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Chlorine in PDB 6z01: Dna Topoisomerase

Enzymatic activity of Dna Topoisomerase

All present enzymatic activity of Dna Topoisomerase:
5.99.1.2;

Protein crystallography data

The structure of Dna Topoisomerase, PDB code: 6z01 was solved by T.S.Takahashi, D.Gadelle, P.Forterre, C.Mayer, S.Petrella, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.44 / 1.90
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.2, 96.59, 94.56, 90, 113.33, 90
R / Rfree (%) 18 / 21.7

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Chlorine atom in the Dna Topoisomerase (pdb code 6z01). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 12 binding sites of Chlorine where determined in the Dna Topoisomerase, PDB code: 6z01:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 12 in 6z01

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Chlorine binding site 1 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl601

b:40.4
occ:1.00
 O A:HOH1055 3.1 44.5 1.0
O A:HOH1024 3.1 34.6 1.0
N A:GLY271 3.1 35.2 1.0
NH1 A:ARG269 3.2 36.2 1.0
CG A:GLU273 3.3 49.5 1.0
N A:GLU273 3.4 46.0 1.0
CB A:GLU273 3.4 50.4 1.0
CG A:ARG269 3.6 30.8 1.0
CB A:ARG269 3.7 30.7 1.0
N A:ASP272 3.7 38.9 1.0
CA A:GLY271 3.7 35.5 1.0
CD A:ARG269 3.7 32.8 1.0
N A:VAL270 3.8 30.1 1.0
C A:GLY271 3.8 35.2 1.0
CA A:GLU273 4.0 46.0 1.0
OD1 A:ASP272 4.2 44.6 1.0
C A:VAL270 4.2 35.0 1.0
CZ A:ARG269 4.2 35.6 1.0
CA A:VAL270 4.4 30.1 1.0
C A:ARG269 4.4 32.3 1.0
NE A:ARG269 4.4 35.3 1.0
CB A:VAL270 4.4 29.3 1.0
C A:ASP272 4.4 48.9 1.0
CA A:ARG269 4.6 28.4 1.0
O A:GLU273 4.6 43.2 1.0
O A:GLY271 4.6 37.8 1.0
CA A:ASP272 4.6 41.4 1.0
O A:HOH778 4.6 41.6 1.0
CD A:GLU273 4.7 63.5 1.0
C A:GLU273 4.8 45.0 1.0
O A:HOH757 4.8 40.4 1.0

Chlorine binding site 2 out of 12 in 6z01

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Chlorine binding site 2 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl602

b:30.9
occ:1.00
 N A:GLY148 3.0 32.5 1.0
O A:HOH1193 3.1 38.5 1.0
N A:GLY150 3.1 31.3 1.0
N A:HIS152 3.2 25.1 1.0
C A:GLY150 3.4 33.7 1.0
CA A:GLY150 3.5 27.3 1.0
CA A:GLY148 3.5 32.3 1.0
CB A:HIS152 3.5 29.8 1.0
C A:GLY148 3.5 36.5 1.0
CB A:ARG155 3.6 27.0 1.0
N A:ASN151 3.6 28.1 1.0
CD A:ARG155 3.7 31.9 1.0
O A:GLY150 3.8 31.0 1.0
N A:ARG149 3.9 34.8 1.0
O A:GLY148 3.9 35.7 1.0
CA A:HIS152 3.9 28.0 1.0
C A:MSE147 4.1 28.1 1.0
O A:HOH1034 4.1 44.5 1.0
C A:ARG149 4.2 37.0 1.0
CG A:ARG155 4.2 27.8 1.0
C A:ASN151 4.2 31.5 1.0
CA A:MSE147 4.3 31.1 1.0
CA A:ASN151 4.4 28.3 1.0
O A:HIS152 4.4 26.0 1.0
O A:HOH947 4.5 40.6 1.0
CA A:ARG149 4.7 37.0 1.0
C A:HIS152 4.7 23.6 1.0
CB A:MSE147 4.7 38.4 1.0
CA A:ARG155 4.7 19.8 1.0
CG A:HIS152 4.9 25.9 1.0
NE A:ARG155 4.9 34.1 1.0

Chlorine binding site 3 out of 12 in 6z01

Go back to Chlorine Binding Sites List in 6z01
Chlorine binding site 3 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl603

b:33.6
occ:1.00
 O A:HOH705 2.7 49.2 1.0
O A:HOH869 3.2 24.1 1.0
O A:HOH1148 3.2 30.9 1.0
N A:SER513 3.2 21.2 1.0
CA A:ALA512 3.6 23.5 1.0
C A:ALA512 3.9 25.1 1.0
CB A:SER513 4.0 20.8 1.0
CB A:ALA512 4.0 22.9 1.0
CA A:SER513 4.2 23.1 1.0
NH2 A:ARG149 4.4 45.6 1.0
NH1 A:ARG149 4.5 46.1 1.0
CE A:LYS222 4.6 33.5 1.0
O A:LYS511 4.7 26.7 1.0
O A:SER513 4.7 20.3 1.0
O A:HOH1161 4.8 36.7 1.0
CZ A:ARG149 4.8 42.3 1.0
O A:HOH1196 4.8 39.1 1.0
N A:ALA512 4.8 24.2 1.0
NZ A:LYS222 4.9 34.5 1.0
O A:HOH1260 5.0 45.0 1.0
C A:SER513 5.0 23.7 1.0

Chlorine binding site 4 out of 12 in 6z01

Go back to Chlorine Binding Sites List in 6z01
Chlorine binding site 4 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl604

b:34.2
occ:1.00
 OG A:SER513 2.9 24.0 1.0
O A:HOH1142 3.0 30.7 1.0
O A:HOH1235 3.0 20.9 1.0
CB A:SER513 3.5 20.8 1.0
CB A:LYS515 4.3 28.0 1.0
O A:HOH997 4.3 26.2 1.0
CA A:SER513 4.4 23.1 1.0
CD A:LYS515 4.5 30.8 1.0
O A:HOH1196 4.6 39.1 1.0
O A:HOH1129 5.0 42.4 1.0

Chlorine binding site 5 out of 12 in 6z01

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Chlorine binding site 5 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl605

b:63.7
occ:1.00
 O A:HOH703 2.7 67.5 1.0
NZ A:LYS443 4.2 70.0 1.0

Chlorine binding site 6 out of 12 in 6z01

Go back to Chlorine Binding Sites List in 6z01
Chlorine binding site 6 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl606

b:43.8
occ:1.00
 N A:GLU141 3.0 31.2 1.0
CG A:GLU141 3.1 44.7 1.0
CB A:GLU141 3.5 40.6 1.0
CZ2 A:TRP197 3.8 25.1 1.0
O A:HOH823 3.8 43.3 1.0
O A:HOH817 3.8 34.3 1.0
CA A:GLU141 3.9 35.8 1.0
CA A:VAL140 4.0 30.3 1.0
C A:VAL140 4.0 31.6 1.0
CD A:GLU141 4.0 65.8 1.0
O A:MSE139 4.1 28.2 1.0
OE1 A:GLU141 4.1 66.6 1.0
O A:HOH1061 4.5 40.1 1.0
NZ A:LYS206 4.5 52.7 1.0
CG1 A:VAL140 4.5 26.0 1.0
O A:HOH1059 4.5 42.3 1.0
CH2 A:TRP197 4.5 24.4 1.0
CE2 A:TRP197 4.7 29.3 1.0
O A:GLU141 4.8 33.2 1.0
O A:HOH1090 4.8 41.7 1.0
C A:GLU141 4.8 34.5 1.0
CB A:VAL140 4.9 28.8 1.0
C A:MSE139 4.9 29.2 1.0
OE2 A:GLU141 5.0 67.9 1.0
N A:VAL140 5.0 24.5 1.0
CE A:LYS206 5.0 53.4 1.0
NE1 A:TRP197 5.0 25.2 1.0

Chlorine binding site 7 out of 12 in 6z01

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Chlorine binding site 7 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl601

b:36.7
occ:1.00
 O B:HOH1110 2.6 36.1 1.0
CB B:GLU273 3.1 43.8 1.0
NH1 B:ARG269 3.1 23.8 1.0
N B:GLY271 3.2 27.8 1.0
N B:GLU273 3.2 30.0 1.0
CG B:GLU273 3.3 46.6 1.0
CB B:ARG269 3.5 25.8 1.0
CG B:ARG269 3.5 22.3 1.0
CD B:ARG269 3.7 29.3 1.0
N B:VAL270 3.7 21.5 1.0
CA B:GLU273 3.8 35.0 1.0
N B:ASP272 3.8 27.7 1.0
CA B:GLY271 3.9 30.7 1.0
C B:GLY271 4.0 32.2 1.0
CZ B:ARG269 4.2 28.8 1.0
C B:VAL270 4.2 25.5 1.0
C B:ARG269 4.3 23.1 1.0
OD1 B:ASP272 4.3 35.0 1.0
CD B:GLU273 4.3 57.4 1.0
CA B:VAL270 4.3 23.8 1.0
C B:ASP272 4.4 36.9 1.0
NE B:ARG269 4.4 25.6 1.0
CA B:ARG269 4.4 22.6 1.0
CB B:VAL270 4.5 22.9 1.0
O B:HOH976 4.5 34.9 1.0
O B:GLU273 4.6 37.0 1.0
OE1 B:GLU273 4.6 58.8 1.0
C B:GLU273 4.7 37.8 1.0
CA B:ASP272 4.7 33.5 1.0
O B:HOH971 4.8 31.3 1.0
O B:GLY271 4.8 30.2 1.0
O B:HOH1023 4.9 31.0 1.0

Chlorine binding site 8 out of 12 in 6z01

Go back to Chlorine Binding Sites List in 6z01
Chlorine binding site 8 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl602

b:38.7
occ:1.00
 NH2 B:ARG495 3.2 25.9 1.0
NE1 B:TRP494 3.2 21.8 1.0
O B:HOH1116 3.3 31.3 1.0
NE B:ARG488 3.4 33.5 1.0
NH2 B:ARG488 3.5 32.3 1.0
O B:HOH982 3.5 35.3 1.0
O B:HOH1212 3.6 46.0 1.0
CZ B:ARG488 3.8 43.2 1.0
NH1 B:ARG495 4.0 26.8 1.0
CZ B:ARG495 4.0 27.3 1.0
CD1 B:TRP494 4.2 23.3 1.0
CE2 B:TRP494 4.2 22.1 1.0
CG B:ARG488 4.3 30.8 1.0
CD B:ARG488 4.4 35.1 1.0
CZ2 B:TRP494 4.4 27.1 1.0
CE B:LYS484 4.5 19.8 1.0
O B:HOH863 4.5 23.6 1.0
CG B:LYS484 4.5 21.3 1.0
CD B:LYS484 4.9 20.0 1.0

Chlorine binding site 9 out of 12 in 6z01

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Chlorine binding site 9 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl603

b:61.6
occ:1.00
 NE2 B:HIS234 3.0 44.0 1.0
ND2 B:ASN233 3.2 33.5 1.0
CG B:MSE230 3.4 57.1 1.0
CE1 B:TYR53 3.5 47.6 1.0
CD2 B:HIS234 3.9 35.8 1.0
CA B:GLY150 3.9 36.8 1.0
CE1 B:HIS234 3.9 48.5 1.0
CB B:ASN233 4.0 32.1 1.0
CG B:ASN233 4.1 37.9 1.0
OH B:TYR53 4.1 60.3 1.0
O B:ARG149 4.1 39.0 1.0
CZ B:TYR53 4.3 49.2 1.0
O B:MSE230 4.4 27.3 1.0
SE B:MSE230 4.4 105.6 1.0
CD1 B:TYR53 4.5 47.3 1.0
N B:GLY150 4.5 36.7 1.0
C B:ARG149 4.5 44.6 1.0
O B:HOH1301 4.6 44.5 1.0
CB B:MSE230 4.6 29.8 1.0
O B:HOH1131 4.8 53.2 1.0
CA B:MSE230 4.9 31.7 1.0

Chlorine binding site 10 out of 12 in 6z01

Go back to Chlorine Binding Sites List in 6z01
Chlorine binding site 10 out of 12 in the Dna Topoisomerase


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of Dna Topoisomerase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl604

b:64.6
occ:1.00
 N B:MSE139 3.2 43.9 1.0
CG B:MSE139 3.3 60.7 1.0
N B:TRP138 3.3 49.5 1.0
CA B:ASN137 3.5 48.9 1.0
CB B:MSE139 3.6 53.2 1.0
O B:ALA136 3.6 51.4 1.0
C B:ASN137 3.7 52.3 1.0
CE B:MSE139 3.7 69.0 1.0
CA B:MSE139 3.9 51.6 1.0
CD1 B:TRP138 4.0 48.8 1.0
NE1 B:TRP138 4.0 47.8 1.0
SE B:MSE139 4.1 83.2 1.0
C B:TRP138 4.1 45.2 1.0
CG B:TRP138 4.1 46.7 1.0
CE2 B:TRP138 4.2 51.6 1.0
CA B:TRP138 4.2 47.1 1.0
CD2 B:TRP138 4.3 50.6 1.0
N B:ASN137 4.4 43.4 1.0
C B:ALA136 4.4 48.1 1.0
O B:MSE139 4.4 46.1 1.0
CB B:ASN137 4.5 49.3 1.0
O B:ASN137 4.6 49.0 1.0
C B:MSE139 4.7 49.1 1.0
CB B:TRP138 4.8 44.8 1.0
CZ2 B:TRP138 4.9 56.4 1.0
CE3 B:TRP138 5.0 51.5 1.0

Reference:

T.S.Takahashi, S.Petrella, D.Gadelle, P.Forterre, C.Mayer. Structure of A Dna Topoisomerase To Be Published.
Page generated: Mon Jul 29 17:55:16 2024

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