Atomistry » Fluorine » PDB 1dvz-1fk9 » 1e2e
Atomistry »
  Fluorine »
    PDB 1dvz-1fk9 »
      1e2e »

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

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy