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Magnesium in PDB 1e2f: 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: 1e2f 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) 71.70 / 1.60
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.300, 101.300, 49.300, 90.00, 90.00, 90.00
R / Rfree (%) 21 / 26.4

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 1e2f). 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 and A Magnesium-Ion, PDB code: 1e2f:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1e2f

Go back to Magnesium Binding Sites List in 1e2f
Magnesium binding site 1 out of 2 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:16.9
occ:1.00
O2B A:ANP302 2.0 19.0 0.7
O A:HOH2276 2.0 20.2 1.0
O A:HOH2277 2.1 18.2 1.0
OG A:SER20 2.1 14.8 1.0
O A:HOH2286 2.1 19.8 1.0
O3G A:ANP302 2.1 20.1 0.7
O2B A:ADP303 2.1 13.6 0.3
O A:HOH2293 2.2 19.1 0.3
PB A:ANP302 3.2 21.2 0.7
CB A:SER20 3.3 13.5 1.0
PB A:ADP303 3.3 13.4 0.3
PG A:ANP302 3.4 21.4 0.7
O3B A:ADP303 3.5 15.8 0.3
N3B A:ANP302 3.6 22.4 0.7
O2P A:TMP301 3.8 12.0 0.3
O A:HOH2292 3.9 44.1 1.0
N A:SER20 3.9 15.8 1.0
O2P A:TMP301 4.0 28.8 0.7
O1A A:ADP303 4.1 14.5 0.3
OD2 A:ASP96 4.1 18.5 1.0
O2A A:ANP302 4.2 20.5 0.7
O3P A:TMP301 4.2 12.3 0.3
CA A:SER20 4.2 13.2 1.0
O A:HOH2143 4.2 25.9 1.0
P A:TMP301 4.2 19.7 0.3
O1P A:TMP301 4.3 18.1 0.3
O1B A:ANP302 4.3 22.0 0.7
O3A A:ANP302 4.3 20.5 0.7
OD1 A:ASP96 4.3 16.6 1.0
O1G A:ANP302 4.4 25.3 0.7
O1B A:ADP303 4.4 12.5 0.3
O A:HOH2297 4.4 27.5 0.3
O2G A:ANP302 4.4 25.8 0.7
O3A A:ADP303 4.4 11.0 0.3
O A:HOH2145 4.5 43.3 1.0
CG A:ASP96 4.7 15.6 1.0
PA A:ANP302 4.7 19.8 0.7
PA A:ADP303 4.7 13.7 0.3
CE A:LYS19 4.8 20.6 1.0
CB A:LYS19 4.8 16.4 1.0
C A:LYS19 4.9 15.5 1.0

Magnesium binding site 2 out of 2 in 1e2f

Go back to Magnesium Binding Sites List in 1e2f
Magnesium binding site 2 out of 2 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:25.1
occ:0.50
O A:HOH2161 2.1 28.8 1.0
O A:HOH2067 2.1 32.9 1.0
O A:HOH2163 2.2 32.8 1.0
O A:HOH2158 4.1 45.0 1.0
OE1 A:GLN119 4.2 18.5 1.0
OD2 A:ASP115 4.3 26.8 1.0
OD1 A:ASP115 4.3 26.9 1.0
CD A:GLN119 4.5 18.1 1.0
O A:HOH2167 4.6 35.2 1.0
NE2 A:GLN119 4.7 21.2 1.0
CG A:ASP115 4.8 25.7 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: Mon Dec 14 05:51:18 2020

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