Chlorine in PDB 7sxq: Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag

Enzymatic activity of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag

All present enzymatic activity of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag:
2.7.7.7;

Protein crystallography data

The structure of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag, PDB code: 7sxq was solved by N.Nieto, P.Chheda, R.Kerns, S.Nelson, R.Honzatko, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.97 / 2.50
Space group P 65
Cell size a, b, c (Å), α, β, γ (°) 143.999, 143.999, 165.006, 90, 90, 120
R / Rfree (%) 20.1 / 22.5

Other elements in 7sxq:

The structure of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag (pdb code 7sxq). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 6 binding sites of Chlorine where determined in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag, PDB code: 7sxq:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6;

Chlorine binding site 1 out of 6 in 7sxq

Go back to Chlorine Binding Sites List in 7sxq
Chlorine binding site 1 out of 6 in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl703

b:52.2
occ:1.00
 HZ3 A:LYS417 2.3 68.5 1.0
H A:GLU615 2.3 69.3 1.0
H A:GLN413 2.6 78.2 1.0
HD2 A:LYS417 2.9 63.8 1.0
H A:LYS412 2.9 78.3 0.5
H A:LYS412 2.9 80.4 0.5
HB2 A:CYS614 3.1 68.8 1.0
HB3 A:PHE411 3.1 70.1 1.0
N A:GLU615 3.1 57.8 1.0
NZ A:LYS417 3.1 57.1 1.0
HA A:CYS614 3.1 67.1 1.0
HA A:ILE414 3.4 62.1 1.0
O A:GLU615 3.5 60.4 1.0
N A:GLN413 3.5 65.2 1.0
HD1 A:PHE411 3.5 68.0 1.0
HZ1 A:LYS417 3.5 68.5 1.0
N A:LYS412 3.6 67.0 0.5
N A:LYS412 3.6 65.2 0.5
HB A:ILE414 3.6 63.7 1.0
HZ2 A:LYS417 3.6 68.5 1.0
N A:ILE414 3.6 56.4 1.0
HB3 A:GLU615 3.6 78.0 1.0
HD13 A:ILE414 3.7 61.8 1.0
HB2 A:LYS412 3.7 84.9 0.5
CD A:LYS417 3.7 53.2 1.0
HB3 A:LYS412 3.7 84.9 0.5
HE3 A:LYS417 3.7 63.5 1.0
CE A:LYS417 3.7 52.9 1.0
CA A:CYS614 3.7 55.9 1.0
C A:GLN413 3.8 58.5 1.0
H A:ILE414 3.8 67.7 1.0
CB A:CYS614 3.8 57.3 1.0
CA A:ILE414 3.9 51.8 1.0
C A:CYS614 3.9 56.4 1.0
CB A:PHE411 4.0 58.4 1.0
HA A:PHE411 4.0 73.5 1.0
CA A:GLU615 4.0 60.3 1.0
HD12 A:ILE414 4.0 61.8 1.0
HD3 A:LYS417 4.1 63.8 1.0
C A:GLU615 4.1 61.0 1.0
O A:GLN413 4.2 56.1 1.0
CD1 A:PHE411 4.2 56.7 1.0
CA A:GLN413 4.2 62.7 1.0
CB A:ILE414 4.2 53.1 1.0
CD1 A:ILE414 4.3 51.5 1.0
CB A:GLU615 4.3 65.0 1.0
CA A:LYS412 4.3 75.9 0.5
CA A:LYS412 4.3 76.2 0.5
HB3 A:CYS614 4.3 68.8 1.0
CA A:PHE411 4.3 61.2 1.0
C A:LYS412 4.4 68.1 0.5
C A:PHE411 4.4 64.0 1.0
C A:LYS412 4.4 68.1 0.5
CB A:LYS412 4.4 70.8 0.5
CB A:LYS412 4.4 70.7 0.5
HB2 A:GLN413 4.5 79.2 1.0
CG A:PHE411 4.5 54.0 1.0
HB2 A:GLU615 4.6 78.0 1.0
HE2 A:LYS417 4.7 63.5 1.0
HB2 A:PHE411 4.7 70.1 1.0
HG3 A:LYS417 4.8 61.7 1.0
HB2 A:LYS412 4.8 84.9 0.5
CG A:LYS417 4.9 51.4 1.0
HG2 A:LYS412 4.9 83.8 0.5
CG1 A:ILE414 4.9 51.9 1.0
HA A:GLU615 4.9 72.3 1.0
HB2 A:LYS417 4.9 58.6 1.0
CB A:GLN413 5.0 66.0 1.0
HA A:GLN413 5.0 75.3 1.0

Chlorine binding site 2 out of 6 in 7sxq

Go back to Chlorine Binding Sites List in 7sxq
Chlorine binding site 2 out of 6 in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl704

b:59.5
occ:1.00
 HD22 A:ASN239 2.3 57.8 1.0
HD1 A:HIS236 2.4 66.2 1.0
HZ3 A:LYS227 2.6 74.1 1.0
ND2 A:ASN239 3.1 48.2 1.0
O A:HOH896 3.1 53.9 1.0
HE2 A:PHE158 3.1 61.0 1.0
ND1 A:HIS236 3.2 55.2 1.0
HD2 A:LYS227 3.3 72.4 1.0
HG21 A:ILE230 3.4 58.6 1.0
NZ A:LYS227 3.4 61.8 1.0
HD21 A:ASN239 3.4 57.8 1.0
HA A:HIS236 3.5 59.2 1.0
HB3 A:ASN239 3.5 59.9 1.0
O A:HOH856 3.6 56.6 1.0
HZ1 A:LYS227 3.6 74.1 1.0
HG22 A:ILE230 3.9 58.6 1.0
HE1 A:HIS236 3.9 67.5 1.0
HZ2 A:LYS227 4.0 74.1 1.0
CE2 A:PHE158 4.0 50.8 1.0
CE1 A:HIS236 4.0 56.3 1.0
CD A:LYS227 4.0 60.3 1.0
CG2 A:ILE230 4.1 48.8 1.0
HD2 A:PHE158 4.1 62.9 1.0
CG A:ASN239 4.1 48.7 1.0
HD3 A:LYS227 4.2 72.4 1.0
CE A:LYS227 4.2 62.6 1.0
CB A:ASN239 4.3 49.9 1.0
CG A:HIS236 4.3 52.2 1.0
HE3 A:LYS227 4.3 75.1 1.0
CA A:HIS236 4.3 49.3 1.0
HB2 A:HIS236 4.3 60.1 1.0
O A:HIS236 4.4 48.7 1.0
CD2 A:PHE158 4.5 52.5 1.0
HB2 A:ASP240 4.5 58.6 1.0
HB A:ILE230 4.5 62.4 1.0
CB A:HIS236 4.6 50.1 1.0
HG13 A:ILE230 4.6 60.6 1.0
HD22 A:ASN243 4.6 58.2 1.0
H A:ASP240 4.8 57.5 1.0
HB2 A:ASN239 4.8 59.9 1.0
HA A:LYS227 4.8 63.8 1.0
HG23 A:ILE230 4.8 58.6 1.0
CB A:ILE230 4.8 52.0 1.0
N A:ASP240 4.9 47.9 1.0
HA A:ASP240 4.9 59.8 1.0
C A:HIS236 4.9 50.2 1.0
OD1 A:ASP240 5.0 58.5 1.0
O A:HOH825 5.0 61.6 1.0

Chlorine binding site 3 out of 6 in 7sxq

Go back to Chlorine Binding Sites List in 7sxq
Chlorine binding site 3 out of 6 in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl705

b:63.2
occ:1.00
 HZ2 A:LYS531 2.2 68.3 1.0
HD22 A:ASN234 2.6 66.0 1.0
HD21 A:ASN529 2.6 67.0 1.0
HD21 B:ASN433 3.0 63.6 1.0
NZ A:LYS531 3.1 56.9 1.0
HE2 A:LYS531 3.2 63.0 1.0
HB2 A:ASN234 3.2 64.3 1.0
HE3 A:LYS531 3.4 63.0 1.0
CE A:LYS531 3.4 52.5 1.0
HZ1 A:LYS531 3.4 68.3 1.0
ND2 A:ASN234 3.5 55.0 1.0
ND2 A:ASN529 3.5 55.8 1.0
ND2 B:ASN433 3.6 53.0 1.0
HZ3 A:LYS531 3.7 68.3 1.0
O B:HOH977 3.8 62.9 1.0
HD22 B:ASN433 3.9 63.6 1.0
HD21 A:ASN234 4.0 66.0 1.0
OD1 A:ASN529 4.0 54.7 1.0
CB A:ASN234 4.0 53.6 1.0
HD22 A:ASN529 4.1 67.0 1.0
O A:GLU233 4.2 52.2 1.0
CG A:ASN529 4.2 53.9 1.0
CG A:ASN234 4.3 54.2 1.0
HB3 A:ASN234 4.3 64.3 1.0
O A:HOH915 4.4 54.9 1.0
CG B:ASN433 4.6 52.9 1.0
O A:HOH952 4.7 59.1 1.0
OD1 B:ASN433 4.8 57.3 1.0
C A:GLU233 4.9 53.4 1.0
CD A:LYS531 4.9 48.8 1.0

Chlorine binding site 4 out of 6 in 7sxq

Go back to Chlorine Binding Sites List in 7sxq
Chlorine binding site 4 out of 6 in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl704

b:49.4
occ:1.00
 HZ3 B:LYS417 2.3 66.8 1.0
H B:GLU615 2.3 63.1 1.0
H B:GLN413 2.6 63.5 1.0
HD2 B:LYS417 2.8 59.4 1.0
H B:LYS412 2.8 63.8 0.5
H B:LYS412 2.9 65.3 0.5
NZ B:LYS417 3.1 55.6 1.0
N B:GLU615 3.2 52.6 1.0
HA B:CYS614 3.2 63.7 1.0
HB3 B:PHE411 3.3 63.5 1.0
HB2 B:CYS614 3.3 65.7 1.0
N B:GLN413 3.4 52.9 1.0
HA B:ILE414 3.4 58.2 1.0
HB3 B:LYS412 3.4 67.4 0.5
HZ1 B:LYS417 3.4 66.8 1.0
O B:GLU615 3.4 53.2 1.0
HB2 B:LYS412 3.4 65.8 0.5
HD1 B:PHE411 3.5 64.4 1.0
HB B:ILE414 3.5 60.0 1.0
N B:LYS412 3.5 53.1 0.5
N B:LYS412 3.5 54.5 0.5
HD13 B:ILE414 3.5 60.6 1.0
CD B:LYS417 3.6 49.5 1.0
N B:ILE414 3.6 48.2 1.0
HZ2 B:LYS417 3.7 66.8 1.0
C B:GLN413 3.7 50.7 1.0
H B:ILE414 3.7 57.8 1.0
CE B:LYS417 3.7 49.7 1.0
HB3 B:GLU615 3.7 69.1 1.0
CA B:CYS614 3.8 53.1 1.0
HE3 B:LYS417 3.8 59.7 1.0
HD3 B:LYS417 3.9 59.4 1.0
CA B:ILE414 3.9 48.5 1.0
C B:CYS614 4.0 53.0 1.0
CB B:CYS614 4.0 54.8 1.0
CA B:GLU615 4.1 57.1 1.0
HD12 B:ILE414 4.1 60.6 1.0
CB B:PHE411 4.1 52.9 1.0
HA B:PHE411 4.1 63.5 1.0
CB B:ILE414 4.1 50.0 1.0
CA B:GLN413 4.1 55.8 1.0
O B:GLN413 4.1 50.5 1.0
CA B:LYS412 4.2 55.2 0.5
C B:GLU615 4.2 54.7 1.0
CA B:LYS412 4.2 53.7 0.5
C B:LYS412 4.2 56.2 0.5
CB B:LYS412 4.2 56.2 0.5
C B:LYS412 4.2 53.9 0.5
CD1 B:PHE411 4.2 53.6 1.0
CD1 B:ILE414 4.2 50.5 1.0
CB B:LYS412 4.2 54.8 0.5
CB B:GLU615 4.3 57.6 1.0
C B:PHE411 4.4 54.3 1.0
CA B:PHE411 4.4 52.9 1.0
HB2 B:GLU615 4.5 69.1 1.0
HB2 B:GLN413 4.5 67.8 1.0
HB3 B:CYS614 4.6 65.7 1.0
CG B:PHE411 4.6 52.4 1.0
HB2 B:LYS412 4.7 67.4 0.5
HE2 B:LYS417 4.7 59.7 1.0
CG1 B:ILE414 4.8 50.2 1.0
CG B:LYS417 4.8 47.8 1.0
HB2 B:PHE411 4.8 63.5 1.0
HG2 B:LYS412 4.8 67.5 0.5
HG3 B:LYS417 4.8 57.3 1.0
HB3 B:LYS412 4.9 65.8 0.5
HB2 B:LYS417 4.9 53.2 1.0
HA B:GLN413 4.9 66.9 1.0
CB B:GLN413 4.9 56.5 1.0
HA B:GLU615 4.9 68.5 1.0

Chlorine binding site 5 out of 6 in 7sxq

Go back to Chlorine Binding Sites List in 7sxq
Chlorine binding site 5 out of 6 in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl705

b:57.4
occ:1.00
 HZ1 B:LYS227 2.2 75.5 1.0
HD1 B:HIS236 2.4 63.9 1.0
HD22 B:ASN239 2.5 56.1 1.0
HD2 B:LYS227 3.0 72.7 1.0
O B:HOH828 3.0 55.9 1.0
HE2 B:PHE158 3.1 61.4 1.0
NZ B:LYS227 3.1 62.9 1.0
ND1 B:HIS236 3.2 53.3 1.0
HG21 B:ILE230 3.3 57.5 1.0
ND2 B:ASN239 3.3 46.7 1.0
HA B:HIS236 3.3 56.9 1.0
HB3 B:ASN239 3.5 53.7 1.0
O B:HOH940 3.5 51.6 1.0
HZ3 B:LYS227 3.6 75.5 1.0
HE3 B:LYS227 3.6 73.6 1.0
HZ2 B:LYS227 3.6 75.5 1.0
HG22 B:ILE230 3.7 57.5 1.0
CE B:LYS227 3.7 61.3 1.0
HD21 B:ASN239 3.7 56.1 1.0
CD B:LYS227 3.8 60.6 1.0
CG2 B:ILE230 3.9 47.9 1.0
CE2 B:PHE158 4.0 51.2 1.0
HB2 B:HIS236 4.0 57.9 1.0
CE1 B:HIS236 4.1 54.6 1.0
HE1 B:HIS236 4.1 65.5 1.0
HD3 B:LYS227 4.1 72.7 1.0
CA B:HIS236 4.2 47.4 1.0
CG B:HIS236 4.2 51.9 1.0
HB B:ILE230 4.2 58.9 1.0
CG B:ASN239 4.3 46.0 1.0
CB B:ASN239 4.3 44.7 1.0
HD2 B:PHE158 4.3 60.7 1.0
O B:HIS236 4.3 46.9 1.0
CB B:HIS236 4.3 48.2 1.0
HG13 B:ILE230 4.5 58.9 1.0
HA B:LYS227 4.5 64.8 1.0
CB B:ILE230 4.6 49.0 1.0
CD2 B:PHE158 4.6 50.6 1.0
HE2 B:LYS227 4.6 73.6 1.0
HB2 B:ASP240 4.7 58.1 1.0
HG23 B:ILE230 4.7 57.5 1.0
O B:HOH994 4.7 57.2 1.0
HB2 B:ASN239 4.7 53.7 1.0
C B:HIS236 4.7 47.8 1.0
H B:ASP240 4.9 54.5 1.0
HZ B:PHE158 4.9 60.0 1.0
HG3 B:LYS227 4.9 65.7 1.0
CZ B:PHE158 5.0 50.0 1.0
HD22 B:ASN243 5.0 56.8 1.0
CG B:LYS227 5.0 54.7 1.0

Chlorine binding site 6 out of 6 in 7sxq

Go back to Chlorine Binding Sites List in 7sxq
Chlorine binding site 6 out of 6 in the Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Plasmodium Falciparum Apicoplast Dna Polymerase (Exo-Minus) Without Affinity Tag within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl706

b:64.6
occ:1.00
 HZ2 B:LYS531 2.2 66.5 1.0
HD22 B:ASN234 2.5 65.4 1.0
HD21 B:ASN529 2.6 66.3 1.0
HD21 A:ASN433 3.0 64.5 1.0
NZ B:LYS531 3.0 55.4 1.0
HE2 B:LYS531 3.0 61.9 1.0
HB2 B:ASN234 3.1 61.8 1.0
HZ1 B:LYS531 3.2 66.5 1.0
ND2 B:ASN234 3.3 54.5 1.0
ND2 B:ASN529 3.4 55.2 1.0
CE B:LYS531 3.4 51.6 1.0
HE3 B:LYS531 3.5 61.9 1.0
HZ3 B:LYS531 3.7 66.5 1.0
ND2 A:ASN433 3.7 53.7 1.0
O A:HOH1000 3.7 61.3 1.0
HD21 B:ASN234 3.8 65.4 1.0
OD1 B:ASN529 3.8 53.2 1.0
CB B:ASN234 3.9 51.5 1.0
HD22 B:ASN529 4.0 66.3 1.0
O B:HOH802 4.0 55.8 1.0
HD22 A:ASN433 4.0 64.5 1.0
CG B:ASN529 4.0 52.6 1.0
CG B:ASN234 4.1 55.8 1.0
O B:GLU233 4.1 49.1 1.0
HB3 B:ASN234 4.2 61.8 1.0
CG A:ASN433 4.7 53.1 1.0
O B:HOH838 4.7 58.8 1.0
OD1 A:ASN433 4.8 56.1 1.0
CD B:LYS531 4.9 47.3 1.0
C B:GLU233 4.9 49.9 1.0
O B:HOH979 4.9 54.7 1.0

Reference:

P.R.Chheda, N.Nieto, S.Kaur, J.M.Beck, J.R.Beck, R.Honzatko, R.J.Kerns, S.W.Nelson. Promising Antimalarials Targeting Apicoplast Dna Polymerase From Plasmodium Falciparum. Eur.J.Med.Chem. V. 243 14751 2022.
ISSN: ISSN 0223-5234
PubMed: 36191407
DOI: 10.1016/J.EJMECH.2022.114751
Page generated: Tue Apr 4 21:44:30 2023

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