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Fluorine in PDB 5sd1: Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer)

Enzymatic activity of Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer)

All present enzymatic activity of Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer):
1.5.1.3;

Protein crystallography data

The structure of Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer), PDB code: 5sd1 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) 36.15 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 29.45, 67.32, 72.29, 90, 90, 90
R / Rfree (%) 14.8 / 21.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer) (pdb code 5sd1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer), PDB code: 5sd1:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5sd1

Go back to Fluorine Binding Sites List in 5sd1
Fluorine binding site 1 out of 4 in the Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer)


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 Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:32.0
occ:0.63
 F25 A:I6J202 0.0 32.0 0.6
F25 A:I6J202 1.0 27.1 0.4
C24 A:I6J202 1.2 29.7 0.4
C24 A:I6J202 1.4 29.2 0.6
F26 A:I6J202 1.8 31.7 0.4
F26 A:I6J202 2.2 30.6 0.6
C23 A:I6J202 2.4 28.2 0.6
C23 A:I6J202 2.6 27.6 0.4
C27 A:I6J202 2.6 27.0 0.6
NH2 A:ARG32 2.8 40.4 1.0
O29 A:I6J202 2.9 15.9 0.6
O29 A:I6J202 3.3 28.6 0.4
O28 A:I6J202 3.3 34.1 0.6
CG A:ARG32 3.4 20.4 1.0
C22 A:I6J202 3.5 27.4 0.6
C27 A:I6J202 3.5 26.3 0.4
O A:GLN28 3.5 16.8 1.0
CZ A:ARG32 3.6 39.1 1.0
C22 A:I6J202 3.6 24.9 0.4
CD A:ARG32 3.7 28.1 1.0
CB A:GLN28 3.8 17.1 1.0
NE A:ARG32 3.9 40.3 1.0
CA A:GLN28 4.0 15.6 1.0
C A:GLN28 4.1 14.0 1.0
O A:HOH405 4.1 32.0 1.0
CD2 A:PHE31 4.1 12.2 1.0
C21 A:I6J202 4.3 25.4 0.6
NE2 A:GLN28 4.3 34.3 1.0
NH1 A:ARG32 4.5 49.1 1.0
CG A:GLN28 4.5 21.6 1.0
C20 A:I6J202 4.6 30.2 0.6
CB A:ARG32 4.7 14.6 1.0
O28 A:I6J202 4.7 25.6 0.4
CE2 A:PHE31 4.7 13.1 1.0
C01 A:I6J202 4.8 19.0 0.6
C01 A:I6J202 4.9 18.4 0.4
N A:ARG32 4.9 10.5 1.0
CD A:GLN28 4.9 30.5 1.0

Fluorine binding site 2 out of 4 in 5sd1

Go back to Fluorine Binding Sites List in 5sd1
Fluorine binding site 2 out of 4 in the Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer)


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 Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:27.1
occ:0.37
 F25 A:I6J202 0.0 27.1 0.4
F25 A:I6J202 1.0 32.0 0.6
C24 A:I6J202 1.0 29.2 0.6
C24 A:I6J202 1.4 29.7 0.4
F26 A:I6J202 2.0 30.6 0.6
C23 A:I6J202 2.2 28.2 0.6
F26 A:I6J202 2.2 31.7 0.4
C23 A:I6J202 2.4 27.6 0.4
C27 A:I6J202 2.8 27.0 0.6
O29 A:I6J202 2.8 15.9 0.6
CD2 A:PHE31 3.2 12.2 1.0
O A:GLN28 3.3 16.8 1.0
O29 A:I6J202 3.4 28.6 0.4
C22 A:I6J202 3.4 24.9 0.4
C22 A:I6J202 3.5 27.4 0.6
C27 A:I6J202 3.5 26.3 0.4
CG A:ARG32 3.7 20.4 1.0
O28 A:I6J202 3.7 34.1 0.6
NH2 A:ARG32 3.7 40.4 1.0
CA A:GLN28 3.8 15.6 1.0
CB A:GLN28 3.8 17.1 1.0
C A:GLN28 3.9 14.0 1.0
CE2 A:PHE31 3.9 13.1 1.0
C01 A:I6J202 4.1 19.0 0.6
C01 A:I6J202 4.1 18.4 0.4
C21 A:I6J202 4.2 25.4 0.6
CG A:PHE31 4.2 16.4 1.0
CD A:ARG32 4.2 28.1 1.0
CB A:PHE31 4.3 10.5 1.0
CZ A:ARG32 4.4 39.1 1.0
N A:ARG32 4.5 10.5 1.0
CG A:GLN28 4.5 21.6 1.0
C20 A:I6J202 4.6 30.2 0.6
NE A:ARG32 4.6 40.3 1.0
O28 A:I6J202 4.7 25.6 0.4
CB A:ARG32 4.7 14.6 1.0
O A:HOH405 4.7 32.0 1.0
NE2 A:GLN28 4.8 34.3 1.0
C21 A:I6J202 4.9 27.1 0.4
CA A:ARG32 5.0 12.6 1.0

Fluorine binding site 3 out of 4 in 5sd1

Go back to Fluorine Binding Sites List in 5sd1
Fluorine binding site 3 out of 4 in the Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer)


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 Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:30.6
occ:0.63
 F26 A:I6J202 0.0 30.6 0.6
F26 A:I6J202 1.4 31.7 0.4
C24 A:I6J202 1.4 29.2 0.6
C24 A:I6J202 1.6 29.7 0.4
C22 A:I6J202 1.9 24.9 0.4
C23 A:I6J202 2.0 27.6 0.4
F25 A:I6J202 2.0 27.1 0.4
F25 A:I6J202 2.2 32.0 0.6
C23 A:I6J202 2.5 28.2 0.6
C21 A:I6J202 2.8 25.4 0.6
C22 A:I6J202 2.8 27.4 0.6
C20 A:I6J202 2.8 30.2 0.6
C01 A:I6J202 3.1 19.0 0.6
C01 A:I6J202 3.2 18.4 0.4
CG A:GLN28 3.2 21.6 1.0
CB A:GLN28 3.3 17.1 1.0
C21 A:I6J202 3.4 27.1 0.4
NE2 A:GLN28 3.4 34.3 1.0
C27 A:I6J202 3.5 26.3 0.4
CD A:GLN28 3.5 30.5 1.0
C16 A:I6J202 3.7 22.7 0.6
CA A:GLN28 3.7 15.6 1.0
C27 A:I6J202 3.7 27.0 0.6
C19 A:I6J202 3.7 24.6 0.6
O29 A:I6J202 4.0 28.6 0.4
C20 A:I6J202 4.2 26.6 0.4
O28 A:I6J202 4.3 25.6 0.4
O15 A:I6J202 4.3 23.8 0.4
O28 A:I6J202 4.3 34.1 0.6
O29 A:I6J202 4.3 15.9 0.6
C16 A:I6J202 4.4 22.6 0.4
C17 A:I6J202 4.4 22.0 0.6
O15 A:I6J202 4.4 22.3 0.6
OE1 A:GLN28 4.4 34.7 1.0
C18 A:I6J202 4.4 23.6 0.6
O A:GLN28 4.4 16.8 1.0
C02 A:I6J202 4.5 13.9 0.4
NH2 A:ARG32 4.5 40.4 1.0
CD2 A:PHE31 4.5 12.2 1.0
C A:GLN28 4.5 14.0 1.0
C02 A:I6J202 4.6 13.8 0.6
N A:GLN28 4.9 16.9 1.0

Fluorine binding site 4 out of 4 in 5sd1

Go back to Fluorine Binding Sites List in 5sd1
Fluorine binding site 4 out of 4 in the Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer)


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 Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:31.7
occ:0.37
 F26 A:I6J202 0.0 31.7 0.4
F26 A:I6J202 1.4 30.6 0.6
C24 A:I6J202 1.4 29.7 0.4
F25 A:I6J202 1.8 32.0 0.6
C24 A:I6J202 1.8 29.2 0.6
F25 A:I6J202 2.2 27.1 0.4
C23 A:I6J202 2.4 27.6 0.4
C22 A:I6J202 2.5 24.9 0.4
C23 A:I6J202 2.8 28.2 0.6
NE2 A:GLN28 2.8 34.3 1.0
C22 A:I6J202 3.0 27.4 0.6
C20 A:I6J202 3.1 30.2 0.6
CB A:GLN28 3.2 17.1 1.0
C21 A:I6J202 3.3 25.4 0.6
NH2 A:ARG32 3.3 40.4 1.0
CD A:GLN28 3.4 30.5 1.0
CG A:GLN28 3.5 21.6 1.0
C27 A:I6J202 3.5 27.0 0.6
C27 A:I6J202 3.6 26.3 0.4
O28 A:I6J202 3.9 34.1 0.6
O29 A:I6J202 3.9 28.6 0.4
C21 A:I6J202 3.9 27.1 0.4
CA A:GLN28 4.1 15.6 1.0
C19 A:I6J202 4.1 24.6 0.6
O29 A:I6J202 4.3 15.9 0.6
C20 A:I6J202 4.3 26.6 0.4
OE1 A:GLN28 4.4 34.7 1.0
O28 A:I6J202 4.4 25.6 0.4
CZ A:ARG32 4.4 39.1 1.0
O A:HOH405 4.4 32.0 1.0
C01 A:I6J202 4.4 19.0 0.6
C01 A:I6J202 4.5 18.4 0.4
C16 A:I6J202 4.5 22.7 0.6
O A:GLN28 4.5 16.8 1.0
C A:GLN28 4.6 14.0 1.0

Reference:

S.J.Mayclin, J.W.Fairman, D.M.Dranow, D.G.Conrady, D.Fox Iii, C.M.Lukacs, D.D.Lorimer, P.S.Horanyi, T.E.Edwards, J.Abendroth. Crystal Structure of Dihydrofolate Reductase From Mycobacterium Tuberculosis Bound to Nadp and Sddc Inhibitor Sddc-1235 (Enantiomer) To Be Published.
Page generated: Thu Aug 1 14:12:31 2024

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