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Chlorine in PDB 4dph: Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph

Enzymatic activity of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph

All present enzymatic activity of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph:
1.5.1.3; 2.1.1.45;

Protein crystallography data

The structure of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph, PDB code: 4dph was solved by Y.Yuthavong, T.Vilaivan, S.Kamchonwongpaisan, S.A.Charman, D.N.Mclennan, K.L.White, L.Vivas, E.Bongard, P.Chitnumsub, B.Tarnchompoo, C.Thongphanchang, S.Taweechai, J.Vanichtanakul, U.Arwon, P.Fantauzzi, J.Yuvaniyama, W.N.Charman, D.Matthews, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 54.66 / 2.38
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 57.951, 156.447, 164.653, 90.00, 90.00, 90.00
R / Rfree (%) 21.9 / 28.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph (pdb code 4dph). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph, PDB code: 4dph:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 4dph

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Chlorine binding site 1 out of 6 in the Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:57.0
occ:1.00
 CL3 A:P65701 0.0 57.0 1.0
C16 A:P65701 1.5 52.2 1.0
C15 A:P65701 2.5 53.7 1.0
C17 A:P65701 2.6 48.6 1.0
CL2 A:P65701 2.7 58.4 1.0
CD1 A:LEU46 3.6 40.7 1.0
CG A:LEU46 3.7 44.7 1.0
O A:SER111 3.7 41.2 1.0
C14 A:P65701 3.8 51.8 1.0
C12 A:P65701 3.9 45.9 1.0
C13 A:P65701 4.4 49.1 1.0
C A:SER111 4.4 40.6 1.0
CD A:PRO113 4.4 42.2 1.0
CB A:LEU46 4.5 45.4 1.0
N A:LEU46 4.5 47.3 1.0
O A:HOH1026 4.6 38.3 1.0
O A:HOH968 4.6 45.9 1.0
OG A:SER111 4.6 42.9 1.0
CB A:SER111 4.7 41.1 1.0
CA A:ILE112 4.8 39.9 1.0
CD2 A:LEU46 4.9 42.3 1.0
N A:ILE112 4.9 40.2 1.0
O11 A:P65701 5.0 40.4 1.0

Chlorine binding site 2 out of 6 in 4dph

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Chlorine binding site 2 out of 6 in the Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:58.4
occ:1.00
 CL2 A:P65701 0.0 58.4 1.0
C15 A:P65701 1.5 53.7 1.0
C16 A:P65701 2.4 52.2 1.0
C14 A:P65701 2.6 51.8 1.0
CL3 A:P65701 2.7 57.0 1.0
CD A:PRO113 3.4 42.2 1.0
CG A:PRO113 3.6 41.9 1.0
C17 A:P65701 3.7 48.6 1.0
C13 A:P65701 3.9 49.1 1.0
C12 A:P65701 4.3 45.9 1.0
O A:HOH1026 4.7 38.3 1.0
CD1 A:LEU46 4.8 40.7 1.0
CE2 A:PHE116 4.8 51.3 1.0
N A:PRO113 4.8 41.7 1.0
O A:SER111 4.9 41.2 1.0
CB A:PRO113 5.0 42.5 1.0

Chlorine binding site 3 out of 6 in 4dph

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Chlorine binding site 3 out of 6 in the Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl701

b:52.6
occ:1.00
 CL1 A:P65701 0.0 52.6 1.0
C13 A:P65701 1.5 49.1 1.0
C12 A:P65701 2.5 45.9 1.0
C14 A:P65701 2.6 51.8 1.0
O11 A:P65701 2.8 40.4 1.0
CE A:MET55 3.4 45.7 1.0
C17 A:P65701 3.8 48.6 1.0
C15 A:P65701 3.9 53.7 1.0
SD A:MET55 4.1 48.9 1.0
CG2 A:ILE112 4.1 36.7 1.0
C10 A:P65701 4.2 34.2 1.0
CD2 A:PHE116 4.3 48.9 1.0
C16 A:P65701 4.4 52.2 1.0
CE2 A:PHE58 4.4 35.5 1.0
CD2 A:LEU119 4.5 36.2 1.0
CG1 A:ILE112 4.7 36.9 1.0
CG A:PHE116 4.7 47.0 1.0
CB A:PHE116 4.7 45.1 1.0
C9 A:P65701 4.9 31.4 1.0
CE2 A:PHE116 4.9 51.3 1.0
CD2 A:PHE58 4.9 34.8 1.0
O A:HOH901 5.0 35.2 1.0
CD1 A:ILE112 5.0 35.0 1.0

Chlorine binding site 4 out of 6 in 4dph

Go back to Chlorine Binding Sites List in 4dph
Chlorine binding site 4 out of 6 in the Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:78.9
occ:1.00
 CL3 B:P65701 0.0 78.9 1.0
C16 B:P65701 1.5 76.3 1.0
C17 B:P65701 2.5 74.5 1.0
C15 B:P65701 2.5 76.6 1.0
CL2 B:P65701 3.0 79.8 1.0
CG1 B:VAL45 3.6 73.1 1.0
CG B:LEU46 3.7 69.9 1.0
N B:LEU46 3.8 71.4 1.0
C12 B:P65701 3.8 73.4 1.0
C14 B:P65701 3.8 75.8 1.0
O B:SER111 3.8 96.8 1.0
CD1 B:LEU46 4.2 68.2 1.0
CB B:LEU46 4.2 70.5 1.0
C13 B:P65701 4.3 74.7 1.0
CA B:VAL45 4.3 72.9 1.0
C B:VAL45 4.4 72.3 1.0
O2D B:NDP702 4.4 86.5 1.0
OG B:SER111 4.5 97.1 1.0
C B:SER111 4.5 96.8 1.0
CB B:SER111 4.5 97.0 1.0
CB B:VAL45 4.6 73.0 1.0
CA B:LEU46 4.6 70.5 1.0
CD2 B:LEU46 4.7 69.5 1.0
O11 B:P65701 5.0 70.1 1.0

Chlorine binding site 5 out of 6 in 4dph

Go back to Chlorine Binding Sites List in 4dph
Chlorine binding site 5 out of 6 in the Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:79.8
occ:1.00
 CL2 B:P65701 0.0 79.8 1.0
C15 B:P65701 1.5 76.6 1.0
C14 B:P65701 2.4 75.8 1.0
C16 B:P65701 2.5 76.3 1.0
CL3 B:P65701 3.0 78.9 1.0
CD B:PRO113 3.6 96.8 1.0
C13 B:P65701 3.7 74.7 1.0
C17 B:P65701 3.8 74.5 1.0
CG B:PRO113 3.8 97.2 1.0
C12 B:P65701 4.3 73.4 1.0
O B:SER111 4.5 96.8 1.0
CE B:MET55 4.7 63.6 1.0
CL1 B:P65701 4.9 77.4 1.0
CD1 B:LEU46 4.9 68.2 1.0

Chlorine binding site 6 out of 6 in 4dph

Go back to Chlorine Binding Sites List in 4dph
Chlorine binding site 6 out of 6 in the Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Quadruple Mutant (N51I+C59R+S108N+I164L) Plasmodium Falciparum Dihydrofolate Reductase-Thymidylate Synthase (Pfdhfr-Ts) Complexed with P65 and Nadph within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl701

b:77.4
occ:1.00
 CL1 B:P65701 0.0 77.4 1.0
C13 B:P65701 1.5 74.7 1.0
C14 B:P65701 2.5 75.8 1.0
C12 B:P65701 2.5 73.4 1.0
O11 B:P65701 2.8 70.1 1.0
C15 B:P65701 3.7 76.6 1.0
C17 B:P65701 3.8 74.5 1.0
CG2 B:ILE112 4.1 96.1 1.0
CE B:MET55 4.2 63.6 1.0
C10 B:P65701 4.2 68.2 1.0
C16 B:P65701 4.3 76.3 1.0
SD B:MET55 4.4 64.2 1.0
CG1 B:ILE112 4.6 95.9 1.0
C8 B:P65701 4.8 66.2 1.0
C9 B:P65701 4.8 67.2 1.0
CE2 B:PHE58 4.8 60.4 1.0
CB B:ILE112 4.9 96.3 1.0
CD2 B:PHE116 4.9 96.0 1.0
CL2 B:P65701 4.9 79.8 1.0
CD B:PRO113 5.0 96.8 1.0

Reference:

Y.Yuthavong, B.Tarnchompoo, T.Vilaivan, P.Chitnumsub, S.Kamchonwongpaisan, S.A.Charman, D.N.Mclennan, K.L.White, L.Vivas, E.Bongard, C.Thongphanchang, S.Taweechai, J.Vanichtanankul, R.Rattanajak, U.Arwon, P.Fantauzzi, J.Yuvaniyama, W.N.Charman, D.Matthews. Malarial Dihydrofolate Reductase As A Paradigm For Drug Development Against A Resistance-Compromised Target Proc.Natl.Acad.Sci.Usa V. 109 16823 2012.
ISSN: ISSN 0027-8424
PubMed: 23035243
DOI: 10.1073/PNAS.1204556109
Page generated: Sun Jul 21 12:16:04 2024

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