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Fluorine in PDB 1z5b: Topoisomerase VI-B, Adp ALF4- Bound Dimer Form

Enzymatic activity of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form

All present enzymatic activity of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form:
5.99.1.3;

Protein crystallography data

The structure of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form, PDB code: 1z5b was solved by K.D.Corbett, J.M.Berger, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 2.00
Space group P 32 1 2
Cell size a, b, c (Å), α, β, γ (°) 74.077, 74.077, 344.381, 90.00, 90.00, 120.00
R / Rfree (%) 17.9 / 20.8

Other elements in 1z5b:

The structure of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms
Aluminium (Al) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form (pdb code 1z5b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form, PDB code: 1z5b:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 1z5b

Go back to Fluorine Binding Sites List in 1z5b
Fluorine binding site 1 out of 8 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3001

b:20.6
occ:1.00
 F1 A:ALF3001 0.0 20.6 1.0
AL A:ALF3001 1.8 19.4 1.0
MG A:MG2001 2.0 20.1 1.0
F3 A:ALF3001 2.5 20.7 1.0
F4 A:ALF3001 2.6 18.7 1.0
O1A A:ADP1001 2.6 18.6 1.0
O A:HOH4002 2.7 14.1 1.0
O3B A:ADP1001 2.8 15.9 1.0
O A:HOH4038 2.8 20.8 1.0
O3A A:ADP1001 2.9 17.7 1.0
N A:GLY111 3.0 7.7 1.0
O1B A:ADP1001 3.0 16.2 1.0
PB A:ADP1001 3.0 18.1 1.0
PA A:ADP1001 3.1 18.6 1.0
CA A:GLY111 3.2 7.2 1.0
OE2 A:GLU38 3.4 9.5 1.0
O A:HOH4136 3.5 28.3 1.0
F2 A:ALF3001 3.6 19.4 1.0
O2A A:ADP1001 3.8 15.5 1.0
N A:VAL112 4.0 7.5 1.0
C A:GLY111 4.1 7.5 1.0
OD1 A:ASN42 4.1 6.0 1.0
C A:LEU110 4.2 8.0 1.0
N A:LEU110 4.2 7.0 1.0
CD A:GLU38 4.5 10.3 1.0
O A:HOH4137 4.5 26.4 1.0
O5' A:ADP1001 4.6 19.9 1.0
O2B A:ADP1001 4.6 15.2 1.0
O A:HOH4006 4.7 16.9 1.0
ND2 A:ASN42 4.8 4.8 1.0
CA A:LEU110 4.8 7.5 1.0
N A:GLY109 4.9 6.7 1.0
CG A:ASN42 4.9 6.3 1.0
NZ A:LYS427 5.0 17.6 1.0

Fluorine binding site 2 out of 8 in 1z5b

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Fluorine binding site 2 out of 8 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3001

b:19.4
occ:1.00
 F2 A:ALF3001 0.0 19.4 1.0
AL A:ALF3001 1.8 19.4 1.0
F4 A:ALF3001 2.5 18.7 1.0
F3 A:ALF3001 2.6 20.7 1.0
O3B A:ADP1001 2.6 15.9 1.0
O A:HOH4002 2.7 14.1 1.0
N A:TYR108 2.8 7.0 1.0
N A:MET107 2.8 7.4 1.0
NZ A:LYS427 2.9 17.6 1.0
CD2 A:TYR108 3.5 7.4 1.0
CB A:TYR108 3.6 7.3 1.0
F1 A:ALF3001 3.6 20.6 1.0
CA A:GLY106 3.7 7.7 1.0
CA A:MET107 3.7 7.2 1.0
C A:MET107 3.7 7.2 1.0
CA A:TYR108 3.7 7.2 1.0
C A:GLY106 3.7 7.7 1.0
CG A:TYR108 3.8 7.1 1.0
CG A:MET107 3.8 6.2 1.0
CE A:LYS427 3.9 15.8 1.0
PB A:ADP1001 4.1 18.1 1.0
N A:GLY109 4.1 6.7 1.0
O A:HOH4006 4.3 16.9 1.0
CB A:MET107 4.3 7.3 1.0
O A:HOH4137 4.4 26.4 1.0
C A:TYR108 4.4 6.9 1.0
CE2 A:TYR108 4.5 7.6 1.0
O1B A:ADP1001 4.6 16.2 1.0
O A:HOH4136 4.6 28.3 1.0
MG A:MG2001 4.7 20.1 1.0
O A:ARG105 4.8 7.6 1.0
O3A A:ADP1001 4.9 17.7 1.0
O A:MET107 4.9 7.4 1.0
O A:GLY106 4.9 7.2 1.0
CD1 A:TYR108 4.9 6.4 1.0
N A:GLY106 5.0 7.7 1.0

Fluorine binding site 3 out of 8 in 1z5b

Go back to Fluorine Binding Sites List in 1z5b
Fluorine binding site 3 out of 8 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3001

b:20.7
occ:1.00
 F3 A:ALF3001 0.0 20.7 1.0
AL A:ALF3001 1.8 19.4 1.0
O A:HOH4136 2.1 28.3 1.0
F1 A:ALF3001 2.5 20.6 1.0
F2 A:ALF3001 2.6 19.4 1.0
MG A:MG2001 2.6 20.1 1.0
O A:HOH4137 2.6 26.4 1.0
O A:HOH4002 2.6 14.1 1.0
O3B A:ADP1001 2.7 15.9 1.0
CA A:GLY106 3.0 7.7 1.0
O1B A:ADP1001 3.1 16.2 1.0
NZ A:LYS427 3.2 17.6 1.0
O A:HOH4038 3.4 20.8 1.0
PB A:ADP1001 3.5 18.1 1.0
F4 A:ALF3001 3.6 18.7 1.0
OE2 A:GLU38 3.7 9.5 1.0
N A:MET107 3.9 7.4 1.0
N A:GLY106 3.9 7.7 1.0
C A:GLY106 4.0 7.7 1.0
OD1 A:ASN42 4.2 6.0 1.0
O3A A:ADP1001 4.4 17.7 1.0
O1A A:ADP1001 4.5 18.6 1.0
O A:ARG105 4.5 7.6 1.0
C A:ARG105 4.6 7.4 1.0
CE A:LYS427 4.6 15.8 1.0
NZ A:LYS98 4.8 5.2 1.0
O2B A:ADP1001 4.8 15.2 1.0
CD A:GLU38 4.9 10.3 1.0
OE1 A:GLU41 5.0 10.8 1.0

Fluorine binding site 4 out of 8 in 1z5b

Go back to Fluorine Binding Sites List in 1z5b
Fluorine binding site 4 out of 8 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F3001

b:18.7
occ:1.00
 F4 A:ALF3001 0.0 18.7 1.0
AL A:ALF3001 1.8 19.4 1.0
F2 A:ALF3001 2.5 19.4 1.0
F1 A:ALF3001 2.6 20.6 1.0
N A:LEU110 2.7 7.0 1.0
O A:HOH4002 2.7 14.1 1.0
O3B A:ADP1001 2.7 15.9 1.0
N A:GLY111 2.7 7.7 1.0
N A:GLY109 3.1 6.7 1.0
CB A:TYR108 3.3 7.3 1.0
CA A:LEU110 3.3 7.5 1.0
O A:HOH4006 3.4 16.9 1.0
CB A:LEU110 3.5 7.6 1.0
C A:LEU110 3.5 8.0 1.0
F3 A:ALF3001 3.6 20.7 1.0
N A:TYR108 3.6 7.0 1.0
O3A A:ADP1001 3.6 17.7 1.0
C A:TYR108 3.7 6.9 1.0
CA A:TYR108 3.7 7.2 1.0
C A:GLY109 3.7 6.8 1.0
CA A:GLY111 3.7 7.2 1.0
PB A:ADP1001 3.8 18.1 1.0
CA A:GLY109 3.8 6.9 1.0
CD2 A:TYR108 4.2 7.4 1.0
CG A:TYR108 4.2 7.1 1.0
MG A:MG2001 4.4 20.1 1.0
PA A:ADP1001 4.6 18.6 1.0
O1B A:ADP1001 4.6 16.2 1.0
O A:TYR108 4.6 7.0 1.0
CG A:LEU110 4.7 9.2 1.0
O2A A:ADP1001 4.7 15.5 1.0
O A:LEU110 4.7 8.3 1.0
NZ A:LYS427 4.8 17.6 1.0
O1A A:ADP1001 4.8 18.6 1.0
N A:MET107 4.8 7.4 1.0
OE2 A:GLU38 4.8 9.5 1.0
O A:GLY109 4.9 5.6 1.0
C A:MET107 4.9 7.2 1.0
O2B A:ADP1001 4.9 15.2 1.0

Fluorine binding site 5 out of 8 in 1z5b

Go back to Fluorine Binding Sites List in 1z5b
Fluorine binding site 5 out of 8 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3002

b:19.2
occ:1.00
 F1 B:ALF3002 0.0 19.2 1.0
AL B:ALF3002 1.8 21.2 1.0
F3 B:ALF3002 2.5 21.2 1.0
O3B B:ADP1002 2.6 18.6 1.0
F4 B:ALF3002 2.6 20.9 1.0
N B:LEU110 2.7 7.1 1.0
O B:HOH3003 2.7 15.8 1.0
N B:GLY111 2.8 7.1 1.0
N B:GLY109 3.2 7.1 1.0
CB B:TYR108 3.4 6.7 1.0
CA B:LEU110 3.4 6.8 1.0
O B:HOH3025 3.5 16.4 1.0
O3A B:ADP1002 3.6 15.6 1.0
C B:LEU110 3.6 6.8 1.0
F2 B:ALF3002 3.6 24.1 1.0
CB B:LEU110 3.6 8.3 1.0
C B:TYR108 3.7 7.0 1.0
PB B:ADP1002 3.7 17.4 1.0
N B:TYR108 3.7 6.7 1.0
CA B:GLY111 3.7 7.4 1.0
C B:GLY109 3.7 7.5 1.0
CA B:TYR108 3.7 7.0 1.0
CA B:GLY109 3.8 7.0 1.0
CD2 B:TYR108 4.3 8.5 1.0
CG B:TYR108 4.3 8.1 1.0
MG B:MG2002 4.4 18.4 1.0
PA B:ADP1002 4.5 17.4 1.0
O1B B:ADP1002 4.5 16.4 1.0
O B:TYR108 4.6 7.2 1.0
O2A B:ADP1002 4.6 16.0 1.0
O1A B:ADP1002 4.7 17.9 1.0
CG B:LEU110 4.7 8.5 1.0
O B:LEU110 4.8 6.9 1.0
O2B B:ADP1002 4.8 16.7 1.0
O B:GLY109 4.9 6.6 1.0
N B:MET107 4.9 7.3 1.0
OE2 B:GLU38 4.9 9.9 1.0
C B:MET107 5.0 6.8 1.0

Fluorine binding site 6 out of 8 in 1z5b

Go back to Fluorine Binding Sites List in 1z5b
Fluorine binding site 6 out of 8 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3002

b:24.1
occ:1.00
 F2 B:ALF3002 0.0 24.1 1.0
AL B:ALF3002 1.8 21.2 1.0
O B:HOH3165 2.4 31.3 1.0
F4 B:ALF3002 2.5 20.9 1.0
F3 B:ALF3002 2.5 21.2 1.0
NZ B:LYS427 2.7 23.3 1.0
O B:HOH3089 2.7 27.3 1.0
O B:HOH3003 2.7 15.8 1.0
O3B B:ADP1002 2.7 18.6 1.0
CA B:GLY106 2.8 7.7 1.0
MG B:MG2002 3.1 18.4 1.0
O1B B:ADP1002 3.3 16.4 1.0
CE B:LYS427 3.5 19.6 1.0
F1 B:ALF3002 3.6 19.2 1.0
PB B:ADP1002 3.6 17.4 1.0
N B:MET107 3.7 7.3 1.0
C B:GLY106 3.8 7.5 1.0
N B:GLY106 3.9 8.0 1.0
O B:HOH3008 3.9 15.3 1.0
OE2 B:GLU38 4.0 9.9 1.0
O B:ARG105 4.2 8.7 1.0
C B:ARG105 4.4 8.2 1.0
O3A B:ADP1002 4.6 15.6 1.0
OD1 B:ASN42 4.6 7.4 1.0
O1A B:ADP1002 4.7 17.9 1.0
O2B B:ADP1002 4.8 16.7 1.0
N B:TYR108 4.8 6.7 1.0
CD B:LYS427 4.9 16.9 1.0
NZ B:LYS98 4.9 9.3 1.0
O B:GLY106 5.0 6.9 1.0

Fluorine binding site 7 out of 8 in 1z5b

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Fluorine binding site 7 out of 8 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3002

b:21.2
occ:1.00
 F3 B:ALF3002 0.0 21.2 1.0
AL B:ALF3002 1.8 21.2 1.0
F2 B:ALF3002 2.5 24.1 1.0
F1 B:ALF3002 2.5 19.2 1.0
O3B B:ADP1002 2.6 18.6 1.0
N B:TYR108 2.7 6.7 1.0
O B:HOH3003 2.8 15.8 1.0
N B:MET107 2.9 7.3 1.0
NZ B:LYS427 3.2 23.3 1.0
CE B:LYS427 3.3 19.6 1.0
CD2 B:TYR108 3.4 8.5 1.0
CB B:TYR108 3.4 6.7 1.0
CA B:TYR108 3.5 7.0 1.0
F4 B:ALF3002 3.6 20.9 1.0
C B:MET107 3.6 6.8 1.0
CG B:TYR108 3.6 8.1 1.0
CA B:MET107 3.6 6.9 1.0
CG B:MET107 3.7 5.1 1.0
C B:GLY106 3.8 7.5 1.0
CA B:GLY106 3.9 7.7 1.0
N B:GLY109 4.1 7.1 1.0
PB B:ADP1002 4.2 17.4 1.0
CB B:MET107 4.2 7.5 1.0
C B:TYR108 4.3 7.0 1.0
CE2 B:TYR108 4.3 9.1 1.0
O B:HOH3025 4.4 16.4 1.0
CD B:LYS427 4.4 16.9 1.0
O B:HOH3089 4.7 27.3 1.0
O1B B:ADP1002 4.7 16.4 1.0
CD1 B:TYR108 4.7 6.9 1.0
O B:MET107 4.8 6.9 1.0
O3A B:ADP1002 4.9 15.6 1.0
O B:HOH3165 4.9 31.3 1.0
O B:GLY106 5.0 6.9 1.0
MG B:MG2002 5.0 18.4 1.0
O B:ARG105 5.0 8.7 1.0
N B:LEU110 5.0 7.1 1.0

Fluorine binding site 8 out of 8 in 1z5b

Go back to Fluorine Binding Sites List in 1z5b
Fluorine binding site 8 out of 8 in the Topoisomerase VI-B, Adp ALF4- Bound Dimer Form


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Topoisomerase VI-B, Adp ALF4- Bound Dimer Form within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F3002

b:20.9
occ:1.00
 F4 B:ALF3002 0.0 20.9 1.0
AL B:ALF3002 1.8 21.2 1.0
MG B:MG2002 2.0 18.4 1.0
F2 B:ALF3002 2.5 24.1 1.0
F1 B:ALF3002 2.6 19.2 1.0
O3B B:ADP1002 2.6 18.6 1.0
O B:HOH3003 2.7 15.8 1.0
O1A B:ADP1002 2.7 17.9 1.0
O B:HOH3008 2.9 15.3 1.0
O1B B:ADP1002 2.9 16.4 1.0
PB B:ADP1002 2.9 17.4 1.0
O3A B:ADP1002 3.0 15.6 1.0
O B:HOH3165 3.2 31.3 1.0
N B:GLY111 3.2 7.1 1.0
PA B:ADP1002 3.3 17.4 1.0
CA B:GLY111 3.4 7.4 1.0
OE2 B:GLU38 3.4 9.9 1.0
F3 B:ALF3002 3.6 21.2 1.0
O2A B:ADP1002 4.0 16.0 1.0
OD1 B:ASN42 4.0 7.4 1.0
N B:VAL112 4.2 7.2 1.0
O B:HOH3089 4.2 27.3 1.0
C B:GLY111 4.3 7.0 1.0
N B:LEU110 4.4 7.1 1.0
C B:LEU110 4.4 6.8 1.0
CD B:GLU38 4.5 8.5 1.0
O2B B:ADP1002 4.5 16.7 1.0
O5' B:ADP1002 4.7 18.2 1.0
O B:HOH3025 4.7 16.4 1.0
NZ B:LYS427 4.8 23.3 1.0
CG B:ASN42 4.9 7.7 1.0
ND2 B:ASN42 4.9 4.0 1.0
N B:GLY109 4.9 7.1 1.0
CA B:GLY106 5.0 7.7 1.0

Reference:

K.D.Corbett, J.M.Berger. Structural Dissection of Atp Turnover in the Prototypical Ghl Atpase Topovi. Structure V. 13 873 2005.
ISSN: ISSN 0969-2126
PubMed: 15939019
DOI: 10.1016/J.STR.2005.03.013
Page generated: Wed Jul 31 13:36:27 2024

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