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Magnesium 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:

Fluorine (F) 3 atoms
Aluminium (Al) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate,A Magnesium-Ion and ALF3, PDB code: 1e2e:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1e2e

Go back to Magnesium Binding Sites List in 1e2e
Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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:Mg401

b:36.5
occ:1.00
 F1 A:AF3901 1.9 61.4 1.0
O A:HOH2013 2.0 48.5 1.0
O2B A:ADP302 2.0 32.4 1.0
OG A:SER20 2.1 35.9 1.0
O A:HOH2172 2.1 32.3 1.0
O A:HOH2012 2.1 34.1 1.0
CB A:SER20 3.2 30.4 1.0
PB A:ADP302 3.2 33.0 1.0
AL A:AF3901 3.2 63.2 1.0
O3B A:ADP302 3.6 39.6 1.0
F3 A:AF3901 3.7 66.5 1.0
O2P A:TMP301 3.8 46.4 1.0
O A:HOH2003 3.8 62.9 1.0
O1A A:ADP302 4.0 35.7 1.0
N A:SER20 4.0 30.2 1.0
CA A:SER20 4.2 29.5 1.0
O3P A:TMP301 4.2 43.3 1.0
OD2 A:ASP96 4.2 31.7 1.0
O1B A:ADP302 4.3 33.1 1.0
O3A A:ADP302 4.4 36.6 1.0
P A:TMP301 4.4 48.4 1.0
OD1 A:ASP96 4.5 26.8 1.0
F2 A:AF3901 4.6 64.9 1.0
PA A:ADP302 4.6 37.1 1.0
O1P A:TMP301 4.6 47.7 1.0
CG A:ASP96 4.7 33.2 1.0
CB A:LYS19 4.9 32.8 1.0
CE A:LYS19 4.9 32.8 1.0
O2A A:ADP302 4.9 36.0 1.0

Magnesium binding site 2 out of 2 in 1e2e

Go back to Magnesium Binding Sites List in 1e2e
Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg 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:Mg402

b:42.4
occ:0.50
 O A:HOH2100 2.2 38.1 1.0
O A:HOH2102 2.2 50.6 1.0
O A:HOH2050 2.3 53.8 1.0
OE1 A:GLN119 4.1 31.0 1.0
OD2 A:ASP115 4.2 46.9 1.0
OD1 A:ASP115 4.2 44.8 1.0
CD A:GLN119 4.3 32.1 1.0
NE2 A:GLN119 4.5 32.5 1.0
CG A:ASP115 4.7 46.5 1.0
O A:HOH2106 4.7 58.0 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: Tue Aug 13 02:50:04 2024

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