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Magnesium in PDB 1e2d: Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion

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

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

Protein crystallography data

The structure of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion, PDB code: 1e2d 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) 33.40 / 1.65
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.000, 101.000, 49.800, 90.00, 90.00, 90.00
R / Rfree (%) 20.1 / 24.2

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion (pdb code 1e2d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion, PDB code: 1e2d:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in 1e2d

Go back to Magnesium Binding Sites List in 1e2d
Magnesium binding site 1 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion


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 and A Magnesium-Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.4
occ:1.00
O2B A:ADP302 2.0 11.5 1.0
O A:HOH2290 2.1 15.1 1.0
O A:HOH2037 2.1 15.4 1.0
O A:HOH2274 2.1 14.3 1.0
O A:HOH2280 2.1 13.2 1.0
OG A:SER20 2.1 12.7 1.0
CB A:SER20 3.2 11.8 1.0
PB A:ADP302 3.3 13.2 1.0
O3B A:ADP302 3.6 15.7 1.0
N A:SER20 3.9 13.2 1.0
O2P A:TMP301 4.0 18.2 1.0
OD2 A:ASP96 4.1 14.4 1.0
O1A A:ADP302 4.1 15.9 1.0
CA A:SER20 4.2 11.9 1.0
O A:HOH2141 4.2 16.3 1.0
O1P A:TMP301 4.2 24.4 1.0
P A:TMP301 4.3 22.4 1.0
O A:HOH2016 4.3 27.2 1.0
O A:HOH2147 4.3 26.8 1.0
O3P A:TMP301 4.3 25.1 1.0
OD1 A:ASP96 4.3 13.9 1.0
O3A A:ADP302 4.3 15.5 1.0
O1B A:ADP302 4.4 14.3 1.0
PA A:ADP302 4.7 14.8 1.0
CG A:ASP96 4.7 13.6 1.0
O A:HOH2017 4.7 32.6 1.0
CB A:LYS19 4.7 10.8 1.0
CE A:LYS19 4.7 17.0 1.0
O A:HOH2287 4.9 26.0 1.0
O2A A:ADP302 5.0 17.0 1.0
C A:LYS19 5.0 11.6 1.0

Magnesium binding site 2 out of 3 in 1e2d

Go back to Magnesium Binding Sites List in 1e2d
Magnesium binding site 2 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion


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 and A Magnesium-Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:23.4
occ:0.50
O A:HOH2166 2.0 22.7 1.0
O A:HOH2076 2.1 32.2 1.0
O A:HOH2159 2.1 22.8 1.0
O A:HOH2164 3.8 44.9 1.0
OE1 A:GLN119 4.1 15.9 1.0
OD2 A:ASP115 4.4 23.8 1.0
OD1 A:ASP115 4.4 24.1 1.0
CD A:GLN119 4.4 15.8 1.0
NE2 A:GLN119 4.7 15.4 1.0
CG A:ASP115 4.8 22.9 1.0

Magnesium binding site 3 out of 3 in 1e2d

Go back to Magnesium Binding Sites List in 1e2d
Magnesium binding site 3 out of 3 in the Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Human Thymidylate Kinase Complexed with Thymidine Monophosphate, Adenosine Diphosphate and A Magnesium-Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg403

b:32.0
occ:1.00
O A:HOH2194 2.1 26.9 1.0
O A:HOH2014 2.2 36.2 1.0
O A:HOH2273 2.2 25.3 1.0
O A:HOH2015 2.3 35.7 1.0
O A:HOH2272 2.3 36.4 1.0
O A:HOH2147 2.4 26.8 1.0
O A:HOH2031 3.6 43.9 1.0
O A:HOH2192 3.8 32.2 1.0
O A:HOH2026 3.9 53.3 1.0
O3P A:TMP301 4.0 25.1 1.0
O1P A:TMP301 4.0 24.4 1.0
O A:HOH2017 4.1 32.6 1.0
OE2 A:GLU149 4.2 31.6 1.0
O A:HOH2079 4.2 21.7 1.0
O A:HOH2274 4.4 14.3 1.0
CD A:GLU149 4.4 37.1 1.0
O A:HOH2275 4.7 27.1 1.0
P A:TMP301 4.7 22.4 1.0
OE1 A:GLU149 4.7 33.5 1.0
O A:HOH2287 5.0 26.0 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 02:49:51 2024

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