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Magnesium in PDB 1e9d: Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp

Enzymatic activity of Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp

All present enzymatic activity of Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp:
2.7.4.9;

Protein crystallography data

The structure of Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp, PDB code: 1e9d 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) 70.00 / 1.70
Space group P 43 21 2
Cell size a, b, c (Å), α, β, γ (°) 101.600, 101.600, 48.600, 90.00, 90.00, 90.00
R / Rfree (%) 20.2 / 25.7

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp (pdb code 1e9d). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp, PDB code: 1e9d:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in 1e9d

Go back to Magnesium Binding Sites List in 1e9d
Magnesium binding site 1 out of 2 in the Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg401

b:13.6
occ:1.00
O2B A:ADP302 2.0 13.1 1.0
OG A:SER20 2.1 10.6 1.0
O A:HOH2192 2.1 10.8 1.0
O A:HOH2187 2.2 11.1 1.0
O A:HOH2026 2.2 11.9 1.0
O A:HOH2188 2.2 16.9 1.0
CB A:SER20 3.1 10.1 1.0
PB A:ADP302 3.2 13.2 1.0
O3B A:ADP302 3.4 14.0 1.0
N A:SER20 3.9 10.2 1.0
OP2 A:ATM301 4.0 15.6 1.0
O A:HOH2100 4.0 52.6 1.0
O A:HOH2010 4.0 30.0 1.0
O1A A:ADP302 4.1 13.3 1.0
CA A:SER20 4.1 10.5 1.0
OD2 A:ASP96 4.1 9.9 1.0
O A:HOH2099 4.2 12.5 1.0
O3A A:ADP302 4.3 14.2 1.0
O1B A:ADP302 4.3 13.2 1.0
OP1 A:ATM301 4.3 21.8 1.0
OD1 A:ASP96 4.4 7.6 1.0
P A:ATM301 4.4 17.6 1.0
PA A:ADP302 4.6 15.1 1.0
OP3 A:ATM301 4.7 19.5 1.0
CG A:ASP96 4.7 9.9 1.0
O A:HOH2198 4.8 27.5 1.0
CB A:LYS19 4.9 10.1 1.0

Magnesium binding site 2 out of 2 in 1e9d

Go back to Magnesium Binding Sites List in 1e9d
Magnesium binding site 2 out of 2 in the Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutant Human Thymidylate Kinase (F105Y) Complexed with Aztmp and Adp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg402

b:19.3
occ:0.50
O A:HOH2109 1.8 24.9 1.0
O A:HOH2110 2.0 21.8 1.0
O A:HOH2051 2.5 31.3 1.0
OD2 A:ASP115 3.9 21.1 1.0
OD1 A:ASP115 4.0 22.7 1.0
OE1 A:GLN119 4.2 11.5 1.0
CD A:GLN119 4.2 11.5 1.0
NE2 A:GLN119 4.2 16.7 1.0
CG A:ASP115 4.4 22.3 1.0
O A:HOH2115 4.8 31.7 1.0
CG A:GLN119 4.9 12.6 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 05:51:38 2020

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