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Fluorine in PDB 1e2e: Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3

Enzymatic activity of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3

All present enzymatic activity of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3:
2.7.4.9;

Protein crystallography data

The structure of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3, PDB code: 1e2e was solved by N.Ostermann, I.Schlichting, R.Brundiers, M.Konrad, J.Reinstein, T.Veit, R.S.Goody, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 71.80 / 2.00
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.600, 101.600, 49.900, 90.00, 90.00, 90.00
R / Rfree (%) 21.4 / 27.2

Other elements in 1e2e:

The structure of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3 also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Aluminium (Al) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3 (pdb code 1e2e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3, PDB code: 1e2e:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 1e2e

Go back to Fluorine Binding Sites List in 1e2e
Fluorine binding site 1 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:61.4
occ:1.00
 F1 A:AF3901 0.0 61.4 1.0
AL A:AF3901 1.6 63.2 1.0
MG A:MG401 1.9 36.5 1.0
O2P A:TMP301 2.3 46.4 1.0
O A:HOH2012 2.5 34.1 1.0
F3 A:AF3901 2.6 66.5 1.0
O2B A:ADP302 2.7 32.4 1.0
O A:HOH2013 2.7 48.5 1.0
F2 A:AF3901 2.9 64.9 1.0
O3B A:ADP302 3.0 39.6 1.0
PB A:ADP302 3.2 33.0 1.0
P A:TMP301 3.4 48.4 1.0
O A:HOH2172 3.4 32.3 1.0
O3P A:TMP301 3.4 43.3 1.0
NH2 A:ARG97 3.8 41.9 1.0
OG A:SER20 3.9 35.9 1.0
NZ A:LYS19 3.9 29.5 1.0
CE A:LYS19 4.0 32.8 1.0
O1B A:ADP302 4.0 33.1 1.0
O1P A:TMP301 4.1 47.7 1.0
NE A:ARG97 4.3 37.6 1.0
CZ A:ARG97 4.6 39.2 1.0
O5' A:TMP301 4.6 46.6 1.0
O3A A:ADP302 4.8 36.6 1.0
OD1 A:ASP15 4.9 77.2 1.0
O1A A:ADP302 4.9 35.7 1.0

Fluorine binding site 2 out of 3 in 1e2e

Go back to Fluorine Binding Sites List in 1e2e
Fluorine binding site 2 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:64.9
occ:1.00
 F2 A:AF3901 0.0 64.9 1.0
AL A:AF3901 1.6 63.2 1.0
CA A:ASP15 2.5 60.4 1.0
O3B A:ADP302 2.5 39.6 1.0
OD1 A:ASP15 2.8 77.2 1.0
F3 A:AF3901 2.9 66.5 1.0
F1 A:AF3901 2.9 61.4 1.0
CB A:ASP15 2.9 64.1 1.0
N A:ARG16 2.9 54.9 1.0
CG A:ASP15 3.0 70.7 1.0
NZ A:LYS19 3.0 29.5 1.0
C A:ASP15 3.2 57.4 1.0
NH2 A:ARG97 3.4 41.9 1.0
PB A:ADP302 3.5 33.0 1.0
O A:HOH2058 3.5 35.7 1.0
N A:ASP15 3.5 58.4 1.0
O1B A:ADP302 3.6 33.1 1.0
O2P A:TMP301 3.7 46.4 1.0
OD2 A:ASP15 4.0 70.0 1.0
O A:VAL14 4.0 46.0 1.0
O2B A:ADP302 4.1 32.4 1.0
CE A:LYS19 4.1 32.8 1.0
C A:VAL14 4.1 58.5 1.0
CA A:ARG16 4.2 50.9 1.0
O A:ASP15 4.4 49.3 1.0
MG A:MG401 4.6 36.5 1.0
CZ A:ARG97 4.6 39.2 1.0
O3A A:ADP302 4.8 36.6 1.0
N A:ALA17 4.9 42.3 1.0
O A:HOH2012 4.9 34.1 1.0

Fluorine binding site 3 out of 3 in 1e2e

Go back to Fluorine Binding Sites List in 1e2e
Fluorine binding site 3 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:66.5
occ:1.00
 F3 A:AF3901 0.0 66.5 1.0
AL A:AF3901 1.6 63.2 1.0
F1 A:AF3901 2.6 61.4 1.0
O3B A:ADP302 2.8 39.6 1.0
O2P A:TMP301 2.9 46.4 1.0
F2 A:AF3901 2.9 64.9 1.0
O A:HOH2058 3.1 35.7 1.0
MG A:MG401 3.7 36.5 1.0
O A:HOH2172 3.7 32.3 1.0
PB A:ADP302 4.0 33.0 1.0
O A:HOH2013 4.0 48.5 1.0
O2B A:ADP302 4.1 32.4 1.0
P A:TMP301 4.2 48.4 1.0
O A:HOH2120 4.3 44.7 1.0
O1P A:TMP301 4.6 47.7 1.0
N A:ARG16 4.6 54.9 1.0
O1A A:ADP302 4.7 35.7 1.0
CB A:ASP15 4.8 64.1 1.0
CG A:ASP15 4.9 70.7 1.0
CA A:ASP15 4.9 60.4 1.0
O A:HOH2012 5.0 34.1 1.0

Reference:

N.Ostermann, I.Schlichting, R.Brundiers, M.Konrad, J.Reinstein, T.Veit, R.S.Goody, A.Lavie. Insights Into the Phosphoryltransfer Mechanism of Human Thymidylate Kinase Gained From Crystal Structures of Enzyme Complexes Along the Reaction Coordinate Structure V. 8 629 2000.
ISSN: ISSN 0969-2126
PubMed: 10873853
DOI: 10.1016/S0969-2126(00)00149-0
Page generated: Wed Jul 31 11:07:40 2024

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