Magnesium in PDB 1nmy: Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp

All present enzymatic activity of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp:
2.7.4.9;

The structure of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp, PDB code: 1nmy was solved by N.Ostermann, D.Segura-Pena, C.Meier, T.Veit, M.Monnerjahn, M.Konrad, A.Lavie, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.80 / 1.60
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	101.258, 101.258, 49.781, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22

The structure of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp also contains other interesting chemical elements:

Fluorine

(F)

2 atoms

The binding sites of Magnesium atom in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp (pdb code 1nmy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp, PDB code: 1nmy:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg401 b:11.2 occ:1.00 O2B A:ANP303 2.0 12.3 0.5 O2B A:ADP302 2.0 10.3 0.5 O A:HOH506 2.1 13.9 1.0 O A:HOH507 2.1 7.5 0.3 O2G A:ANP303 2.1 13.2 0.5 O A:HOH505 2.1 16.0 1.0 O A:HOH504 2.1 11.2 1.0 OG A:SER20 2.1 10.2 1.0 PB A:ANP303 3.2 15.2 0.5 CB A:SER20 3.3 8.8 1.0 PB A:ADP302 3.3 7.8 0.5 PG A:ANP303 3.4 13.2 0.5 O3B A:ADP302 3.5 13.5 0.5 N3B A:ANP303 3.5 15.8 0.5 O A:HOH682 3.8 34.4 1.0 N A:SER20 3.9 9.8 1.0 O1A A:ADP302 4.0 8.4 0.5 OP1 A:FDM301 4.0 10.0 0.5 OP3 A:FDM301 4.0 22.1 0.5 CA A:SER20 4.2 7.5 1.0 OD2 A:ASP96 4.2 11.1 1.0 O1B A:ANP303 4.3 15.2 0.5 O2A A:ANP303 4.3 13.0 0.5 O A:HOH522 4.3 16.3 1.0 OP2 A:FDM301 4.3 14.7 0.5 O3A A:ANP303 4.3 14.6 0.5 O1G A:ANP303 4.3 17.0 0.5 OP3 A:FDM301 4.3 13.7 0.5 O3A A:ADP302 4.3 7.2 0.5 OD1 A:ASP96 4.3 10.6 1.0 O1B A:ADP302 4.3 7.4 0.5 O3G A:ANP303 4.3 16.3 0.5 P1 A:FDM301 4.4 15.9 0.5 PA A:ADP302 4.6 7.7 0.5 CG A:ASP96 4.7 9.8 1.0 CE A:LYS19 4.7 15.8 1.0 CB A:LYS19 4.8 9.8 1.0 PA A:ANP303 4.8 14.5 0.5 O A:HOH508 4.8 15.0 0.3 O2A A:ADP302 4.9 9.3 0.5 C A:LYS19 5.0 10.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Human Thymidylate Kinase with Fltmp and Appnhp within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:18.6 occ:0.50 O A:HOH501 2.1 23.2 1.0 O A:HOH502 2.2 21.7 1.0 O A:HOH503 2.3 30.4 1.0 O A:HOH835 3.8 36.2 1.0 OD1 A:ASP115 4.1 20.3 1.0 OD2 A:ASP115 4.1 21.2 1.0 OE1 A:GLN119 4.2 12.8 1.0 CD A:GLN119 4.4 11.7 1.0 CG A:ASP115 4.6 17.7 1.0 NE2 A:GLN119 4.6 13.7 1.0 O A:HOH520 4.7 35.5 1.0

N.Ostermann, D.Segura-Pena, C.Meier, T.Veit, M.Monnerjahn, M.Konrad, A.Lavie. Structures of Human Thymidylate Kinase in Complex with Prodrugs: Implications For the Structure-Based Design of Novel Compounds Biochemistry V. 42 2568 2003.
ISSN: ISSN 0006-2960
PubMed: 12614151
DOI: 10.1021/BI027302T