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Chlorine in PDB 5xmv: Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362

Enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362

All present enzymatic activity of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362:
2.1.2.1;

Protein crystallography data

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362, PDB code: 5xmv 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 / 2.16
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 101.674, 58.843, 234.899, 90.00, 90.14, 90.00
R / Rfree (%) 24.2 / 30.6

Other elements in 5xmv:

The structure of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 also contains other interesting chemical elements:

Fluorine (F) 9 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 (pdb code 5xmv). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362, PDB code: 5xmv:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5;

Chlorine binding site 1 out of 5 in 5xmv

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Chlorine binding site 1 out of 5 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl502

b:41.4
occ:1.00
 CL3 A:8AU502 0.0 41.4 1.0
C25 A:8AU502 1.8 30.6 1.0
C26 A:8AU502 2.7 30.1 1.0
C22 A:8AU502 2.8 29.0 1.0
C13 A:8AU502 3.2 29.4 1.0
C20 A:8AU502 3.2 29.0 1.0
C21 A:8AU502 3.2 28.4 1.0
CZ B:TYR63 3.5 25.5 1.0
CE1 B:TYR63 3.6 26.1 1.0
CZ B:PHE266 3.6 21.3 1.0
C10 A:8AU502 3.7 27.5 1.0
CE2 B:TYR63 3.7 25.3 1.0
CD1 B:TYR63 3.8 26.7 1.0
CD2 B:TYR63 3.9 28.0 1.0
OH B:TYR63 4.0 24.1 1.0
CG B:TYR63 4.0 28.1 1.0
C27 A:8AU502 4.0 29.1 1.0
C29 A:8AU502 4.1 29.8 1.0
N11 A:8AU502 4.1 27.6 1.0
CD1 A:LEU130 4.2 20.6 1.0
CD2 A:LEU130 4.3 21.5 1.0
C19 A:8AU502 4.3 29.3 1.0
CE2 B:PHE266 4.3 20.9 1.0
C16 A:8AU502 4.4 28.7 1.0
C5 A:8AU502 4.5 27.7 1.0
CE1 B:PHE266 4.5 20.3 1.0
C28 A:8AU502 4.6 28.4 1.0
CG A:LEU130 4.7 20.6 1.0
OE2 B:GLU56 4.8 25.6 1.0

Chlorine binding site 2 out of 5 in 5xmv

Go back to Chlorine Binding Sites List in 5xmv
Chlorine binding site 2 out of 5 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl503

b:31.8
occ:1.00
 ND2 A:ASN276 3.2 14.4 1.0
ND2 B:ASN276 3.2 14.9 1.0
NZ B:LYS277 3.3 14.9 1.0
NZ A:LYS277 3.4 14.8 1.0
CE B:LYS277 4.1 14.6 1.0
CG A:ASN276 4.2 14.5 1.0
CG B:LYS277 4.2 15.4 1.0
CG B:ASN276 4.3 15.4 1.0
CE A:LYS277 4.3 14.6 1.0
CG A:LYS277 4.3 14.8 1.0
CD2 B:LEU46 4.4 22.1 1.0
OD1 A:ASN276 4.4 14.8 1.0
CD2 A:LEU46 4.4 22.3 1.0
OD1 B:ASN276 4.5 15.7 1.0
CD B:LYS277 4.8 14.8 1.0
CD A:LYS277 4.9 14.9 1.0

Chlorine binding site 3 out of 5 in 5xmv

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Chlorine binding site 3 out of 5 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl502

b:41.0
occ:1.00
 CL3 B:8AU502 0.0 41.0 1.0
C25 B:8AU502 1.8 31.6 1.0
C26 B:8AU502 2.7 30.2 1.0
C22 B:8AU502 2.8 30.4 1.0
C20 B:8AU502 3.2 29.8 1.0
C21 B:8AU502 3.3 29.5 1.0
CZ A:TYR63 3.3 24.1 1.0
C13 B:8AU502 3.4 31.8 1.0
CE2 A:TYR63 3.5 24.0 1.0
CE1 A:TYR63 3.5 24.5 1.0
OH A:TYR63 3.7 23.6 1.0
CZ A:PHE266 3.8 19.5 1.0
C10 B:8AU502 3.9 31.1 1.0
CD2 A:TYR63 3.9 25.2 1.0
CD1 A:TYR63 3.9 24.4 1.0
C27 B:8AU502 4.0 29.6 1.0
CG A:TYR63 4.1 25.5 1.0
C29 B:8AU502 4.1 31.2 1.0
CD2 B:LEU130 4.3 19.2 1.0
CD1 B:LEU130 4.3 18.4 1.0
C19 B:8AU502 4.3 29.6 1.0
N11 B:8AU502 4.3 30.6 1.0
C16 B:8AU502 4.4 30.5 1.0
CE2 A:PHE266 4.4 18.7 1.0
C28 B:8AU502 4.6 30.5 1.0
C5 B:8AU502 4.6 30.8 1.0
CE1 A:PHE266 4.7 18.7 1.0
CG B:LEU130 4.7 18.2 1.0
OE2 A:GLU56 4.9 23.6 1.0

Chlorine binding site 4 out of 5 in 5xmv

Go back to Chlorine Binding Sites List in 5xmv
Chlorine binding site 4 out of 5 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl502

b:37.4
occ:1.00
 CL3 C:8AU502 0.0 37.4 1.0
C25 C:8AU502 1.8 30.5 1.0
C26 C:8AU502 2.7 29.2 1.0
C22 C:8AU502 2.8 29.9 1.0
C20 C:8AU502 3.2 29.5 1.0
C21 C:8AU502 3.2 28.8 1.0
C13 C:8AU502 3.3 28.2 1.0
C10 C:8AU502 3.8 27.8 1.0
C27 C:8AU502 4.0 28.9 1.0
C29 C:8AU502 4.1 30.0 1.0
CD1 C:LEU130 4.2 20.3 1.0
C19 C:8AU502 4.3 30.2 1.0
C16 C:8AU502 4.3 28.9 1.0
N11 C:8AU502 4.4 28.2 1.0
CD2 C:LEU130 4.4 20.8 1.0
C5 C:8AU502 4.5 27.7 1.0
C28 C:8AU502 4.6 28.6 1.0
CG C:LEU130 4.7 20.4 1.0

Chlorine binding site 5 out of 5 in 5xmv

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Chlorine binding site 5 out of 5 in the Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Plasmodium Vivax Shmt Bound with Plp-Glycine and GS362 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl503

b:18.7
occ:0.50
 NZ C:LYS277 3.1 15.3 1.0
ND2 C:ASN276 3.6 15.2 1.0
CE C:LYS277 3.9 15.4 1.0
CG C:LYS277 4.1 16.2 1.0
CD2 C:LEU46 4.1 23.2 1.0
CG C:ASN276 4.5 15.2 1.0
CD C:LYS277 4.6 15.7 1.0
OD1 C:ASN276 4.7 14.6 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: Sat Jul 12 10:42:40 2025

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