.4 1.0
CD2 H:TYR108 3.9 31.6 1.0
CG H:ARG107 4.0 15.2 1.0
CB H:SER105 4.0 11.9 1.0
O4 E:FAD259 4.1 19.5 1.0
CB H:ARG107 4.1 14.7 1.0
C2 H:UFP260 4.1 17.0 1.0
CZ H:TYR108 4.2 35.2 1.0
P H:UFP260 4.2 12.9 1.0
C4 E:FAD259 4.3 20.2 1.0
NE H:ARG107 4.3 15.3 1.0
OH H:TYR108 4.4 38.8 1.0
O2P H:UFP260 4.4 14.8 1.0
OE2 E:GLU92 4.5 17.6 1.0
CZ H:ARG107 4.5 17.2 1.0
C9A E:FAD259 4.5 20.7 1.0
O5' H:UFP260 4.5 13.0 1.0
C1' H:UFP260 4.7 16.5 1.0
C10 E:FAD259 4.7 19.8 1.0
C7 E:FAD259 4.8 20.2 1.0

Reference:

L.Baugh, I.Phan, D.W.Begley, M.C.Clifton, B.Armour, D.M.Dranow, B.M.Taylor, M.M.Muruthi, J.Abendroth, J.W.Fairman, D.Fox, S.H.Dieterich, B.L.Staker, A.S.Gardberg, R.Choi, S.N.Hewitt, A.J.Napuli, J.Myers, L.K.Barrett, Y.Zhang, M.Ferrell, E.Mundt, K.Thompkins, N.Tran, S.Lyons-Abbott, A.Abramov, A.Sekar, D.Serbzhinskiy, D.Lorimer, G.W.Buchko, R.Stacy, L.J.Stewart, T.E.Edwards, W.C.Van Voorhis, P.J.Myler. Increasing the Structural Coverage of Tuberculosis Drug Targets. Tuberculosis (Edinb) V. 95 142 2015.
ISSN: ISSN 1472-9792
PubMed: 25613812
DOI: 10.1016/J.TUBE.2014.12.003
Page generated: Wed Jul 31 18:59:56 2024

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