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Magnesium in PDB 1e2g: Human Thymidylate Kinase Complexed with Adp, Tdp and A Magnesium-Ion

Enzymatic activity of Human Thymidylate Kinase Complexed with Adp, Tdp and A Magnesium-Ion

All present enzymatic activity of Human Thymidylate Kinase Complexed with Adp, Tdp and A Magnesium-Ion:
2.7.4.9;

Protein crystallography data

The structure of Human Thymidylate Kinase Complexed with Adp, Tdp and A Magnesium-Ion, PDB code: 1e2g 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) 50.50 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.100, 101.100, 49.200, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 24

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Thymidylate Kinase Complexed with Adp, Tdp and A Magnesium-Ion (pdb code 1e2g). 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 Adp, Tdp and A Magnesium-Ion, PDB code: 1e2g:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1e2g

Go back to Magnesium Binding Sites List in 1e2g
Magnesium binding site 1 out of 2 in the Human Thymidylate Kinase Complexed with Adp, Tdp 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 Adp, Tdp and A Magnesium-Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:21.5
occ:1.00
O2B A:ADP302 2.0 17.0 1.0
OG A:SER20 2.1 17.9 1.0
O A:HOH2259 2.1 19.8 1.0
O A:HOH2252 2.1 24.1 1.0
O A:HOH2267 2.2 20.8 1.0
O A:HOH2124 2.3 19.9 1.0
CB A:SER20 3.2 14.3 1.0
PB A:ADP302 3.3 19.2 1.0
O3B A:ADP302 3.6 24.2 1.0
N A:SER20 4.0 13.4 1.0
O2P A:TMP301 4.0 19.9 0.3
O A:HOH2268 4.0 28.2 1.0
O1A A:ADP302 4.0 18.5 1.0
CA A:SER20 4.1 12.6 1.0
OD2 A:ASP96 4.1 19.3 1.0
O2B A:TYD304 4.3 16.3 0.7
OD1 A:ASP96 4.3 17.0 1.0
O A:HOH2126 4.3 34.5 1.0
NH1 A:ARG97 4.3 16.8 0.7
O1P A:TMP301 4.3 22.6 0.3
O1B A:ADP302 4.4 20.1 1.0
O3A A:ADP302 4.4 19.6 1.0
O3P A:TMP301 4.4 20.6 0.3
P A:TMP301 4.4 20.9 0.3
O A:HOH2030 4.5 28.7 1.0
O1B A:TYD304 4.5 24.8 0.7
CG A:ASP96 4.7 13.2 1.0
PA A:ADP302 4.7 19.7 1.0
NH1 A:ARG16 4.7 26.8 0.5
CZ A:ARG97 4.8 19.3 0.7
PB A:TYD304 4.8 23.4 0.7
O A:HOH2125 4.8 25.6 1.0
CB A:LYS19 4.9 15.5 1.0
NZ A:LYS19 5.0 19.7 1.0
NH2 A:ARG97 5.0 19.2 0.7

Magnesium binding site 2 out of 2 in 1e2g

Go back to Magnesium Binding Sites List in 1e2g
Magnesium binding site 2 out of 2 in the Human Thymidylate Kinase Complexed with Adp, Tdp 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 Adp, Tdp and A Magnesium-Ion within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:22.5
occ:0.50
O A:HOH2144 2.0 26.2 1.0
O A:HOH2142 2.1 25.4 1.0
O A:HOH2061 2.2 30.9 1.0
O A:HOH2063 4.0 43.4 1.0
O A:HOH2060 4.1 58.3 1.0
OD2 A:ASP115 4.1 26.4 1.0
OD1 A:ASP115 4.2 23.4 1.0
OE1 A:GLN119 4.2 18.3 1.0
CD A:GLN119 4.5 18.4 1.0
CG A:ASP115 4.6 23.6 1.0
NE2 A:GLN119 4.6 21.9 1.0
O A:HOH2062 4.9 38.5 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 02:50:44 2024

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