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Magnesium in PDB 1e9b: Human Thymidylate Kinase Complexed with Aztmp and Appnp

Enzymatic activity of Human Thymidylate Kinase Complexed with Aztmp and Appnp

All present enzymatic activity of Human Thymidylate Kinase Complexed with Aztmp and Appnp:
2.7.4.9;

Protein crystallography data

The structure of Human Thymidylate Kinase Complexed with Aztmp and Appnp, PDB code: 1e9b was solved by N.Ostermann, A.Lavie, S.Padiyar, R.Brundiers, T.Veit, J.Reintein, R.S.Goody, M.Konrad, I.Schlichting, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 44.50 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 100.100, 100.100, 49.700, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 23

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Human Thymidylate Kinase Complexed with Aztmp and Appnp (pdb code 1e9b). 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 Aztmp and Appnp, PDB code: 1e9b:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1e9b

Go back to Magnesium Binding Sites List in 1e9b
Magnesium binding site 1 out of 2 in the Human Thymidylate Kinase Complexed with Aztmp and Appnp


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 Aztmp and Appnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:18.4
occ:1.00
O2B A:ANP303 2.0 20.6 0.7
O2B A:ADP302 2.1 11.8 0.3
OG A:SER20 2.1 15.5 1.0
O A:HOH2030 2.1 20.0 1.0
O A:HOH2283 2.1 19.6 1.0
O A:HOH2148 2.1 16.8 1.0
O A:HOH2289 2.1 9.2 0.3
O3G A:ANP303 2.1 24.6 0.7
CB A:SER20 3.2 14.1 1.0
PB A:ADP302 3.2 10.9 0.3
PB A:ANP303 3.3 22.1 0.7
O3B A:ADP302 3.4 12.1 0.3
PG A:ANP303 3.4 25.0 0.7
N3B A:ANP303 3.7 23.4 0.7
O A:HOH2278 3.8 36.4 1.0
N A:SER20 3.9 12.2 1.0
OP1 A:ATM301 3.9 11.0 0.3
O A:HOH2012 4.0 36.6 1.0
OP1 A:ATM301 4.0 36.9 0.7
O2A A:ADP302 4.0 13.9 0.3
O2A A:ANP303 4.1 22.4 0.7
CA A:SER20 4.1 13.3 1.0
OP2 A:ATM301 4.1 31.7 0.7
OD2 A:ASP96 4.1 17.1 1.0
OP2 A:ATM301 4.2 17.4 0.3
O1B A:ADP302 4.2 8.8 0.3
O A:HOH2146 4.2 22.6 1.0
P A:ATM301 4.3 17.5 0.3
O1G A:ANP303 4.3 25.6 0.7
OD1 A:ASP96 4.3 16.1 1.0
O3A A:ADP302 4.3 10.9 0.3
O3A A:ANP303 4.3 21.7 0.7
O1B A:ANP303 4.4 23.4 0.7
OP3 A:ATM301 4.5 18.5 0.3
O A:HOH2290 4.5 27.7 0.3
O2G A:ANP303 4.5 26.8 0.7
O A:HOH2011 4.6 50.7 1.0
P A:ATM301 4.6 33.3 0.7
PA A:ANP303 4.6 23.1 0.7
PA A:ADP302 4.7 12.8 0.3
CG A:ASP96 4.7 14.5 1.0
CB A:LYS19 4.7 15.0 1.0
CE A:LYS19 4.7 23.2 1.0
C A:LYS19 4.9 14.4 1.0

Magnesium binding site 2 out of 2 in 1e9b

Go back to Magnesium Binding Sites List in 1e9b
Magnesium binding site 2 out of 2 in the Human Thymidylate Kinase Complexed with Aztmp and Appnp


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 Aztmp and Appnp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:23.4
occ:0.50
O A:HOH2163 2.1 27.1 1.0
O A:HOH2078 2.2 31.1 1.0
O A:HOH2162 2.3 28.4 1.0
OE1 A:GLN119 4.1 18.5 1.0
OD2 A:ASP115 4.3 27.1 1.0
CD A:GLN119 4.4 16.7 1.0
OD1 A:ASP115 4.4 25.9 1.0
NE2 A:GLN119 4.6 18.8 1.0
O A:HOH2173 4.6 38.6 1.0
CG A:ASP115 4.8 25.1 1.0

Reference:

N.Ostermann, A.Lavie, S.Padiyar, R.Brundiers, T.Veit, J.Reintein, R.S.Goody, M.Konrad, I.Schlichting. Potentiating Azt Activation: Structures of Wildtype and Mutant Human Thymidylate Kinase Suggest Reasons For the Mutants' Improved Kinetics with the Hiv Prodrug Metabolite Aztmp J.Mol.Biol. V. 304 43 2000.
ISSN: ISSN 0022-2836
PubMed: 11071809
DOI: 10.1006/JMBI.2000.4175
Page generated: Mon Dec 14 05:51:36 2020

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