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Fluorine in PDB 5xmq: Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011

Enzymatic activity of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011

All present enzymatic activity of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011, PDB code: 5xmq was solved by P.Chitnumsub, A.Jaruwat, U.Leartsakulpanich, G.Schwertz, F.Diederich, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.319, 58.362, 236.453, 90.00, 90.07, 90.00
R / Rfree (%) 21.7 / 27.6

Other elements in 5xmq:

The structure of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 (pdb code 5xmq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011, PDB code: 5xmq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5xmq

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Fluorine binding site 1 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:58.6
occ:1.00
 F33 A:8A6502 0.0 58.6 1.0
C23 A:8A6502 1.3 63.9 1.0
F31 A:8A6502 2.2 66.7 1.0
F32 A:8A6502 2.2 62.9 1.0
C18 A:8A6502 2.3 63.5 1.0
C19 A:8A6502 2.8 62.2 1.0
NZ A:LYS355 3.0 39.0 1.0
C17 A:8A6502 3.5 61.7 1.0
CD A:LYS355 3.7 32.7 1.0
CE A:LYS355 3.9 36.7 1.0
CG A:LYS355 4.1 29.9 1.0
C20 A:8A6502 4.1 60.6 1.0
CD A:PRO367 4.1 36.2 1.0
O A:ALA364 4.2 62.4 1.0
CG A:PRO367 4.2 35.5 1.0
CE1 B:TYR63 4.4 37.3 1.0
CD1 B:TYR63 4.4 35.7 1.0
C16 A:8A6502 4.7 59.3 1.0
C21 A:8A6502 4.9 59.7 1.0

Fluorine binding site 2 out of 9 in 5xmq

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Fluorine binding site 2 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:62.9
occ:1.00
 F32 A:8A6502 0.0 62.9 1.0
C23 A:8A6502 1.3 63.9 1.0
F31 A:8A6502 2.1 66.7 1.0
F33 A:8A6502 2.2 58.6 1.0
C18 A:8A6502 2.3 63.5 1.0
C17 A:8A6502 2.7 61.7 1.0
O A:LYS355 3.2 22.9 1.0
CG A:LYS355 3.4 29.9 1.0
CG A:PRO367 3.4 35.5 1.0
C19 A:8A6502 3.6 62.2 1.0
C A:LYS355 3.6 24.4 1.0
CD A:LYS355 3.7 32.7 1.0
CB A:PRO367 4.0 36.0 1.0
N A:ASN356 4.0 25.6 1.0
NZ A:LYS355 4.0 39.0 1.0
CD A:PRO367 4.1 36.2 1.0
CA A:ASN356 4.1 25.8 1.0
CB A:LYS355 4.1 26.2 1.0
C16 A:8A6502 4.1 59.3 1.0
N9 A:8A6502 4.4 47.8 1.0
CA A:LYS355 4.5 24.0 1.0
CE A:LYS355 4.5 36.7 1.0
N A:THR357 4.6 27.1 1.0
C A:ASN356 4.6 26.6 1.0
C20 A:8A6502 4.7 60.6 1.0
C8 A:8A6502 4.7 55.3 1.0
C15 A:8A6502 4.9 55.1 1.0
C14 A:8A6502 4.9 56.1 1.0
C21 A:8A6502 4.9 59.7 1.0

Fluorine binding site 3 out of 9 in 5xmq

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Fluorine binding site 3 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F502

b:66.7
occ:1.00
 F31 A:8A6502 0.0 66.7 1.0
C23 A:8A6502 1.3 63.9 1.0
F32 A:8A6502 2.1 62.9 1.0
F33 A:8A6502 2.2 58.6 1.0
C18 A:8A6502 2.3 63.5 1.0
C19 A:8A6502 2.9 62.2 1.0
C17 A:8A6502 3.3 61.7 1.0
O A:ALA364 3.5 62.4 1.0
CD A:PRO367 3.7 36.2 1.0
CG A:PRO367 3.8 35.5 1.0
CG2 A:THR357 3.9 31.8 1.0
CB A:PRO367 4.0 36.0 1.0
CB A:ALA364 4.1 73.0 1.0
C20 A:8A6502 4.2 60.6 1.0
C A:ALA364 4.3 70.5 1.0
CA A:ALA364 4.3 75.1 1.0
C16 A:8A6502 4.5 59.3 1.0
N A:PRO367 4.7 37.9 1.0
N9 A:8A6502 4.7 47.8 1.0
N A:THR357 4.8 27.1 1.0
C21 A:8A6502 4.8 59.7 1.0
CA A:PRO367 4.9 35.9 1.0
CD A:LYS355 5.0 32.7 1.0

Fluorine binding site 4 out of 9 in 5xmq

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Fluorine binding site 4 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:59.1
occ:1.00
 F33 B:8A6502 0.0 59.1 1.0
C23 B:8A6502 1.3 60.5 1.0
F31 B:8A6502 2.2 62.7 1.0
F32 B:8A6502 2.2 60.5 1.0
C18 B:8A6502 2.3 60.5 1.0
C19 B:8A6502 2.8 58.8 1.0
NZ B:LYS355 3.1 36.6 1.0
C17 B:8A6502 3.5 58.1 1.0
CD B:LYS355 3.8 31.6 1.0
CG B:PRO367 3.9 38.5 1.0
CG B:LYS355 3.9 28.9 1.0
CE B:LYS355 4.1 34.8 1.0
CD B:PRO367 4.1 39.6 1.0
C20 B:8A6502 4.1 57.4 1.0
O B:ALA364 4.3 68.7 1.0
C16 B:8A6502 4.7 56.9 1.0
CB B:PRO367 4.8 37.6 1.0
C21 B:8A6502 4.9 58.7 1.0
CD2 A:TYR63 4.9 35.5 1.0

Fluorine binding site 5 out of 9 in 5xmq

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Fluorine binding site 5 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:60.5
occ:1.00
 F32 B:8A6502 0.0 60.5 1.0
C23 B:8A6502 1.3 60.5 1.0
F31 B:8A6502 2.1 62.7 1.0
F33 B:8A6502 2.2 59.1 1.0
C18 B:8A6502 2.3 60.5 1.0
C17 B:8A6502 2.7 58.1 1.0
O B:LYS355 3.1 23.2 1.0
CG B:LYS355 3.3 28.9 1.0
C B:LYS355 3.4 23.1 1.0
CG B:PRO367 3.5 38.5 1.0
C19 B:8A6502 3.6 58.8 1.0
N B:ASN356 3.7 25.1 1.0
CA B:ASN356 3.8 26.1 1.0
CD B:LYS355 4.0 31.6 1.0
CB B:PRO367 4.1 37.6 1.0
CB B:LYS355 4.1 25.3 1.0
C16 B:8A6502 4.1 56.9 1.0
N9 B:8A6502 4.2 50.0 1.0
NZ B:LYS355 4.2 36.6 1.0
CA B:LYS355 4.4 23.6 1.0
N B:THR357 4.4 26.3 1.0
C B:ASN356 4.4 25.4 1.0
CD B:PRO367 4.5 39.6 1.0
C8 B:8A6502 4.6 55.0 1.0
CE B:LYS355 4.7 34.8 1.0
C20 B:8A6502 4.7 57.4 1.0
C14 B:8A6502 4.9 54.7 1.0
C15 B:8A6502 4.9 53.0 1.0
C21 B:8A6502 4.9 58.7 1.0

Fluorine binding site 6 out of 9 in 5xmq

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Fluorine binding site 6 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F502

b:62.7
occ:1.00
 F31 B:8A6502 0.0 62.7 1.0
C23 B:8A6502 1.3 60.5 1.0
F32 B:8A6502 2.1 60.5 1.0
F33 B:8A6502 2.2 59.1 1.0
C18 B:8A6502 2.2 60.5 1.0
C19 B:8A6502 3.0 58.8 1.0
C17 B:8A6502 3.2 58.1 1.0
CG2 B:THR357 3.6 29.4 1.0
CG B:PRO367 3.6 38.5 1.0
CB B:PRO367 3.8 37.6 1.0
O B:ALA364 3.9 68.7 1.0
CD B:PRO367 4.1 39.6 1.0
C20 B:8A6502 4.2 57.4 1.0
N B:THR357 4.3 26.3 1.0
C16 B:8A6502 4.4 56.9 1.0
N9 B:8A6502 4.4 50.0 1.0
CB B:THR357 4.7 29.0 1.0
C B:ALA364 4.7 74.0 1.0
C21 B:8A6502 4.8 58.7 1.0
OG1 B:THR357 4.9 33.0 1.0
C B:ASN356 4.9 25.4 1.0
C8 B:8A6502 4.9 55.0 1.0
CA B:ALA364 4.9 76.6 1.0
CA B:ASN356 4.9 26.1 1.0
CA B:THR357 5.0 28.7 1.0
CB B:ALA364 5.0 73.0 1.0
N B:PRO367 5.0 41.4 1.0
CA B:PRO367 5.0 37.3 1.0

Fluorine binding site 7 out of 9 in 5xmq

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Fluorine binding site 7 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:53.1
occ:1.00
 F33 C:8A6502 0.0 53.1 1.0
C23 C:8A6502 1.3 58.1 1.0
F32 C:8A6502 2.2 59.9 1.0
F31 C:8A6502 2.2 55.7 1.0
C18 C:8A6502 2.3 59.1 1.0
C19 C:8A6502 2.7 58.1 1.0
NZ C:LYS355 2.8 41.4 1.0
CE C:LYS355 3.6 38.3 1.0
C17 C:8A6502 3.6 59.0 1.0
CG C:PRO367 4.0 34.6 1.0
CD C:PRO367 4.0 35.5 1.0
O C:ALA364 4.1 71.1 1.0
C20 C:8A6502 4.1 57.6 1.0
CG C:LYS355 4.1 30.2 1.0
CD C:LYS355 4.3 34.1 1.0
C16 C:8A6502 4.8 58.8 1.0
CB C:PRO367 4.9 33.6 1.0
C21 C:8A6502 4.9 58.5 1.0
C22 C:8A6502 5.0 55.2 1.0

Fluorine binding site 8 out of 9 in 5xmq

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Fluorine binding site 8 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:59.9
occ:1.00
 F32 C:8A6502 0.0 59.9 1.0
C23 C:8A6502 1.3 58.1 1.0
F31 C:8A6502 2.1 55.7 1.0
F33 C:8A6502 2.2 53.1 1.0
C18 C:8A6502 2.3 59.1 1.0
C17 C:8A6502 2.7 59.0 1.0
CG C:LYS355 3.0 30.2 1.0
O C:LYS355 3.1 24.4 1.0
C19 C:8A6502 3.5 58.1 1.0
C C:LYS355 3.6 23.9 1.0
CE C:LYS355 3.7 38.3 1.0
NZ C:LYS355 3.8 41.4 1.0
CD C:LYS355 3.8 34.1 1.0
CG C:PRO367 3.8 34.6 1.0
CB C:LYS355 4.1 26.6 1.0
C16 C:8A6502 4.1 58.8 1.0
N C:ASN356 4.1 23.9 1.0
CA C:ASN356 4.3 24.8 1.0
CA C:LYS355 4.4 23.7 1.0
CB C:PRO367 4.6 33.6 1.0
C15 C:8A6502 4.6 56.2 1.0
CD C:PRO367 4.6 35.5 1.0
C20 C:8A6502 4.6 57.6 1.0
N9 C:8A6502 4.6 55.4 1.0
C21 C:8A6502 4.9 58.5 1.0
C14 C:8A6502 4.9 56.8 1.0
C8 C:8A6502 4.9 60.2 1.0
N C:LYS355 4.9 22.7 1.0

Fluorine binding site 9 out of 9 in 5xmq

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Fluorine binding site 9 out of 9 in the Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Plasmodium Vivax Shmt(C346A) Bound with Plp-Glycine and MF011 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F502

b:55.7
occ:1.00
 F31 C:8A6502 0.0 55.7 1.0
C23 C:8A6502 1.3 58.1 1.0
F32 C:8A6502 2.1 59.9 1.0
F33 C:8A6502 2.2 53.1 1.0
C18 C:8A6502 2.3 59.1 1.0
C17 C:8A6502 3.0 59.0 1.0
C19 C:8A6502 3.2 58.1 1.0
CG C:PRO367 3.5 34.6 1.0
CG2 C:THR357 3.6 27.7 1.0
CB C:PRO367 3.8 33.6 1.0
CD C:PRO367 4.0 35.5 1.0
N C:THR357 4.1 25.5 1.0
O C:ALA364 4.1 71.1 1.0
N9 C:8A6502 4.1 55.4 1.0
C16 C:8A6502 4.3 58.8 1.0
C20 C:8A6502 4.4 57.6 1.0
O C:LYS355 4.5 24.4 1.0
CA C:ASN356 4.5 24.8 1.0
C C:ASN356 4.6 24.8 1.0
CG C:LYS355 4.6 30.2 1.0
C8 C:8A6502 4.7 60.2 1.0
CB C:THR357 4.7 27.1 1.0
NZ C:LYS355 4.7 41.4 1.0
N C:ASN356 4.8 23.9 1.0
C C:LYS355 4.8 23.9 1.0
C21 C:8A6502 4.8 58.5 1.0
CA C:THR357 4.8 27.3 1.0
N C:PRO367 4.9 37.4 1.0
OG1 C:THR357 4.9 30.3 1.0
CA C:PRO367 4.9 34.0 1.0

Reference:

G.Schwertz, M.S.Frei, M.C.Witschel, M.Rottmann, U.Leartsakulpanich, P.Chitnumsub, A.Jaruwat, W.Ittarat, A.Schafer, R.A.Aponte, N.Trapp, K.Mark, P.Chaiyen, F.Diederich. Conformational Aspects in the Design of Inhibitors For Serine Hydroxymethyltransferase (Shmt): Biphenyl, Aryl Sulfonamide, and Aryl Sulfone Motifs Chemistry V. 23 14345 2017.
ISSN: ISSN 1521-3765
PubMed: 28967982
DOI: 10.1002/CHEM.201703244
Page generated: Thu Aug 1 16:56:22 2024

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