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Fluorine in PDB 2bef: Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3

Enzymatic activity of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3

All present enzymatic activity of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3:
2.7.4.6;

Protein crystallography data

The structure of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3, PDB code: 2bef was solved by Y.W.Xu, J.Cherfils, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 15.00 / 2.30
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.560, 71.560, 153.750, 90.00, 90.00, 120.00
R / Rfree (%) 19.3 / n/a

Other elements in 2bef:

The structure of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 (pdb code 2bef). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3, PDB code: 2bef:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 2bef

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Fluorine binding site 1 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F157

b:33.5
occ:1.00
 F1 A:BEF157 0.0 33.5 1.0
BE A:BEF157 1.6 29.8 1.0
ND1 A:HIS122 2.6 12.3 1.0
O3B A:ADP158 2.6 12.7 1.0
F3 A:BEF157 2.7 33.1 1.0
F2 A:BEF157 2.7 29.3 1.0
CA A:HIS122 3.2 2.2 1.0
NH2 A:ARG92 3.2 23.5 1.0
N A:GLY123 3.2 6.6 1.0
O1B A:ADP158 3.3 15.4 1.0
PB A:ADP158 3.4 9.9 1.0
CG A:HIS122 3.4 8.1 1.0
CE1 A:HIS122 3.4 5.6 1.0
NH2 A:ARG109 3.5 5.4 1.0
CB A:HIS122 3.5 4.8 1.0
O A:HOH626 3.6 8.9 1.0
C A:HIS122 3.7 6.6 1.0
O A:GLY123 3.7 12.8 1.0
MG A:MG156 3.9 10.7 1.0
O A:ILE121 4.1 8.7 1.0
O2B A:ADP158 4.2 8.6 1.0
C A:GLY123 4.3 8.1 1.0
CA A:GLY123 4.3 3.5 1.0
CZ A:ARG92 4.4 21.0 1.0
N A:HIS122 4.4 6.9 1.0
NE2 A:HIS122 4.4 8.1 1.0
CD2 A:HIS122 4.4 9.3 1.0
O3' A:ADP158 4.6 12.1 1.0
CZ A:ARG109 4.6 10.3 1.0
O3A A:ADP158 4.7 16.8 1.0
C A:ILE121 4.7 8.8 1.0
NH1 A:ARG109 4.9 10.9 1.0
O A:HIS122 4.9 9.3 1.0
OH A:TYR56 4.9 14.7 1.0

Fluorine binding site 2 out of 9 in 2bef

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Fluorine binding site 2 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F157

b:29.3
occ:1.00
 F2 A:BEF157 0.0 29.3 1.0
BE A:BEF157 1.7 29.8 1.0
OH A:TYR56 2.6 14.7 1.0
F1 A:BEF157 2.7 33.5 1.0
F3 A:BEF157 2.7 33.1 1.0
O3B A:ADP158 2.9 12.7 1.0
NZ A:LYS16 2.9 10.9 1.0
O3' A:ADP158 3.1 12.1 1.0
ND1 A:HIS122 3.2 12.3 1.0
CE A:LYS16 3.2 12.9 1.0
CZ A:TYR56 3.5 16.2 1.0
CB A:HIS122 3.5 4.8 1.0
CE1 A:TYR56 3.6 12.3 1.0
CG A:HIS122 3.7 8.1 1.0
C4' A:ADP158 3.8 10.8 1.0
C5' A:ADP158 3.8 13.5 1.0
CA A:HIS122 3.8 2.2 1.0
C3' A:ADP158 4.1 14.9 1.0
NH2 A:ARG109 4.2 5.4 1.0
PB A:ADP158 4.2 9.9 1.0
CE1 A:HIS122 4.3 5.6 1.0
O A:ILE121 4.4 8.7 1.0
MG A:MG156 4.6 10.7 1.0
O1B A:ADP158 4.7 15.4 1.0
N A:HIS122 4.7 6.9 1.0
CD A:LYS16 4.7 11.3 1.0
CE2 A:TYR56 4.8 16.7 1.0
O2' A:ADP158 4.8 19.1 1.0
O3A A:ADP158 4.9 16.8 1.0
CD1 A:TYR56 4.9 12.8 1.0
O5' A:ADP158 4.9 12.6 1.0
C A:ILE121 4.9 8.8 1.0

Fluorine binding site 3 out of 9 in 2bef

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Fluorine binding site 3 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F157

b:33.1
occ:1.00
 F3 A:BEF157 0.0 33.1 1.0
BE A:BEF157 1.7 29.8 1.0
MG A:MG156 2.1 10.7 1.0
F1 A:BEF157 2.7 33.5 1.0
ND1 A:HIS122 2.7 12.3 1.0
O A:HOH619 2.7 17.8 1.0
F2 A:BEF157 2.7 29.3 1.0
O A:HOH626 2.8 8.9 1.0
CE1 A:HIS122 3.1 5.6 1.0
O3B A:ADP158 3.1 12.7 1.0
O1B A:ADP158 3.1 15.4 1.0
O1A A:ADP158 3.4 13.4 1.0
CE1 A:TYR56 3.4 12.3 1.0
PB A:ADP158 3.6 9.9 1.0
C5' A:ADP158 3.7 13.5 1.0
O A:HOH693 4.0 17.5 1.0
CG A:HIS122 4.0 8.1 1.0
O A:HOH737 4.1 15.5 1.0
OH A:TYR56 4.1 14.7 1.0
O3A A:ADP158 4.1 16.8 1.0
PA A:ADP158 4.2 13.8 1.0
CZ A:TYR56 4.2 16.2 1.0
CD1 A:TYR56 4.3 12.8 1.0
NE2 A:HIS122 4.4 8.1 1.0
O5' A:ADP158 4.4 12.6 1.0
C4' A:ADP158 4.6 10.8 1.0
O3' A:ADP158 4.7 12.1 1.0
CB A:HIS122 4.7 4.8 1.0
NE2 A:HIS59 4.8 12.2 1.0
CD2 A:HIS122 4.9 9.3 1.0
O A:HOH677 4.9 22.9 1.0
O A:GLY123 4.9 12.8 1.0
O2B A:ADP158 5.0 8.6 1.0
NH2 A:ARG92 5.0 23.5 1.0

Fluorine binding site 4 out of 9 in 2bef

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Fluorine binding site 4 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F157

b:34.5
occ:1.00
 F1 B:BEF157 0.0 34.5 1.0
BE B:BEF157 1.6 26.4 1.0
MG B:MG156 2.2 15.2 1.0
F3 B:BEF157 2.6 27.2 1.0
F2 B:BEF157 2.6 29.3 1.0
O1B B:ADP158 2.8 20.8 1.0
O B:HOH620 2.8 11.6 1.0
ND1 B:HIS122 2.9 12.9 1.0
O B:HOH779 2.9 20.8 1.0
O3B B:ADP158 3.0 18.4 1.0
O1A B:ADP158 3.3 17.6 1.0
CE1 B:HIS122 3.3 6.5 1.0
PB B:ADP158 3.4 17.6 1.0
CE1 B:TYR56 3.7 14.3 1.0
NH2 B:ARG92 3.8 32.6 1.0
C5' B:ADP158 3.9 10.0 1.0
O B:HOH706 4.1 17.9 1.0
CG B:HIS122 4.1 10.3 1.0
O3A B:ADP158 4.2 19.1 1.0
OH B:TYR56 4.2 16.9 1.0
PA B:ADP158 4.3 16.4 1.0
O B:GLY123 4.3 10.8 1.0
CZ B:TYR56 4.5 14.6 1.0
O B:HOH638 4.5 7.1 1.0
NE2 B:HIS122 4.6 11.4 1.0
O5' B:ADP158 4.6 16.2 1.0
O2B B:ADP158 4.7 18.0 1.0
C4' B:ADP158 4.7 14.2 1.0
CD1 B:TYR56 4.7 15.7 1.0
O3' B:ADP158 4.7 12.4 1.0
CB B:HIS122 4.7 7.0 1.0
N B:GLY123 4.7 8.2 1.0
CZ B:ARG92 4.8 29.9 1.0
O B:HOH699 5.0 19.7 1.0
CA B:HIS122 5.0 5.9 1.0

Fluorine binding site 5 out of 9 in 2bef

Go back to Fluorine Binding Sites List in 2bef
Fluorine binding site 5 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F157

b:29.3
occ:1.00
 F2 B:BEF157 0.0 29.3 1.0
BE B:BEF157 1.6 26.4 1.0
NH2 B:ARG92 2.4 32.6 1.0
F1 B:BEF157 2.6 34.5 1.0
F3 B:BEF157 2.6 27.2 1.0
O3B B:ADP158 2.8 18.4 1.0
N B:GLY123 2.8 8.2 1.0
CA B:HIS122 3.0 5.9 1.0
ND1 B:HIS122 3.1 12.9 1.0
NH2 B:ARG109 3.1 2.6 1.0
C B:HIS122 3.4 6.3 1.0
O1B B:ADP158 3.6 20.8 1.0
CG B:HIS122 3.6 10.3 1.0
CB B:HIS122 3.6 7.0 1.0
PB B:ADP158 3.6 17.6 1.0
O B:GLY123 3.6 10.8 1.0
CZ B:ARG92 3.7 29.9 1.0
CE1 B:HIS122 3.9 6.5 1.0
O B:HOH620 3.9 11.6 1.0
O B:ILE121 4.0 12.6 1.0
CA B:GLY123 4.0 6.5 1.0
N B:HIS122 4.2 10.2 1.0
C B:GLY123 4.3 8.4 1.0
O2B B:ADP158 4.3 18.0 1.0
CZ B:ARG109 4.3 6.6 1.0
NH1 B:ARG92 4.3 30.9 1.0
MG B:MG156 4.3 15.2 1.0
O3' B:ADP158 4.5 12.4 1.0
C B:ILE121 4.6 8.0 1.0
O B:HIS122 4.6 7.6 1.0
CD2 B:HIS122 4.6 9.4 1.0
NE B:ARG92 4.7 27.4 1.0
NH1 B:ARG109 4.7 4.1 1.0
NE2 B:HIS122 4.7 11.4 1.0
OH B:TYR56 4.8 16.9 1.0

Fluorine binding site 6 out of 9 in 2bef

Go back to Fluorine Binding Sites List in 2bef
Fluorine binding site 6 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F157

b:27.2
occ:1.00
 F3 B:BEF157 0.0 27.2 1.0
BE B:BEF157 1.6 26.4 1.0
OH B:TYR56 2.4 16.9 1.0
F1 B:BEF157 2.6 34.5 1.0
F2 B:BEF157 2.6 29.3 1.0
O3B B:ADP158 2.9 18.4 1.0
O3' B:ADP158 3.1 12.4 1.0
ND1 B:HIS122 3.2 12.9 1.0
NZ B:LYS16 3.4 13.6 1.0
CZ B:TYR56 3.4 14.6 1.0
CE1 B:TYR56 3.5 14.3 1.0
CB B:HIS122 3.5 7.0 1.0
CE B:LYS16 3.6 10.7 1.0
C4' B:ADP158 3.7 14.2 1.0
CA B:HIS122 3.8 5.9 1.0
CG B:HIS122 3.8 10.3 1.0
C3' B:ADP158 3.9 12.7 1.0
C5' B:ADP158 3.9 10.0 1.0
PB B:ADP158 4.2 17.6 1.0
NH2 B:ARG109 4.2 2.6 1.0
CE1 B:HIS122 4.4 6.5 1.0
O1B B:ADP158 4.5 20.8 1.0
O B:ILE121 4.5 12.6 1.0
CE2 B:TYR56 4.7 18.2 1.0
MG B:MG156 4.7 15.2 1.0
N B:HIS122 4.7 10.2 1.0
CD1 B:TYR56 4.8 15.7 1.0
O1A B:ADP158 4.9 17.6 1.0
C B:HIS122 4.9 6.3 1.0
O5' B:ADP158 4.9 16.2 1.0
N B:GLY123 4.9 8.2 1.0
O3A B:ADP158 4.9 19.1 1.0
NH2 B:ARG92 4.9 32.6 1.0

Fluorine binding site 7 out of 9 in 2bef

Go back to Fluorine Binding Sites List in 2bef
Fluorine binding site 7 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F157

b:32.3
occ:1.00
 F1 C:BEF157 0.0 32.3 1.0
BE C:BEF157 1.6 26.1 1.0
MG C:MG156 2.3 19.4 1.0
F3 C:BEF157 2.6 25.8 1.0
F2 C:BEF157 2.6 28.7 1.0
O C:HOH643 2.8 20.7 1.0
ND1 C:HIS122 2.8 7.0 1.0
O3B C:ADP158 2.9 17.3 1.0
O1B C:ADP158 3.0 17.0 1.0
O C:HOH777 3.1 21.7 1.0
CE1 C:HIS122 3.2 2.0 1.0
O1A C:ADP158 3.2 19.3 1.0
PB C:ADP158 3.4 17.0 1.0
CE1 C:TYR56 3.4 15.6 1.0
C5' C:ADP158 3.5 16.4 1.0
O3A C:ADP158 3.9 19.9 1.0
PA C:ADP158 4.0 17.8 1.0
OH C:TYR56 4.1 15.6 1.0
CG C:HIS122 4.1 4.8 1.0
O5' C:ADP158 4.2 20.3 1.0
CZ C:TYR56 4.3 14.3 1.0
CD1 C:TYR56 4.3 12.3 1.0
O C:HOH610 4.4 14.3 1.0
C4' C:ADP158 4.4 17.3 1.0
O C:HOH778 4.4 32.7 1.0
O3' C:ADP158 4.4 18.9 1.0
NE2 C:HIS122 4.5 7.2 1.0
CB C:HIS122 4.8 5.2 1.0
O2B C:ADP158 4.8 16.4 1.0
O C:GLY123 4.8 13.1 1.0
C3' C:ADP158 4.9 16.0 1.0
CD2 C:HIS122 5.0 7.0 1.0
NE2 C:HIS59 5.0 26.2 1.0

Fluorine binding site 8 out of 9 in 2bef

Go back to Fluorine Binding Sites List in 2bef
Fluorine binding site 8 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F157

b:28.7
occ:1.00
 F2 C:BEF157 0.0 28.7 1.0
BE C:BEF157 1.6 26.1 1.0
O3B C:ADP158 2.3 17.3 1.0
F1 C:BEF157 2.6 32.3 1.0
F3 C:BEF157 2.7 25.8 1.0
NH2 C:ARG109 2.9 9.2 1.0
ND1 C:HIS122 3.0 7.0 1.0
PB C:ADP158 3.2 17.0 1.0
CA C:HIS122 3.2 5.6 1.0
N C:GLY123 3.3 13.2 1.0
O1B C:ADP158 3.3 17.0 1.0
CG C:HIS122 3.6 4.8 1.0
CB C:HIS122 3.7 5.2 1.0
C C:HIS122 3.7 8.6 1.0
CE1 C:HIS122 3.8 2.0 1.0
O C:ILE121 3.9 8.0 1.0
O C:GLY123 4.0 13.1 1.0
O2B C:ADP158 4.1 16.4 1.0
CZ C:ARG109 4.2 8.4 1.0
MG C:MG156 4.2 19.4 1.0
O C:HOH777 4.2 21.7 1.0
NH1 C:ARG92 4.3 23.9 1.0
O3' C:ADP158 4.3 18.9 1.0
N C:HIS122 4.4 7.5 1.0
CA C:GLY123 4.5 5.3 1.0
O3A C:ADP158 4.5 19.9 1.0
NH1 C:ARG109 4.6 8.1 1.0
C C:ILE121 4.6 7.9 1.0
CD2 C:HIS122 4.6 7.0 1.0
NZ C:LYS16 4.6 11.6 1.0
C C:GLY123 4.7 8.5 1.0
NE2 C:HIS122 4.7 7.2 1.0
CZ C:ARG92 4.8 22.4 1.0
OH C:TYR56 4.9 15.6 1.0
NH2 C:ARG92 4.9 26.6 1.0
O C:HIS122 5.0 9.3 1.0

Fluorine binding site 9 out of 9 in 2bef

Go back to Fluorine Binding Sites List in 2bef
Fluorine binding site 9 out of 9 in the Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of Ndp Kinase Complexed with Mg, Adp, and BEF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F157

b:25.8
occ:1.00
 F3 C:BEF157 0.0 25.8 1.0
BE C:BEF157 1.6 26.1 1.0
OH C:TYR56 2.3 15.6 1.0
F1 C:BEF157 2.6 32.3 1.0
F2 C:BEF157 2.7 28.7 1.0
NZ C:LYS16 2.8 11.6 1.0
ND1 C:HIS122 3.0 7.0 1.0
O3B C:ADP158 3.1 17.3 1.0
CE C:LYS16 3.1 12.4 1.0
O3' C:ADP158 3.2 18.9 1.0
CZ C:TYR56 3.3 14.3 1.0
CE1 C:TYR56 3.3 15.6 1.0
CB C:HIS122 3.5 5.2 1.0
CG C:HIS122 3.7 4.8 1.0
C4' C:ADP158 3.8 17.3 1.0
CA C:HIS122 3.9 5.6 1.0
C5' C:ADP158 3.9 16.4 1.0
C3' C:ADP158 4.0 16.0 1.0
CE1 C:HIS122 4.2 2.0 1.0
NH2 C:ARG109 4.2 9.2 1.0
PB C:ADP158 4.4 17.0 1.0
O C:ILE121 4.5 8.0 1.0
CE2 C:TYR56 4.6 14.1 1.0
CD C:LYS16 4.6 4.9 1.0
CD1 C:TYR56 4.7 12.3 1.0
N C:HIS122 4.7 7.5 1.0
O2' C:ADP158 4.8 17.5 1.0
O1B C:ADP158 4.8 17.0 1.0
MG C:MG156 4.9 19.4 1.0
CD2 C:HIS122 4.9 7.0 1.0
C C:ILE121 4.9 7.9 1.0
O3A C:ADP158 5.0 19.9 1.0

Reference:

Y.W.Xu, S.Morera, J.Janin, J.Cherfils. ALF3 Mimics the Transition State of Protein Phosphorylation in the Crystal Structure of Nucleoside Diphosphate Kinase and Mgadp. Proc.Natl.Acad.Sci.Usa V. 94 3579 1997.
ISSN: ISSN 0027-8424
PubMed: 9108019
DOI: 10.1073/PNAS.94.8.3579
Page generated: Wed Jul 31 13:53:19 2024

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